diff --git a/src/multiqc/config.vsh.yaml b/src/multiqc/config.vsh.yaml index 32a93a15..2eb9e673 100644 --- a/src/multiqc/config.vsh.yaml +++ b/src/multiqc/config.vsh.yaml @@ -120,65 +120,73 @@ functionality: example: path/to/multiqc_config.yml description: | Specific config file to load, after those in MultiQC dir / home dir / working dir - + - name: "--profile_runtime" + type: boolean_true + description: | + Add analysis of how long MultiQC takes to run to the report - name: "MultiQC behaviour" arguments: - name: "--verbose" type: boolean_true - description: Increase output verbosity. - - name: "--force" - type: boolean_true - description: Overwrite any existing reports + description: | + Increase output verbosity. - name: "--quiet" type: boolean_true - description: Only show log warnings + description: | + Only show log warnings - name: "--strict" type: boolean_true - description: Don't catch exceptions, run additional code checks to help development. + description: | + Don't catch exceptions, run additional code checks to help development. - name: "--development" type: boolean_true - description: Development mode. Do not compress and minimise JS, export uncompressed plot data. + description: | + Development mode. Do not compress and minimise JS, export uncompressed plot data. - name: "--require_logs" type: boolean_true - description: Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error. + description: | + Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error. - name: "--no_megaqc_upload" type: boolean_true - description: Don't upload generated report to MegaQC, even if MegaQC options are found. + description: | + Don't upload generated report to MegaQC, even if MegaQC options are found. - name: "--no_ansi" type: boolean_true - description: Disable coloured log output. + description: | + Disable coloured log output. - name: "Output format" arguments: - name: "--flat" type: boolean_true - description: Use only flat plots (static images). + description: | + Use only flat plots (static images). - name: "--interactive" type: boolean_true - description: Use only interactive plots (in-browser Javascript). - - name: "--export" - type: boolean_true - description: Export plots as static images in addition to the report. + description: | + Use only interactive plots (in-browser Javascript). - name: "--data_dir" type: boolean_true - description: Force the parsed data directory to be created. + description: | + Force the parsed data directory to be created. - name: "--no_data_dir" type: boolean_true - description: Prevent the parsed data directory from being created. + description: | + Prevent the parsed data directory from being created. - name: "--zip_data_dir" type: boolean_true - description: Compress the data directory. + description: | + Compress the data directory. - name: "--data_format" type: string choices: [tsv, csv, json, yaml] - description: Output parsed data in a different format. - - name: "--no_report" - type: boolean_true - description: Do not generate a report, only export data and plots. + description: | + Output parsed data in a different format than the default 'txt'. - name: "--pdf" type: boolean_true - description: Creates PDF report with the 'simple' template. Requires Pandoc to be installed. + description: | + Creates PDF report with the 'simple' template. Requires Pandoc to be installed. resources: - type: bash_script @@ -192,7 +200,7 @@ functionality: platforms: - type: docker - image: quay.io/biocontainers/multiqc:1.20--pyhdfd78af_0 + image: quay.io/biocontainers/multiqc:1.20--pyhdfd78af_2 setup: - type: docker run: | diff --git a/src/multiqc/rna-seq/data/SRR3192396_1.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192396_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..14554796 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_1.fastq.gz_trimming_report.txt @@ -0,0 +1,155 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192396_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192396_1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2200.70 s (21 us/read; 2.87 M reads/minute). + +=== Summary === + +Total reads processed: 105,089,150 +Reads with adapters: 31,907,642 (30.4%) +Reads written (passing filters): 105,089,150 (100.0%) + +Total basepairs processed: 10,614,004,150 bp +Quality-trimmed: 223,928,038 bp (2.1%) +Total written (filtered): 10,345,268,814 bp (97.5%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 31907642 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 29.0% + C: 30.8% + G: 18.8% + T: 21.4% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 22534133 26272287.5 0 22534133 +2 7424483 6568071.9 0 7424483 +3 1447916 1642018.0 0 1447916 +4 343385 410504.5 0 343385 +5 88652 102626.1 0 88652 +6 13787 25656.5 0 13787 +7 3613 6414.1 0 3613 +8 2961 1603.5 0 2961 +9 3515 400.9 0 2662 853 +10 4242 100.2 1 2597 1645 +11 3413 25.1 1 2440 973 +12 2534 6.3 1 2396 138 +13 2448 1.6 1 2395 53 +14 2629 1.6 1 2583 46 +15 2103 1.6 1 2054 49 +16 1982 1.6 1 1930 52 +17 1694 1.6 1 1620 74 +18 1618 1.6 1 1568 50 +19 895 1.6 1 861 34 +20 1097 1.6 1 1054 43 +21 873 1.6 1 848 25 +22 864 1.6 1 826 38 +23 1038 1.6 1 974 64 +24 918 1.6 1 857 61 +25 747 1.6 1 723 24 +26 628 1.6 1 590 38 +27 789 1.6 1 743 46 +28 793 1.6 1 749 44 +29 881 1.6 1 840 41 +30 878 1.6 1 834 44 +31 848 1.6 1 785 63 +32 774 1.6 1 731 43 +33 1003 1.6 1 965 38 +34 769 1.6 1 733 36 +35 993 1.6 1 934 59 +36 688 1.6 1 646 42 +37 891 1.6 1 843 48 +38 470 1.6 1 432 38 +39 572 1.6 1 541 31 +40 416 1.6 1 370 46 +41 505 1.6 1 477 28 +42 222 1.6 1 176 46 +43 196 1.6 1 173 23 +44 138 1.6 1 94 44 +45 216 1.6 1 185 31 +46 193 1.6 1 157 36 +47 130 1.6 1 88 42 +48 153 1.6 1 101 52 +49 126 1.6 1 95 31 +50 87 1.6 1 69 18 +51 81 1.6 1 49 32 +52 118 1.6 1 73 45 +53 79 1.6 1 51 28 +54 47 1.6 1 17 30 +55 60 1.6 1 19 41 +56 71 1.6 1 46 25 +57 55 1.6 1 29 26 +58 63 1.6 1 33 30 +59 42 1.6 1 28 14 +60 50 1.6 1 12 38 +61 49 1.6 1 26 23 +62 74 1.6 1 39 35 +63 74 1.6 1 52 22 +64 58 1.6 1 41 17 +65 74 1.6 1 40 34 +66 65 1.6 1 34 31 +67 83 1.6 1 41 42 +68 49 1.6 1 33 16 +69 92 1.6 1 62 30 +70 105 1.6 1 52 53 +71 63 1.6 1 39 24 +72 50 1.6 1 16 34 +73 37 1.6 1 5 32 +74 37 1.6 1 4 33 +75 27 1.6 1 3 24 +76 32 1.6 1 2 30 +77 20 1.6 1 0 20 +78 52 1.6 1 0 52 +79 29 1.6 1 1 28 +80 38 1.6 1 0 38 +81 59 1.6 1 2 57 +82 59 1.6 1 0 59 +83 40 1.6 1 0 40 +84 35 1.6 1 0 35 +85 33 1.6 1 0 33 +86 56 1.6 1 0 56 +87 66 1.6 1 0 66 +88 39 1.6 1 0 39 +89 51 1.6 1 0 51 +90 54 1.6 1 0 54 +91 30 1.6 1 0 30 +92 40 1.6 1 0 40 +93 14 1.6 1 0 14 +94 133 1.6 1 1 132 +95 45 1.6 1 0 45 +96 31 1.6 1 0 31 +97 56 1.6 1 0 56 +98 30 1.6 1 0 30 +99 9 1.6 1 0 9 +100 21 1.6 1 0 21 +101 68 1.6 1 0 68 + + +RUN STATISTICS FOR INPUT FILE: SRR3192396_1.fastq.gz +============================================= +105089150 sequences processed in total + diff --git a/src/multiqc/rna-seq/data/SRR3192396_1Log.final.out b/src/multiqc/rna-seq/data/SRR3192396_1Log.final.out new file mode 100644 index 00000000..ac263484 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_1Log.final.out @@ -0,0 +1,34 @@ + Started job on | May 03 04:15:10 + Started mapping on | May 03 04:19:43 + Finished on | May 03 05:44:43 + Mapping speed, Million of reads per hour | 73.70 + + Number of input reads | 104413184 + Average input read length | 196 + UNIQUE READS: + Uniquely mapped reads number | 97833503 + Uniquely mapped reads % | 93.70% + Average mapped length | 195.57 + Number of splices: Total | 40714338 + Number of splices: Annotated (sjdb) | 40114995 + Number of splices: GT/AG | 40194421 + Number of splices: GC/AG | 336796 + Number of splices: AT/AC | 41871 + Number of splices: Non-canonical | 141250 + Mismatch rate per base, % | 0.25% + Deletion rate per base | 0.02% + Deletion average length | 1.56 + Insertion rate per base | 0.01% + Insertion average length | 1.61 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 3659822 + % of reads mapped to multiple loci | 3.51% + Number of reads mapped to too many loci | 11548 + % of reads mapped to too many loci | 0.01% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 2.77% + % of reads unmapped: other | 0.02% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff --git a/src/multiqc/rna-seq/data/SRR3192396_1Log.out b/src/multiqc/rna-seq/data/SRR3192396_1Log.out new file mode 100644 index 00000000..efc17cd1 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_1Log.out @@ -0,0 +1,408 @@ +STAR version=STAR_2.5.1b +STAR compilation time,server,dir=Tue Jan 26 13:48:00 CET 2016 milou-b.uppmax.uu.se:/sw/apps/bioinfo/star/2.5.1b/src/source +##### DEFAULT parameters: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 1 +runDirPerm User_RWX +runRNGseed 777 +genomeDir ./GenomeDir/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn Read1 Read2 +readFilesCommand - +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outTmpDir - +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +##### Command Line: +STAR --runThreadN 4 --outQSconversionAdd 0 --outSAMattributes Standard --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --readFilesIn SRR3192396_1_val_1.fq.gz SRR3192396_2_val_2.fq.gz --outFileNamePrefix SRR3192396_1 --outStd SAM +##### Initial USER parameters from Command Line: +outFileNamePrefix SRR3192396_1 +outStd SAM +###### All USER parameters from Command Line: +runThreadN 4 ~RE-DEFINED +outQSconversionAdd 0 ~RE-DEFINED +outSAMattributes Standard ~RE-DEFINED +genomeLoad NoSharedMemory ~RE-DEFINED +readFilesCommand zcat ~RE-DEFINED +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ~RE-DEFINED +readFilesIn SRR3192396_1_val_1.fq.gz SRR3192396_2_val_2.fq.gz ~RE-DEFINED +outFileNamePrefix SRR3192396_1 ~RE-DEFINED +outStd SAM ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runThreadN 4 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +readFilesIn SRR3192396_1_val_1.fq.gz SRR3192396_2_val_2.fq.gz +readFilesCommand zcat +outFileNamePrefix SRR3192396_1 +outStd SAM +outQSconversionAdd 0 +outSAMattributes Standard + +------------------------------- +##### Final effective command line: +STAR --runThreadN 4 --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --genomeLoad NoSharedMemory --readFilesIn SRR3192396_1_val_1.fq.gz SRR3192396_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix SRR3192396_1 --outStd SAM --outQSconversionAdd 0 --outSAMattributes Standard + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 4 +runDirPerm User_RWX +runRNGseed 777 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn SRR3192396_1_val_1.fq.gz SRR3192396_2_val_2.fq.gz +readFilesCommand zcat +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outFileNamePrefix SRR3192396_1 +outTmpDir - +outStd SAM +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +---------------------------------------- + + + Input read files for mate 1, from input string SRR3192396_1_val_1.fq.gz +-rw-rw-r-- 1 phil b2013064 8606188876 May 3 03:47 SRR3192396_1_val_1.fq.gz + + readsCommandsFile: +exec > "SRR3192396_1_STARtmp/tmp.fifo.read1" +echo FILE 0 +zcat "SRR3192396_1_val_1.fq.gz" + + + Input read files for mate 2, from input string SRR3192396_2_val_2.fq.gz +-rw-rw-r-- 1 phil b2013064 8729624604 May 3 03:47 SRR3192396_2_val_2.fq.gz + + readsCommandsFile: +exec > "SRR3192396_1_STARtmp/tmp.fifo.read2" +echo FILE 0 +zcat "SRR3192396_2_val_2.fq.gz" + +Finished loading and checking parameters +Reading genome generation parameters: +versionGenome 20201 ~RE-DEFINED +genomeFastaFiles genome.fa ~RE-DEFINED +genomeSAindexNbases 14 ~RE-DEFINED +genomeChrBinNbits 18 ~RE-DEFINED +genomeSAsparseD 1 ~RE-DEFINED +sjdbOverhang 100 ~RE-DEFINED +sjdbFileChrStartEnd - ~RE-DEFINED +sjdbGTFfile genes.gtf ~RE-DEFINED +sjdbGTFchrPrefix - ~RE-DEFINED +sjdbGTFfeatureExon exon ~RE-DEFINED +sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED +sjdbGTFtagExonParentGene gene_id ~RE-DEFINED +sjdbInsertSave Basic ~RE-DEFINED +Genome version is compatible with current STAR version +Number of real (reference) chromosmes= 25 +1 1 249250621 0 +2 2 243199373 249298944 +3 3 198022430 492568576 +4 4 191154276 690749440 +5 5 180915260 882114560 +6 6 171115067 1063256064 +7 7 159138663 1234436096 +8 8 146364022 1393819648 +9 9 141213431 1540358144 +10 10 135534747 1681653760 +11 11 135006516 1817444352 +12 12 133851895 1952710656 +13 13 115169878 2086666240 +14 14 107349540 2202009600 +15 15 102531392 2309488640 +16 16 90354753 2412249088 +17 17 81195210 2502688768 +18 18 78077248 2583953408 +19 19 59128983 2662072320 +20 20 63025520 2721316864 +21 21 48129895 2784493568 +22 22 51304566 2832728064 +23 X 155270560 2884108288 +24 Y 59373566 3039559680 +25 MT 16569 3099066368 +--sjdbOverhang = 100 taken from the generated genome +Started loading the genome: Tue May 3 04:15:10 2016 + +checking Genome sizefile size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +checking SA sizefile size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 +Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 +nGenome=3168538239; nSAbyte=24152204822 +GstrandBit=32 SA number of indices=5855079956 +Shared memory is not used for genomes. Allocated a private copy of the genome. +Genome file size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3168538239 bytes +SA file size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24152204822 bytes +Loading SAindex ... done: 1565873619 bytes +Finished loading the genome: Tue May 3 04:19:43 2016 + +Processing splice junctions database sjdbN=344327, sjdbOverhang=100 +alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 +Created thread # 1 +Created thread # 2 +Created thread # 3 +Starting to map file # 0 +mate 1: SRR3192396_1_val_1.fq.gz +mate 2: SRR3192396_2_val_2.fq.gz +Thread #3 end of input stream, nextChar=-1 +Completed: thread #2 +Completed: thread #0 +Completed: thread #1 +Joined thread # 1 +Joined thread # 2 +Completed: thread #3 +Joined thread # 3 +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192396_1Log.progress.out b/src/multiqc/rna-seq/data/SRR3192396_1Log.progress.out new file mode 100644 index 00000000..6c94b5b1 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_1Log.progress.out @@ -0,0 +1,84 @@ + Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped + M/hr number length unique length MMrate multi multi+ MM short other +May 03 04:20:43 82.3 1371127 196 93.8% 195.9 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:21:43 88.5 2951213 196 93.8% 196.0 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:22:43 90.6 4530028 196 93.8% 196.0 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:23:45 89.2 5997922 196 93.8% 196.0 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:24:47 91.1 7694685 196 93.7% 195.8 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:25:50 92.1 9392101 196 93.7% 195.7 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:26:50 92.4 10963679 196 93.7% 195.5 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:27:51 91.5 12409961 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:28:51 91.7 13965629 196 93.7% 195.7 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:29:53 92.3 15633432 196 93.7% 195.7 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:30:55 92.7 17305188 196 93.7% 195.7 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:31:58 91.9 18754909 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:33:01 92.2 20428561 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:34:04 92.4 22103174 196 93.7% 195.5 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:35:04 92.5 23660217 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:36:11 91.9 25216781 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:37:13 92.2 26886896 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:38:15 92.5 28559260 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:39:16 92.8 30232464 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:40:24 92.6 31907782 196 93.7% 195.5 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:41:24 92.6 33466428 196 93.7% 195.5 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:42:24 92.6 35023163 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:43:25 92.9 36690097 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:44:25 92.9 38247627 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:45:26 92.6 39695858 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:46:26 92.7 41256000 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:47:28 92.8 42929406 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:48:31 92.9 44597705 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:49:31 92.7 46041962 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.7% 0.0% +May 03 04:50:32 92.9 47708658 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:51:34 93.0 49378645 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:52:37 93.1 51050503 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:53:38 93.1 52612045 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:54:39 93.0 54175275 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:55:41 93.2 55843336 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:56:46 92.6 57177107 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:57:46 91.4 57955597 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 04:58:57 90.2 58957038 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:00:05 89.0 59848486 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:01:05 88.1 60740536 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:02:05 87.3 61632971 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:03:09 86.5 62637634 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:04:15 85.7 63641982 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:05:20 85.0 64648620 196 93.7% 195.5 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:06:25 84.3 65649447 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:07:28 83.6 66538709 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:08:28 83.1 67538872 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:09:33 82.5 68541233 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:10:37 82.0 69544167 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:11:41 81.5 70548123 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:12:43 81.0 71551670 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:13:47 80.5 72552423 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:14:59 79.7 73441029 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:15:59 79.4 74442278 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:17:05 78.9 75444934 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:18:09 78.5 76448454 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:19:09 78.1 77341351 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:20:14 77.7 78344670 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:21:18 77.3 79345266 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:22:18 76.8 80123352 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:23:24 76.5 81236322 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:24:29 76.2 82239974 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:25:32 75.9 83243463 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:26:35 75.6 84248542 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:27:38 75.3 85250006 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:28:43 75.0 86250432 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:29:46 74.5 87028244 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:30:53 74.2 88029279 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:31:57 74.0 89031637 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:33:01 73.7 90034353 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:34:01 73.4 90926464 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:35:04 73.2 91927967 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:36:07 73.0 92928072 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:37:13 72.7 93927625 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:38:14 72.8 95263246 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:39:17 72.9 96712373 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:40:20 73.1 98274088 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:41:20 73.3 99715346 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:42:20 73.4 101031731 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:43:24 73.5 102570026 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +May 03 05:44:26 73.7 104110079 196 93.7% 195.6 0.2% 3.5% 0.0% 0.0% 2.8% 0.0% +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192396_1Log.std.out b/src/multiqc/rna-seq/data/SRR3192396_1Log.std.out new file mode 100644 index 00000000..f13f9ca3 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_1Log.std.out @@ -0,0 +1,4 @@ +May 03 04:15:10 ..... Started STAR run +May 03 04:15:10 ..... Loading genome +May 03 04:19:43 ..... Started mapping +May 03 05:44:43 ..... Finished successfully diff --git a/src/multiqc/rna-seq/data/SRR3192396_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192396_1_fastqc.html new file mode 100644 index 00000000..223e4f2f --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192396_1.fastq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192396_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192396_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences105089150
Sequences flagged as poor quality0
Sequence length101
%GC50

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA5497210.5230996729919312No Hit
GTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGT5142410.48933786218653397No Hit
TTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCA4936080.46970405603242577No Hit
GTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGC4483180.42660731388540113No Hit
GCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTT4232160.40272092789788483No Hit
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG2985540.28409593188259685No Hit
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT2442730.23244359669861253No Hit
CACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTC2381730.22663900126701947No Hit
AGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTG2330200.22173554548685567No Hit
CAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTT1982130.18861414332497695No Hit
ATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGAT1970400.18749794817067225No Hit
GGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACC1914390.1821681876768439No Hit
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA1798730.17116229410933478No Hit
GGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAA1697180.16149907007526465No Hit
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1594120.1516921585149371No Hit
CTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACG1509320.14362281929200113No Hit
AATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGA1353330.12877923172848957No Hit
CCCGCTTCTTCGGTTCCCGCCTCCTCCCCGTTCACCGCCGGGGCGGCTCG1315070.12513851334795267No Hit
GGACCTTGAGAGCTTGTTTGGAGGTTCTAGCAGGGGAGCGCAGCTACTCG1295380.12326486606847614No Hit
CGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCA1292960.12303458539725558No Hit
GGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAA1289350.12269106753646786No Hit
GGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTC1211690.11530115145093475No Hit
GCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCC1132960.10780941705209339No Hit
GCTTGTTTGGAGGTTCTAGCAGGGGAGCGCAGCTACTCGTATACCCTTGA1090680.1037861663168843No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
ACTTCGC271700.026.1998677
CTCGCTA901300.024.1103618
TCGCTAT941000.023.4211949
GATGTGT773900.022.3604852
GTCTCGC1013000.021.7377576
GGGGTCT2234000.021.6014923
TAAGCGT383850.021.23180682-83
CCCTACG676450.020.53985832-33
CTACGTT687050.020.28531334-35
GGATGTG870150.020.0312461
CACTTCG367300.019.7814256
TCTCGCT1125850.019.740247
GGGGGTC1492900.019.2224862
GGTCTTA1232550.019.2103315
GGTCTCG1179100.019.122615
CTTCGCT390150.018.8298038
GGGGGGT820100.018.6849231
TTCGCTG390850.018.6502829
ACTACCC751600.018.54490328-29
AACGAAC882750.018.45718876-77
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192396_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192396_1_fastqc.zip new file mode 100644 index 00000000..4b340d8c Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192396_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192396_1_star_aligned.bam_counts.txt.summary b/src/multiqc/rna-seq/data/SRR3192396_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..18e1f3b1 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_1_star_aligned.bam_counts.txt.summary @@ -0,0 +1,12 @@ +Status SRR3192396_1_star_aligned.bam +Assigned 71898412 +Unassigned_Ambiguity 3195747 +Unassigned_MultiMapping 8363965 +Unassigned_NoFeatures 22980875 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_FragmentLength 0 +Unassigned_Chimera 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_Duplicate 0 diff --git a/src/multiqc/rna-seq/data/SRR3192396_1_val_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192396_1_val_1_fastqc.html new file mode 100644 index 00000000..b0e0cf7c --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_1_val_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192396_1_val_1.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192396_1_val_1.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192396_1_val_1.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences104413184
Sequences flagged as poor quality0
Sequence length20-101
%GC50

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA5394750.5166732584268285No Hit
GTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGT5053360.48397719582998255No Hit
TTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCA4747810.45471364995439656No Hit
GTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGC4312370.41301010416462347No Hit
GCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTT4153970.3978396061554832No Hit
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG2895370.27729927285810957No Hit
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT2375140.22747510505952964No Hit
CACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTC2309440.22118279622619302No Hit
AGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTG2287110.21904417740962676No Hit
CAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTT1944860.18626574973520585No Hit
ATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGAT1941760.18596885236255223No Hit
GGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACC1876390.17970814873340132No Hit
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA1765570.16909454652776415No Hit
GGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAA1677580.16066744981170195No Hit
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1569410.1503076469730106No Hit
CTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACG1475960.14135762778769392No Hit
AATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGA1334940.12785167053233432No Hit
CGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCA1284600.12303044029382344No Hit
GGACCTTGAGAGCTTGTTTGGAGGTTCTAGCAGGGGAGCGCAGCTACTCG1271360.12176240119255437No Hit
GGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAA1261300.12079892133162035No Hit
GGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTC1189670.11393867655640115No Hit
GCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCC1106580.10598086923582371No Hit
CCCGCTTCTTCGGTTCCCGCCTCCTCCCCGTTCACCGCCGGGGCGGCTCG1068100.10229551088107801No Hit
GCTTGTTTGGAGGTTCTAGCAGGGGAGCGCAGCTACTCGTATACCCTTGA1050700.10062905466037698No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
ACTTCGC270350.024.916447
CTCGCTA873000.023.8377238
TCGCTAT911850.023.0302669
GTCTCGC963900.021.9355416
GATGTGT754850.021.7361372
GGGGGGT686000.021.6415351
TAAGCGT372200.021.58756682-83
GGGGTCT2165150.020.9934773
CCCTACG662900.020.2215532-33
CTACGTT677300.019.83046734-35
TCTCGCT1078600.019.7616967
GGATGTG858650.019.2219811
GGTCTCG1131150.019.1178475
CACTTCG364200.018.915266
TGCGGAC1530450.018.87812292-93
GGGGGTC1429350.018.7635172
AACGAAC866950.018.75679276-77
CGAACCT874150.018.5719378-79
ACTACCC734250.018.25302328-29
GGTCTTA1213100.018.2118135
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192396_1_val_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192396_1_val_1_fastqc.zip new file mode 100644 index 00000000..4ed0e7b1 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192396_1_val_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192396_2.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192396_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..27d8f45f --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_2.fastq.gz_trimming_report.txt @@ -0,0 +1,158 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192396_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192396_2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2246.39 s (21 us/read; 2.81 M reads/minute). + +=== Summary === + +Total reads processed: 105,089,150 +Reads with adapters: 32,883,672 (31.3%) +Reads written (passing filters): 105,089,150 (100.0%) + +Total basepairs processed: 10,614,004,150 bp +Quality-trimmed: 373,151,687 bp (3.5%) +Total written (filtered): 10,194,057,791 bp (96.0%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 32883672 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 31.6% + C: 30.7% + G: 21.2% + T: 16.5% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 22961688 26272287.5 0 22961688 +2 7631789 6568071.9 0 7631789 +3 1774925 1642018.0 0 1774925 +4 352001 410504.5 0 352001 +5 85236 102626.1 0 85236 +6 14948 25656.5 0 14948 +7 5781 6414.1 0 5781 +8 2947 1603.5 0 2947 +9 4332 400.9 0 2702 1630 +10 4609 100.2 1 2721 1888 +11 4651 25.1 1 2206 2445 +12 3142 6.3 1 2694 448 +13 2715 1.6 1 2575 140 +14 3889 1.6 1 3787 102 +15 1551 1.6 1 1462 89 +16 1876 1.6 1 1792 84 +17 2296 1.6 1 2204 92 +18 601 1.6 1 550 51 +19 1322 1.6 1 1268 54 +20 814 1.6 1 765 49 +21 433 1.6 1 359 74 +22 766 1.6 1 684 82 +23 971 1.6 1 903 68 +24 1405 1.6 1 1323 82 +25 724 1.6 1 646 78 +26 873 1.6 1 777 96 +27 666 1.6 1 582 84 +28 1132 1.6 1 1082 50 +29 813 1.6 1 701 112 +30 2529 1.6 1 2431 98 +31 221 1.6 1 135 86 +32 751 1.6 1 699 52 +33 325 1.6 1 276 49 +34 449 1.6 1 361 88 +35 770 1.6 1 667 103 +36 704 1.6 1 618 86 +37 862 1.6 1 800 62 +38 468 1.6 1 419 49 +39 551 1.6 1 501 50 +40 361 1.6 1 277 84 +41 438 1.6 1 366 72 +42 838 1.6 1 728 110 +43 196 1.6 1 84 112 +44 356 1.6 1 275 81 +45 580 1.6 1 458 122 +46 175 1.6 1 84 91 +47 203 1.6 1 111 92 +48 183 1.6 1 124 59 +49 204 1.6 1 120 84 +50 256 1.6 1 172 84 +51 197 1.6 1 157 40 +52 104 1.6 1 52 52 +53 62 1.6 1 33 29 +54 86 1.6 1 34 52 +55 150 1.6 1 52 98 +56 78 1.6 1 37 41 +57 113 1.6 1 40 73 +58 100 1.6 1 45 55 +59 81 1.6 1 36 45 +60 100 1.6 1 51 49 +61 126 1.6 1 46 80 +62 98 1.6 1 59 39 +63 259 1.6 1 152 107 +64 161 1.6 1 133 28 +65 187 1.6 1 139 48 +66 100 1.6 1 39 61 +67 68 1.6 1 31 37 +68 69 1.6 1 5 64 +69 35 1.6 1 1 34 +70 48 1.6 1 1 47 +71 41 1.6 1 2 39 +72 36 1.6 1 1 35 +73 39 1.6 1 0 39 +74 45 1.6 1 1 44 +75 49 1.6 1 0 49 +76 69 1.6 1 0 69 +77 17 1.6 1 0 17 +78 59 1.6 1 1 58 +79 33 1.6 1 0 33 +80 51 1.6 1 1 50 +81 14 1.6 1 0 14 +82 41 1.6 1 0 41 +83 52 1.6 1 0 52 +84 67 1.6 1 1 66 +85 21 1.6 1 0 21 +86 47 1.6 1 1 46 +87 31 1.6 1 0 31 +88 31 1.6 1 1 30 +89 24 1.6 1 0 24 +90 12 1.6 1 0 12 +91 40 1.6 1 0 40 +92 41 1.6 1 0 41 +93 29 1.6 1 0 29 +94 48 1.6 1 0 48 +95 21 1.6 1 0 21 +96 7 1.6 1 0 7 +97 28 1.6 1 0 28 +98 52 1.6 1 0 52 +99 32 1.6 1 0 32 +100 24 1.6 1 0 24 +101 33 1.6 1 0 33 + + +RUN STATISTICS FOR INPUT FILE: SRR3192396_2.fastq.gz +============================================= +105089150 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 105089150 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 675966 (0.64%) diff --git a/src/multiqc/rna-seq/data/SRR3192396_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192396_2_fastqc.html new file mode 100644 index 00000000..b15870da --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192396_2.fastq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192396_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192396_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences105089150
Sequences flagged as poor quality0
Sequence length101
%GC51

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[WARN]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG18232941.7349973807952581No Hit
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG9742020.9270243407621053No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA5580380.5310139058123508No Hit
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT4745480.45156707424125136No Hit
GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT4377870.41658629839521966No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA3006860.2861246855645897No Hit
GGTCGACCCGTGCGGAGGAGCGAGGAGGAAGGACGCGCGAGGGCCGGGAC2863310.27246485483991445No Hit
GCAGGTCGACCCGTGCGGAGGAGCGAGGAGGAAGGACGCGCGAGGGCCGG2559660.2435703400398614No Hit
CTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCT2538750.24158060085175298No Hit
GTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAG2234040.2125852193114132No Hit
CTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCT2204830.20980567451539955No Hit
GCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGC2078640.19779777455617445No Hit
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT2056590.19569955604360678No Hit
GGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGC1939770.18458328000559523No Hit
CTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTG1908310.18158963127972774No Hit
CGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGG1718730.16354970993675372No Hit
CTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGA1456980.13864228609708995No Hit
ACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCT1406430.13383208447304026No Hit
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT1392570.1325132042651406No Hit
CTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTG1343420.1278362228641111No Hit
GCTGCAGGTCGACCCGTGCGGAGGAGCGAGGAGGAAGGACGCGCGAGGGC1264330.12031023183649311No Hit
TGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTA1210380.11517649538510873No Hit
CGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTA1199910.11418019843152218No Hit
CGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGT1104760.10512598113125857No Hit
CCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCG1085750.10331704081724896No Hit
GGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGC1067520.10158232319892205No Hit
GGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTC1067230.10155472758129645No Hit
CCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTT1058660.10073922950180869No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGGTGGC4048850.071.389711
GGGCGAT649050.068.75771
GGCGATC699600.063.800112
TGGCGCG4578150.062.8249324
GGCGCGT4665550.061.7385
GTGGCGC4742300.060.678353
GGTGGCG4791650.060.1574362
GCGCGTG5153550.056.009166
CGCGTGC5228750.055.1259167
GCGTGCC5264150.054.8354848
CGTGCCT5347000.054.026389
GCGATCT917550.049.001433
CGATCTG1080600.041.5857054
TAGTCCC5492350.034.29420516-17
TGTAGTC5553700.033.9951414-15
CCTGTAG5628950.033.6584312-13
TGCCTGT6075400.031.2204410-11
AGGTCGA855550.030.9285643
GTCCCAG6422700.029.44554118-19
TACTCGG6943050.027.3357726-27
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192396_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192396_2_fastqc.zip new file mode 100644 index 00000000..221e4399 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192396_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192396_2_val_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192396_2_val_2_fastqc.html new file mode 100644 index 00000000..8792035e --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192396_2_val_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192396_2_val_2.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192396_2_val_2.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192396_2_val_2.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences104413184
Sequences flagged as poor quality0
Sequence length20-101
%GC51

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG17466871.6728605843491946No Hit
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG9508320.9106436214032128No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA5287700.5064207217356765No Hit
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT4573930.43806058054890845No Hit
GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT3363360.32212024106074577No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA2925850.2802184444447169No Hit
GGTCGACCCGTGCGGAGGAGCGAGGAGGAAGGACGCGCGAGGGCCGGGAC2669490.25566598945972185No Hit
CTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCT2494630.2389190621751368No Hit
GCAGGTCGACCCGTGCGGAGGAGCGAGGAGGAAGGACGCGCGAGGGCCGG2387570.22866556775052466No Hit
CTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCT2159310.2068043437886158No Hit
GTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAG2127190.20372810391454016No Hit
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT2002620.19179761820116512No Hit
GCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGC1959740.1876908571239433No Hit
GGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGC1898100.18178738807543693No Hit
CTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTG1850970.17727359027764156No Hit
CGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGG1367040.13092599493948964No Hit
ACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCT1362830.1305227891527568No Hit
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT1315570.1259965408199792No Hit
CTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTG1312920.12574274145303335No Hit
GCTGCAGGTCGACCCGTGCGGAGGAGCGAGGAGGAAGGACGCGCGAGGGC1184600.11345310569209344No Hit
TGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTA1184260.11342054275444756No Hit
CTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGA1176140.1126428631847871No Hit
CGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTA1168800.11193988682502011No Hit
CGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGT1083740.10379340601278858No Hit
CCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCG1078480.10328963821273757No Hit
CCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTT1048630.10043080383412117No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGGTGGC4004350.069.607011
GGGCGAT630100.067.476991
GGCGATC676600.062.8641132
TGGCGCG4575550.060.605684
GGCGCGT4639400.059.7893755
GTGGCGC4722950.058.782073
GGTGGCG4758300.058.4172672
GCGCGTG5129050.054.1901786
CGCGTGC5235300.053.078917
GCGTGCC5269650.052.772018
CGTGCCT5345350.052.0683179
GCGATCT904750.047.3244483
CGATCTG1062400.040.2976464
TAGTCCC5500250.033.13526516-17
TGTAGTC5552150.032.87983314-15
CCTGTAG5613550.032.6474412-13
TGCCTGT6063500.030.23705110-11
AGGTCGA852350.029.6042793
GTCCCAG6400950.028.59918418-19
TACTCGG6917100.026.5314626-27
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192396_2_val_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192396_2_val_2_fastqc.zip new file mode 100644 index 00000000..76f97dbb Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192396_2_val_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192397_1.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192397_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..c3948eab --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_1.fastq.gz_trimming_report.txt @@ -0,0 +1,155 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192397_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192397_1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2021.96 s (22 us/read; 2.74 M reads/minute). + +=== Summary === + +Total reads processed: 92,494,632 +Reads with adapters: 29,457,331 (31.8%) +Reads written (passing filters): 92,494,632 (100.0%) + +Total basepairs processed: 9,341,957,832 bp +Quality-trimmed: 155,135,737 bp (1.7%) +Total written (filtered): 9,145,059,528 bp (97.9%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29457331 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 30.4% + C: 30.4% + G: 17.5% + T: 21.8% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 20977783 23123658.0 0 20977783 +2 6579269 5780914.5 0 6579269 +3 1366985 1445228.6 0 1366985 +4 338775 361307.2 0 338775 +5 87544 90326.8 0 87544 +6 15846 22581.7 0 15846 +7 6972 5645.4 0 6972 +8 6831 1411.4 0 6831 +9 6466 352.8 0 5640 826 +10 7319 88.2 1 5638 1681 +11 6080 22.1 1 5119 961 +12 5774 5.5 1 5601 173 +13 5766 1.4 1 5695 71 +14 5830 1.4 1 5748 82 +15 4397 1.4 1 4326 71 +16 4689 1.4 1 4618 71 +17 4171 1.4 1 4090 81 +18 3641 1.4 1 3570 71 +19 1455 1.4 1 1411 44 +20 1583 1.4 1 1547 36 +21 1093 1.4 1 1055 38 +22 958 1.4 1 910 48 +23 765 1.4 1 712 53 +24 581 1.4 1 545 36 +25 549 1.4 1 512 37 +26 444 1.4 1 405 39 +27 632 1.4 1 602 30 +28 622 1.4 1 592 30 +29 722 1.4 1 662 60 +30 724 1.4 1 680 44 +31 438 1.4 1 368 70 +32 579 1.4 1 541 38 +33 937 1.4 1 912 25 +34 860 1.4 1 804 56 +35 1644 1.4 1 1590 54 +36 678 1.4 1 641 37 +37 1182 1.4 1 1119 63 +38 472 1.4 1 426 46 +39 486 1.4 1 453 33 +40 327 1.4 1 283 44 +41 384 1.4 1 348 36 +42 241 1.4 1 218 23 +43 272 1.4 1 255 17 +44 208 1.4 1 164 44 +45 328 1.4 1 285 43 +46 279 1.4 1 240 39 +47 161 1.4 1 112 49 +48 172 1.4 1 137 35 +49 160 1.4 1 132 28 +50 105 1.4 1 81 24 +51 142 1.4 1 119 23 +52 168 1.4 1 122 46 +53 161 1.4 1 113 48 +54 94 1.4 1 64 30 +55 65 1.4 1 33 32 +56 92 1.4 1 80 12 +57 93 1.4 1 62 31 +58 91 1.4 1 69 22 +59 168 1.4 1 140 28 +60 83 1.4 1 53 30 +61 62 1.4 1 29 33 +62 60 1.4 1 28 32 +63 50 1.4 1 30 20 +64 61 1.4 1 33 28 +65 37 1.4 1 10 27 +66 54 1.4 1 15 39 +67 51 1.4 1 21 30 +68 63 1.4 1 22 41 +69 43 1.4 1 22 21 +70 102 1.4 1 46 56 +71 104 1.4 1 27 77 +72 50 1.4 1 24 26 +73 34 1.4 1 4 30 +74 33 1.4 1 2 31 +75 34 1.4 1 0 34 +76 21 1.4 1 0 21 +77 27 1.4 1 1 26 +78 36 1.4 1 0 36 +79 36 1.4 1 0 36 +80 47 1.4 1 0 47 +81 46 1.4 1 0 46 +82 41 1.4 1 0 41 +83 53 1.4 1 0 53 +84 35 1.4 1 0 35 +85 29 1.4 1 0 29 +86 67 1.4 1 0 67 +87 20 1.4 1 0 20 +88 37 1.4 1 0 37 +89 60 1.4 1 0 60 +90 79 1.4 1 1 78 +91 56 1.4 1 0 56 +92 46 1.4 1 0 46 +93 28 1.4 1 0 28 +94 80 1.4 1 0 80 +95 60 1.4 1 0 60 +96 22 1.4 1 1 21 +97 52 1.4 1 0 52 +98 39 1.4 1 0 39 +99 23 1.4 1 0 23 +100 18 1.4 1 0 18 +101 99 1.4 1 1 98 + + +RUN STATISTICS FOR INPUT FILE: SRR3192397_1.fastq.gz +============================================= +92494632 sequences processed in total + diff --git a/src/multiqc/rna-seq/data/SRR3192397_1Log.final.out b/src/multiqc/rna-seq/data/SRR3192397_1Log.final.out new file mode 100644 index 00000000..075fa397 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_1Log.final.out @@ -0,0 +1,34 @@ + Started job on | May 03 01:49:26 + Started mapping on | May 03 01:53:48 + Finished on | May 03 02:58:56 + Mapping speed, Million of reads per hour | 84.72 + + Number of input reads | 91969895 + Average input read length | 196 + UNIQUE READS: + Uniquely mapped reads number | 87095738 + Uniquely mapped reads % | 94.70% + Average mapped length | 196.47 + Number of splices: Total | 35803790 + Number of splices: Annotated (sjdb) | 35270329 + Number of splices: GT/AG | 35325123 + Number of splices: GC/AG | 305371 + Number of splices: AT/AC | 39160 + Number of splices: Non-canonical | 134136 + Mismatch rate per base, % | 0.21% + Deletion rate per base | 0.02% + Deletion average length | 1.56 + Insertion rate per base | 0.01% + Insertion average length | 1.49 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 3124558 + % of reads mapped to multiple loci | 3.40% + Number of reads mapped to too many loci | 10279 + % of reads mapped to too many loci | 0.01% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 1.87% + % of reads unmapped: other | 0.02% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff --git a/src/multiqc/rna-seq/data/SRR3192397_1Log.out b/src/multiqc/rna-seq/data/SRR3192397_1Log.out new file mode 100644 index 00000000..10724d6a --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_1Log.out @@ -0,0 +1,408 @@ +STAR version=STAR_2.5.1b +STAR compilation time,server,dir=Tue Jan 26 13:48:00 CET 2016 milou-b.uppmax.uu.se:/sw/apps/bioinfo/star/2.5.1b/src/source +##### DEFAULT parameters: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 1 +runDirPerm User_RWX +runRNGseed 777 +genomeDir ./GenomeDir/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn Read1 Read2 +readFilesCommand - +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outTmpDir - +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +##### Command Line: +STAR --runThreadN 4 --outQSconversionAdd 0 --outSAMattributes Standard --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --readFilesIn SRR3192397_1_val_1.fq.gz SRR3192397_2_val_2.fq.gz --outFileNamePrefix SRR3192397_1 --outStd SAM +##### Initial USER parameters from Command Line: +outFileNamePrefix SRR3192397_1 +outStd SAM +###### All USER parameters from Command Line: +runThreadN 4 ~RE-DEFINED +outQSconversionAdd 0 ~RE-DEFINED +outSAMattributes Standard ~RE-DEFINED +genomeLoad NoSharedMemory ~RE-DEFINED +readFilesCommand zcat ~RE-DEFINED +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ~RE-DEFINED +readFilesIn SRR3192397_1_val_1.fq.gz SRR3192397_2_val_2.fq.gz ~RE-DEFINED +outFileNamePrefix SRR3192397_1 ~RE-DEFINED +outStd SAM ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runThreadN 4 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +readFilesIn SRR3192397_1_val_1.fq.gz SRR3192397_2_val_2.fq.gz +readFilesCommand zcat +outFileNamePrefix SRR3192397_1 +outStd SAM +outQSconversionAdd 0 +outSAMattributes Standard + +------------------------------- +##### Final effective command line: +STAR --runThreadN 4 --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --genomeLoad NoSharedMemory --readFilesIn SRR3192397_1_val_1.fq.gz SRR3192397_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix SRR3192397_1 --outStd SAM --outQSconversionAdd 0 --outSAMattributes Standard + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 4 +runDirPerm User_RWX +runRNGseed 777 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn SRR3192397_1_val_1.fq.gz SRR3192397_2_val_2.fq.gz +readFilesCommand zcat +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outFileNamePrefix SRR3192397_1 +outTmpDir - +outStd SAM +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +---------------------------------------- + + + Input read files for mate 1, from input string SRR3192397_1_val_1.fq.gz +-rw-rw-r-- 1 phil b2013064 7578585489 May 3 01:01 SRR3192397_1_val_1.fq.gz + + readsCommandsFile: +exec > "SRR3192397_1_STARtmp/tmp.fifo.read1" +echo FILE 0 +zcat "SRR3192397_1_val_1.fq.gz" + + + Input read files for mate 2, from input string SRR3192397_2_val_2.fq.gz +-rw-rw-r-- 1 phil b2013064 7694217071 May 3 01:01 SRR3192397_2_val_2.fq.gz + + readsCommandsFile: +exec > "SRR3192397_1_STARtmp/tmp.fifo.read2" +echo FILE 0 +zcat "SRR3192397_2_val_2.fq.gz" + +Finished loading and checking parameters +Reading genome generation parameters: +versionGenome 20201 ~RE-DEFINED +genomeFastaFiles genome.fa ~RE-DEFINED +genomeSAindexNbases 14 ~RE-DEFINED +genomeChrBinNbits 18 ~RE-DEFINED +genomeSAsparseD 1 ~RE-DEFINED +sjdbOverhang 100 ~RE-DEFINED +sjdbFileChrStartEnd - ~RE-DEFINED +sjdbGTFfile genes.gtf ~RE-DEFINED +sjdbGTFchrPrefix - ~RE-DEFINED +sjdbGTFfeatureExon exon ~RE-DEFINED +sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED +sjdbGTFtagExonParentGene gene_id ~RE-DEFINED +sjdbInsertSave Basic ~RE-DEFINED +Genome version is compatible with current STAR version +Number of real (reference) chromosmes= 25 +1 1 249250621 0 +2 2 243199373 249298944 +3 3 198022430 492568576 +4 4 191154276 690749440 +5 5 180915260 882114560 +6 6 171115067 1063256064 +7 7 159138663 1234436096 +8 8 146364022 1393819648 +9 9 141213431 1540358144 +10 10 135534747 1681653760 +11 11 135006516 1817444352 +12 12 133851895 1952710656 +13 13 115169878 2086666240 +14 14 107349540 2202009600 +15 15 102531392 2309488640 +16 16 90354753 2412249088 +17 17 81195210 2502688768 +18 18 78077248 2583953408 +19 19 59128983 2662072320 +20 20 63025520 2721316864 +21 21 48129895 2784493568 +22 22 51304566 2832728064 +23 X 155270560 2884108288 +24 Y 59373566 3039559680 +25 MT 16569 3099066368 +--sjdbOverhang = 100 taken from the generated genome +Started loading the genome: Tue May 3 01:49:27 2016 + +checking Genome sizefile size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +checking SA sizefile size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 +Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 +nGenome=3168538239; nSAbyte=24152204822 +GstrandBit=32 SA number of indices=5855079956 +Shared memory is not used for genomes. Allocated a private copy of the genome. +Genome file size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3168538239 bytes +SA file size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24152204822 bytes +Loading SAindex ... done: 1565873619 bytes +Finished loading the genome: Tue May 3 01:53:47 2016 + +Processing splice junctions database sjdbN=344327, sjdbOverhang=100 +alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 +Created thread # 1 +Created thread # 2 +Created thread # 3 +Starting to map file # 0 +mate 1: SRR3192397_1_val_1.fq.gz +mate 2: SRR3192397_2_val_2.fq.gz +Thread #3 end of input stream, nextChar=-1 +Completed: thread #2 +Completed: thread #1 +Completed: thread #0 +Joined thread # 1 +Joined thread # 2 +Completed: thread #3 +Joined thread # 3 +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192397_1Log.progress.out b/src/multiqc/rna-seq/data/SRR3192397_1Log.progress.out new file mode 100644 index 00000000..d18b706a --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_1Log.progress.out @@ -0,0 +1,65 @@ + Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped + M/hr number length unique length MMrate multi multi+ MM short other +May 03 01:54:49 74.0 1253673 197 94.8% 197.0 0.2% 3.3% 0.0% 0.0% 1.9% 0.0% +May 03 01:55:53 81.5 2828417 197 94.8% 197.0 0.2% 3.3% 0.0% 0.0% 1.8% 0.0% +May 03 01:56:54 83.1 4290920 197 94.8% 197.0 0.2% 3.4% 0.0% 0.0% 1.8% 0.0% +May 03 01:57:57 81.6 5643128 197 94.8% 196.9 0.2% 3.4% 0.0% 0.0% 1.8% 0.0% +May 03 01:58:57 82.8 7109118 197 94.7% 196.7 0.2% 3.4% 0.0% 0.0% 1.8% 0.0% +May 03 02:00:00 84.1 8690090 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.8% 0.0% +May 03 02:01:01 84.4 10150924 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:02:02 83.7 11480482 197 94.7% 196.7 0.2% 3.4% 0.0% 0.0% 1.8% 0.0% +May 03 02:03:05 84.2 13033054 197 94.7% 196.7 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:04:06 84.3 14477443 197 94.7% 196.7 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:05:06 84.5 15922768 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:06:09 83.8 17258683 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:07:11 84.3 18813645 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:08:11 84.5 20254808 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:09:16 84.6 21807533 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:10:19 84.1 23141065 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:11:23 84.3 24697752 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:12:27 84.5 26256299 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:13:31 84.6 27809727 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:14:34 84.2 29139924 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:15:38 84.3 30692320 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:16:42 84.5 32246875 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:17:45 84.7 33802666 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:18:47 84.4 35137513 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:19:48 84.4 36579878 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:20:48 84.5 38020297 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:21:48 84.6 39461328 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:22:51 84.3 40794138 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:23:52 84.3 42239056 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:24:56 84.4 43797005 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:26:00 84.5 45352621 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:27:00 84.4 46683228 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:28:02 84.3 48124748 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:29:03 84.4 49568876 197 94.7% 196.6 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:30:04 84.4 51014692 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:31:05 84.6 52572801 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:32:06 84.5 53907499 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:33:08 84.6 55459528 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:34:08 84.6 56902089 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:35:11 84.8 58458320 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:36:11 84.5 59682818 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:37:13 84.5 61124220 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:38:17 84.5 62676564 197 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:39:21 84.6 64232439 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:40:24 84.4 65567546 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:41:24 84.5 67012080 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:42:27 84.6 68564458 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:43:29 84.5 70008206 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:44:33 84.3 71342740 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:45:34 84.5 72900553 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:46:36 84.6 74452708 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:47:38 84.7 76005720 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:48:41 84.5 77338796 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:49:43 84.7 78896178 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:50:46 84.7 80448783 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:51:49 84.8 82000296 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:52:50 84.7 83333359 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:53:53 84.8 84890459 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:54:57 84.8 86446806 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:56:00 84.9 87999058 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:57:04 84.7 89331795 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +May 03 02:58:08 84.8 90889298 196 94.7% 196.5 0.2% 3.4% 0.0% 0.0% 1.9% 0.0% +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192397_1Log.std.out b/src/multiqc/rna-seq/data/SRR3192397_1Log.std.out new file mode 100644 index 00000000..61b52863 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_1Log.std.out @@ -0,0 +1,4 @@ +May 03 01:49:26 ..... Started STAR run +May 03 01:49:27 ..... Loading genome +May 03 01:53:48 ..... Started mapping +May 03 02:58:56 ..... Finished successfully diff --git a/src/multiqc/rna-seq/data/SRR3192397_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192397_1_fastqc.html new file mode 100644 index 00000000..c19ec10e --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192397_1.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192397_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192397_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences92494632
Sequences flagged as poor quality0
Sequence length101
%GC48

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA5340590.5773945886935363No Hit
GTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGT5000560.5406324552975139No Hit
GTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGC4269820.4616289516131055No Hit
GCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTT4235300.4578968431378807No Hit
TTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCA4226500.45694543657409226No Hit
AGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTG2340530.25304495508452857No Hit
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG2113450.22849434116349585No Hit
ATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGAT1943750.21014733049589301No Hit
CAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTT1736700.18776224765130156No Hit
GGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACC1696040.18336631686906976No Hit
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT1658170.17927202521331184No Hit
CACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTC1414570.15293536169753072No Hit
GGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAA1400330.15139581289430937No Hit
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA1377400.14891675010934688No Hit
AATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGA1354150.14640309072206484No Hit
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1287410.1391875368507872No Hit
CGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCA1261740.1364122406584633No Hit
GGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAA1237190.13375803257425792No Hit
CTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTG1228880.1328596020577713No Hit
CTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACG1099610.11888365586448302No Hit
GTGTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGC951170.10283515696348736No Hit
GGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG938590.10147507803479883No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
ACTTCGC253800.024.960487
CTCGCTA695150.023.8074558
TCGCTAT732550.022.942049
ACGGGGT429650.022.5221861
GTCTCGC757850.022.000696
CGCGCGA91200.021.220741
GGGGTCT1958950.020.6201423
GGGGGGT621450.020.5799261
GATGTGT626250.020.1101552
CGAACCT805600.020.0445778-79
AACGAAC809300.020.00562176-77
GGTCTCG870250.019.7048055
TCTCGCT858300.019.6969787
ATAGCGG832550.019.46524888-89
CAAACGA836250.019.38642574-75
CACTTCG332750.019.3379276
TAAGCGT285900.019.20341982-83
GGGGGTC1373050.018.9117532
ACGTAGG871950.018.72773252-53
TCACGTA867700.018.71675550-51
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192397_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192397_1_fastqc.zip new file mode 100644 index 00000000..a9f28635 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192397_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192397_1_star_aligned.bam_counts.txt.summary b/src/multiqc/rna-seq/data/SRR3192397_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..9a723e2d --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_1_star_aligned.bam_counts.txt.summary @@ -0,0 +1,12 @@ +Status SRR3192397_1_star_aligned.bam +Assigned 62966583 +Unassigned_Ambiguity 2741920 +Unassigned_MultiMapping 7199385 +Unassigned_NoFeatures 21598644 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_FragmentLength 0 +Unassigned_Chimera 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_Duplicate 0 diff --git a/src/multiqc/rna-seq/data/SRR3192397_1_val_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192397_1_val_1_fastqc.html new file mode 100644 index 00000000..922b75ff --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_1_val_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192397_1_val_1.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192397_1_val_1.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192397_1_val_1.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences91969895
Sequences flagged as poor quality0
Sequence length20-101
%GC48

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA5242460.5700191350658822No Hit
GTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGT4910330.5339062309465504No Hit
GCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTT4151330.45137922577817446No Hit
GTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGC4115410.4474735999209306No Hit
TTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCA4073220.44288622923838283No Hit
AGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTG2297800.24984262513293073No Hit
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG2057980.22376670104929447No Hit
ATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGAT1918580.20860956729373237No Hit
CAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTT1703260.18519755839669058No Hit
GGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACC1666420.1811918998059093No Hit
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT1617470.17586950599432566No Hit
CACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTC1375260.14953371426595627No Hit
GGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAA1373920.14938801441493438No Hit
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA1352210.14702745936591535No Hit
AATTTGAAGTAGATAGAAACCGACCTGGATTACTCCGGTCTGAACTCAGA1338450.1455313176121382No Hit
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1268450.1379201313647254No Hit
CGGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCA1252710.13620870177137856No Hit
GGATGTGTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAA1223040.13298264611479657No Hit
CTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTG1204630.13098090413172703No Hit
CTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACG1079310.11735470612421599No Hit
GTGTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGC940080.1022160566781119No Hit
GGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTTTG927040.100798201411451No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
ACTTCGC251300.025.992617
GGTTATA833250.025.14731894-95
CGCGCGA88700.023.3595521
CTCGCTA685450.022.9520078
GGGGGGT527550.022.9285491
ACGGGGT418300.022.4574831
TCGCTAT726550.021.9287919
GTCTCGC731500.021.6342246
GGGGTCT1919850.020.0845833
AACGAAC790950.020.0754576-77
CGAACCT788800.020.0725778-79
CACTTCG328300.020.0661966
ATAGCGG775550.019.96929488-89
GATGTGT622600.019.7059042
TAAGCGT271000.019.41685982-83
CAAACGA817850.019.40681674-75
TCTCGCT827300.019.1852117
GGTCTCG850850.019.1514265
GGGGGTC1324600.018.8335442
CTTCGCT354350.018.7353528
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192397_1_val_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192397_1_val_1_fastqc.zip new file mode 100644 index 00000000..69ff4b47 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192397_1_val_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192397_2.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192397_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..89552b12 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_2.fastq.gz_trimming_report.txt @@ -0,0 +1,158 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192397_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192397_2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2040.01 s (22 us/read; 2.72 M reads/minute). + +=== Summary === + +Total reads processed: 92,494,632 +Reads with adapters: 29,937,340 (32.4%) +Reads written (passing filters): 92,494,632 (100.0%) + +Total basepairs processed: 9,341,957,832 bp +Quality-trimmed: 283,316,439 bp (3.0%) +Total written (filtered): 9,015,621,178 bp (96.5%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29937340 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 32.4% + C: 29.8% + G: 20.3% + T: 17.5% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 20943420 23123658.0 0 20943420 +2 6804121 5780914.5 0 6804121 +3 1663664 1445228.6 0 1663664 +4 339911 361307.2 0 339911 +5 77230 90326.8 0 77230 +6 15697 22581.7 0 15697 +7 8480 5645.4 0 8480 +8 6428 1411.4 0 6428 +9 6832 352.8 0 5304 1528 +10 7699 88.2 1 5674 2025 +11 6629 22.1 1 4456 2173 +12 6657 5.5 1 6125 532 +13 5561 1.4 1 5359 202 +14 8517 1.4 1 8363 154 +15 2875 1.4 1 2757 118 +16 3934 1.4 1 3817 117 +17 5541 1.4 1 5398 143 +18 1194 1.4 1 1110 84 +19 2071 1.4 1 1992 79 +20 1014 1.4 1 967 47 +21 421 1.4 1 368 53 +22 657 1.4 1 631 26 +23 699 1.4 1 648 51 +24 1087 1.4 1 1007 80 +25 474 1.4 1 433 41 +26 596 1.4 1 519 77 +27 488 1.4 1 408 80 +28 805 1.4 1 747 58 +29 648 1.4 1 499 149 +30 2186 1.4 1 2112 74 +31 122 1.4 1 67 55 +32 508 1.4 1 469 39 +33 302 1.4 1 232 70 +34 385 1.4 1 333 52 +35 1077 1.4 1 1003 74 +36 593 1.4 1 552 41 +37 1026 1.4 1 959 67 +38 466 1.4 1 420 46 +39 477 1.4 1 417 60 +40 338 1.4 1 253 85 +41 403 1.4 1 349 54 +42 767 1.4 1 676 91 +43 233 1.4 1 125 108 +44 369 1.4 1 305 64 +45 626 1.4 1 558 68 +46 171 1.4 1 111 60 +47 189 1.4 1 105 84 +48 210 1.4 1 125 85 +49 202 1.4 1 119 83 +50 209 1.4 1 142 67 +51 220 1.4 1 182 38 +52 139 1.4 1 69 70 +53 107 1.4 1 54 53 +54 92 1.4 1 48 44 +55 97 1.4 1 53 44 +56 105 1.4 1 51 54 +57 110 1.4 1 71 39 +58 124 1.4 1 71 53 +59 218 1.4 1 162 56 +60 114 1.4 1 75 39 +61 111 1.4 1 44 67 +62 65 1.4 1 50 15 +63 132 1.4 1 74 58 +64 127 1.4 1 61 66 +65 141 1.4 1 60 81 +66 71 1.4 1 16 55 +67 60 1.4 1 6 54 +68 59 1.4 1 4 55 +69 40 1.4 1 1 39 +70 49 1.4 1 0 49 +71 23 1.4 1 0 23 +72 33 1.4 1 1 32 +73 50 1.4 1 0 50 +74 31 1.4 1 1 30 +75 31 1.4 1 0 31 +76 36 1.4 1 0 36 +77 43 1.4 1 0 43 +78 78 1.4 1 0 78 +79 28 1.4 1 0 28 +80 33 1.4 1 0 33 +81 31 1.4 1 0 31 +82 19 1.4 1 0 19 +83 25 1.4 1 1 24 +84 25 1.4 1 1 24 +85 37 1.4 1 0 37 +86 21 1.4 1 0 21 +87 23 1.4 1 0 23 +88 26 1.4 1 0 26 +89 22 1.4 1 1 21 +90 17 1.4 1 0 17 +91 29 1.4 1 0 29 +92 46 1.4 1 0 46 +93 31 1.4 1 0 31 +94 16 1.4 1 0 16 +95 34 1.4 1 0 34 +96 22 1.4 1 1 21 +97 35 1.4 1 0 35 +98 37 1.4 1 0 37 +99 27 1.4 1 0 27 +100 13 1.4 1 2 11 +101 28 1.4 1 0 28 + + +RUN STATISTICS FOR INPUT FILE: SRR3192397_2.fastq.gz +============================================= +92494632 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 92494632 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 524737 (0.57%) diff --git a/src/multiqc/rna-seq/data/SRR3192397_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192397_2_fastqc.html new file mode 100644 index 00000000..3bceee88 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192397_2.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192397_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192397_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences92494632
Sequences flagged as poor quality0
Sequence length101
%GC49

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[WARN]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG16636641.7986600562938615No Hit
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG7723350.835005214140427No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA5526320.5974746729085856No Hit
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT3680110.39787281925723No Hit
GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT3354880.3627107787184882No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA2657150.2872761307921091No Hit
GCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGC1982940.21438433313621919No Hit
CTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCT1909110.20640224829479834No Hit
GTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAG1768970.1912510987664668No Hit
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT1735780.18766278241963275No Hit
CTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCT1714880.1854031918306351No Hit
CTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTG1592660.1721894520322001No Hit
GGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGC1443620.1560760845018552No Hit
CGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGG1272900.13761879716435868No Hit
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT1265670.13683713018070065No Hit
ACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCT1206420.13043135303246572No Hit
CTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTG1160700.12548836347605555No Hit
CAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTG1138200.12305578987546002No Hit
CTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGA1050730.11359902486016701No Hit
CCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTT1046250.11311467242769288No Hit
TGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTA932400.10080585000867943No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGGTGGC3494850.071.837031
GGGCGAT502200.066.510961
TGGCGCG4065950.061.5046924
GGCGATC544800.061.3982
GGCGCGT4128350.060.5750275
GTGGCGC4187500.059.7602423
GGTGGCG4238500.059.177152
GCGCGTG4556150.055.0318156
CGCGTGC4669900.053.6411257
GCGTGCC4722200.053.1737678
CGTGCCT4792550.052.430639
GCGATCT721350.046.797263
CGATCTG840300.040.1614954
TAGTCCC4942050.033.8579116-17
TGTAGTC5010250.033.51652514-15
CCTGTAG5059750.033.33855412-13
TGCCTGT5456800.030.92414710-11
GTCCCAG5716100.029.393118-19
TACTCGG6088450.027.70665626-27
GTAGTCC4928950.026.53200516-17
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192397_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192397_2_fastqc.zip new file mode 100644 index 00000000..909e8faf Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192397_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192397_2_val_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192397_2_val_2_fastqc.html new file mode 100644 index 00000000..5075faf1 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192397_2_val_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192397_2_val_2.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192397_2_val_2.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192397_2_val_2.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences91969895
Sequences flagged as poor quality0
Sequence length20-101
%GC49

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[WARN]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG15957431.7350710251436081No Hit
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG7542610.8201172785942618No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA5246550.5704638458051953No Hit
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT3551340.3861415738269572No Hit
GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT2608560.28363194282215937No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA2586970.2812844355209931No Hit
CTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCT1876000.20397979143066325No Hit
GCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGC1874400.20380582145929382No Hit
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT1691120.18387756123892499No Hit
GTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAG1686770.18340458037926433No Hit
CTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCT1680180.18268804155968646No Hit
CTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTG1546090.16810827064660672No Hit
GGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGC1412320.1535632937278008No Hit
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT1194760.12990772687084182No Hit
ACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCT1171780.1274090831570483No Hit
CTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTG1134570.12336319401038787No Hit
CAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTG1131370.12301525406764899No Hit
CCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTT1036990.11275320038149439No Hit
CGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGG1018160.11070579128094037No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGGTGGC3410100.070.133441
GGGCGAT497150.066.1594241
GGCGATC530850.062.1625752
TGGCGCG4001050.059.589874
GGCGCGT4074550.058.5561945
GTGGCGC4124000.057.8746573
GGTGGCG4148750.057.6016732
GCGCGTG4504150.053.0946246
CGCGTGC4611150.051.808277
GCGTGCC4660000.051.3372048
CGTGCCT4730150.050.5916569
GCGATCT710800.046.790813
CGATCTG833350.039.854694
TAGTCCC4884950.032.82145316-17
TGTAGTC4952150.032.47381614-15
CCTGTAG4983200.032.35709412-13
TGCCTGT5389150.029.9810110-11
GTCCCAG5605050.028.7145118-19
TACTCGG5990400.026.95159126-27
GCTACTC6271950.025.81980124-25
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192397_2_val_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192397_2_val_2_fastqc.zip new file mode 100644 index 00000000..09127821 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192397_2_val_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192398_1.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192398_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..d0cc43dc --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_1.fastq.gz_trimming_report.txt @@ -0,0 +1,154 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192398_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192398_1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1558.02 s (23 us/read; 2.65 M reads/minute). + +=== Summary === + +Total reads processed: 68,765,938 +Reads with adapters: 24,776,219 (36.0%) +Reads written (passing filters): 68,765,938 (100.0%) + +Total basepairs processed: 6,876,593,800 bp +Quality-trimmed: 278,227,662 bp (4.0%) +Total written (filtered): 6,538,840,170 bp (95.1%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24776219 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 28.4% + C: 34.1% + G: 18.8% + T: 18.7% + none/other: 0.1% + +Overview of removed sequences +length count expect max.err error counts +1 16021271 17191484.5 0 16021271 +2 4699932 4297871.1 0 4699932 +3 1508602 1074467.8 0 1508602 +4 453513 268616.9 0 453513 +5 273388 67154.2 0 273388 +6 191192 16788.6 0 191192 +7 169275 4197.1 0 169275 +8 150430 1049.3 0 150430 +9 139426 262.3 0 137722 1704 +10 122228 65.6 1 119552 2676 +11 112758 16.4 1 110925 1833 +12 110789 4.1 1 109262 1527 +13 102395 1.0 1 100897 1498 +14 84764 1.0 1 83584 1180 +15 80197 1.0 1 78962 1235 +16 75853 1.0 1 74641 1212 +17 56820 1.0 1 55824 996 +18 43570 1.0 1 42851 719 +19 33410 1.0 1 32909 501 +20 27061 1.0 1 26606 455 +21 23822 1.0 1 23424 398 +22 25845 1.0 1 25377 468 +23 27296 1.0 1 26836 460 +24 24317 1.0 1 23890 427 +25 19752 1.0 1 19462 290 +26 18553 1.0 1 18238 315 +27 17968 1.0 1 17560 408 +28 20792 1.0 1 20388 404 +29 14527 1.0 1 14226 301 +30 11801 1.0 1 11520 281 +31 9414 1.0 1 9202 212 +32 8692 1.0 1 8464 228 +33 7743 1.0 1 7554 189 +34 15277 1.0 1 14882 395 +35 7217 1.0 1 7004 213 +36 6097 1.0 1 5907 190 +37 5269 1.0 1 5096 173 +38 6084 1.0 1 5893 191 +39 5045 1.0 1 4859 186 +40 4900 1.0 1 4728 172 +41 4024 1.0 1 3890 134 +42 2218 1.0 1 2143 75 +43 1554 1.0 1 1508 46 +44 1651 1.0 1 1585 66 +45 1544 1.0 1 1478 66 +46 1849 1.0 1 1747 102 +47 1504 1.0 1 1438 66 +48 1213 1.0 1 1140 73 +49 1085 1.0 1 1030 55 +50 721 1.0 1 664 57 +51 628 1.0 1 569 59 +52 557 1.0 1 466 91 +53 452 1.0 1 404 48 +54 351 1.0 1 298 53 +55 244 1.0 1 195 49 +56 269 1.0 1 208 61 +57 249 1.0 1 181 68 +58 342 1.0 1 235 107 +59 374 1.0 1 285 89 +60 271 1.0 1 156 115 +61 279 1.0 1 166 113 +62 431 1.0 1 134 297 +63 709 1.0 1 259 450 +64 542 1.0 1 331 211 +65 397 1.0 1 165 232 +66 556 1.0 1 179 377 +67 1036 1.0 1 264 772 +68 1885 1.0 1 462 1423 +69 4722 1.0 1 684 4038 +70 2904 1.0 1 1397 1507 +71 1746 1.0 1 613 1133 +72 1062 1.0 1 489 573 +73 324 1.0 1 239 85 +74 159 1.0 1 124 35 +75 60 1.0 1 32 28 +76 18 1.0 1 7 11 +77 22 1.0 1 5 17 +78 43 1.0 1 5 38 +79 37 1.0 1 1 36 +80 29 1.0 1 5 24 +81 38 1.0 1 1 37 +82 32 1.0 1 0 32 +83 43 1.0 1 2 41 +84 33 1.0 1 3 30 +85 35 1.0 1 4 31 +86 33 1.0 1 0 33 +87 31 1.0 1 2 29 +88 34 1.0 1 7 27 +89 33 1.0 1 2 31 +90 32 1.0 1 3 29 +91 43 1.0 1 5 38 +92 28 1.0 1 4 24 +93 29 1.0 1 3 26 +94 29 1.0 1 3 26 +95 54 1.0 1 14 40 +96 32 1.0 1 7 25 +97 38 1.0 1 5 33 +98 25 1.0 1 2 23 +99 33 1.0 1 3 30 +100 218 1.0 1 1 217 + + +RUN STATISTICS FOR INPUT FILE: SRR3192398_1.fastq.gz +============================================= +68765938 sequences processed in total + diff --git a/src/multiqc/rna-seq/data/SRR3192398_1Log.final.out b/src/multiqc/rna-seq/data/SRR3192398_1Log.final.out new file mode 100644 index 00000000..365819ae --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_1Log.final.out @@ -0,0 +1,34 @@ + Started job on | May 03 03:15:50 + Started mapping on | May 03 03:20:29 + Finished on | May 03 04:03:15 + Mapping speed, Million of reads per hour | 93.39 + + Number of input reads | 66565696 + Average input read length | 194 + UNIQUE READS: + Uniquely mapped reads number | 58676080 + Uniquely mapped reads % | 88.15% + Average mapped length | 193.82 + Number of splices: Total | 24721300 + Number of splices: Annotated (sjdb) | 24432647 + Number of splices: GT/AG | 24441750 + Number of splices: GC/AG | 183461 + Number of splices: AT/AC | 23120 + Number of splices: Non-canonical | 72969 + Mismatch rate per base, % | 0.23% + Deletion rate per base | 0.01% + Deletion average length | 1.50 + Insertion rate per base | 0.01% + Insertion average length | 1.55 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 5170028 + % of reads mapped to multiple loci | 7.77% + Number of reads mapped to too many loci | 16728 + % of reads mapped to too many loci | 0.03% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 4.02% + % of reads unmapped: other | 0.04% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff --git a/src/multiqc/rna-seq/data/SRR3192398_1Log.out b/src/multiqc/rna-seq/data/SRR3192398_1Log.out new file mode 100644 index 00000000..429d9ec0 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_1Log.out @@ -0,0 +1,408 @@ +STAR version=STAR_2.5.1b +STAR compilation time,server,dir=Tue Jan 26 13:48:00 CET 2016 milou-b.uppmax.uu.se:/sw/apps/bioinfo/star/2.5.1b/src/source +##### DEFAULT parameters: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 1 +runDirPerm User_RWX +runRNGseed 777 +genomeDir ./GenomeDir/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn Read1 Read2 +readFilesCommand - +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outTmpDir - +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +##### Command Line: +STAR --runThreadN 4 --outQSconversionAdd 0 --outSAMattributes Standard --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --readFilesIn SRR3192398_1_val_1.fq.gz SRR3192398_2_val_2.fq.gz --outFileNamePrefix SRR3192398_1 --outStd SAM +##### Initial USER parameters from Command Line: +outFileNamePrefix SRR3192398_1 +outStd SAM +###### All USER parameters from Command Line: +runThreadN 4 ~RE-DEFINED +outQSconversionAdd 0 ~RE-DEFINED +outSAMattributes Standard ~RE-DEFINED +genomeLoad NoSharedMemory ~RE-DEFINED +readFilesCommand zcat ~RE-DEFINED +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ~RE-DEFINED +readFilesIn SRR3192398_1_val_1.fq.gz SRR3192398_2_val_2.fq.gz ~RE-DEFINED +outFileNamePrefix SRR3192398_1 ~RE-DEFINED +outStd SAM ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runThreadN 4 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +readFilesIn SRR3192398_1_val_1.fq.gz SRR3192398_2_val_2.fq.gz +readFilesCommand zcat +outFileNamePrefix SRR3192398_1 +outStd SAM +outQSconversionAdd 0 +outSAMattributes Standard + +------------------------------- +##### Final effective command line: +STAR --runThreadN 4 --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --genomeLoad NoSharedMemory --readFilesIn SRR3192398_1_val_1.fq.gz SRR3192398_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix SRR3192398_1 --outStd SAM --outQSconversionAdd 0 --outSAMattributes Standard + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 4 +runDirPerm User_RWX +runRNGseed 777 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn SRR3192398_1_val_1.fq.gz SRR3192398_2_val_2.fq.gz +readFilesCommand zcat +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outFileNamePrefix SRR3192398_1 +outTmpDir - +outStd SAM +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +---------------------------------------- + + + Input read files for mate 1, from input string SRR3192398_1_val_1.fq.gz +-rw-rw-r-- 1 phil b2013064 5196228400 May 3 02:55 SRR3192398_1_val_1.fq.gz + + readsCommandsFile: +exec > "SRR3192398_1_STARtmp/tmp.fifo.read1" +echo FILE 0 +zcat "SRR3192398_1_val_1.fq.gz" + + + Input read files for mate 2, from input string SRR3192398_2_val_2.fq.gz +-rw-rw-r-- 1 phil b2013064 5174289177 May 3 02:55 SRR3192398_2_val_2.fq.gz + + readsCommandsFile: +exec > "SRR3192398_1_STARtmp/tmp.fifo.read2" +echo FILE 0 +zcat "SRR3192398_2_val_2.fq.gz" + +Finished loading and checking parameters +Reading genome generation parameters: +versionGenome 20201 ~RE-DEFINED +genomeFastaFiles genome.fa ~RE-DEFINED +genomeSAindexNbases 14 ~RE-DEFINED +genomeChrBinNbits 18 ~RE-DEFINED +genomeSAsparseD 1 ~RE-DEFINED +sjdbOverhang 100 ~RE-DEFINED +sjdbFileChrStartEnd - ~RE-DEFINED +sjdbGTFfile genes.gtf ~RE-DEFINED +sjdbGTFchrPrefix - ~RE-DEFINED +sjdbGTFfeatureExon exon ~RE-DEFINED +sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED +sjdbGTFtagExonParentGene gene_id ~RE-DEFINED +sjdbInsertSave Basic ~RE-DEFINED +Genome version is compatible with current STAR version +Number of real (reference) chromosmes= 25 +1 1 249250621 0 +2 2 243199373 249298944 +3 3 198022430 492568576 +4 4 191154276 690749440 +5 5 180915260 882114560 +6 6 171115067 1063256064 +7 7 159138663 1234436096 +8 8 146364022 1393819648 +9 9 141213431 1540358144 +10 10 135534747 1681653760 +11 11 135006516 1817444352 +12 12 133851895 1952710656 +13 13 115169878 2086666240 +14 14 107349540 2202009600 +15 15 102531392 2309488640 +16 16 90354753 2412249088 +17 17 81195210 2502688768 +18 18 78077248 2583953408 +19 19 59128983 2662072320 +20 20 63025520 2721316864 +21 21 48129895 2784493568 +22 22 51304566 2832728064 +23 X 155270560 2884108288 +24 Y 59373566 3039559680 +25 MT 16569 3099066368 +--sjdbOverhang = 100 taken from the generated genome +Started loading the genome: Tue May 3 03:15:51 2016 + +checking Genome sizefile size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +checking SA sizefile size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 +Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 +nGenome=3168538239; nSAbyte=24152204822 +GstrandBit=32 SA number of indices=5855079956 +Shared memory is not used for genomes. Allocated a private copy of the genome. +Genome file size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3168538239 bytes +SA file size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24152204822 bytes +Loading SAindex ... done: 1565873619 bytes +Finished loading the genome: Tue May 3 03:20:28 2016 + +Processing splice junctions database sjdbN=344327, sjdbOverhang=100 +alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 +Created thread # 1 +Created thread # 2 +Created thread # 3 +Starting to map file # 0 +mate 1: SRR3192398_1_val_1.fq.gz +mate 2: SRR3192398_2_val_2.fq.gz +Thread #2 end of input stream, nextChar=-1 +Completed: thread #3 +Completed: thread #2 +Completed: thread #1 +Completed: thread #0 +Joined thread # 1 +Joined thread # 2 +Joined thread # 3 +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192398_1Log.progress.out b/src/multiqc/rna-seq/data/SRR3192398_1Log.progress.out new file mode 100644 index 00000000..1955f5a4 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_1Log.progress.out @@ -0,0 +1,44 @@ + Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped + M/hr number length unique length MMrate multi multi+ MM short other +May 03 03:21:29 82.8 1380577 195 88.2% 194.7 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:22:33 83.0 2859985 195 88.2% 194.8 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:23:35 88.4 4566937 195 88.2% 194.8 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:24:36 89.8 6161140 195 88.2% 194.7 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:25:37 90.7 7756625 195 88.2% 194.6 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:26:39 91.0 9353955 194 88.2% 194.5 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:27:40 91.3 10935394 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:28:41 92.3 12617847 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:29:41 91.8 14075765 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:30:43 92.4 15758102 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:31:44 91.8 17216887 194 88.2% 194.5 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:32:45 92.5 18901593 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:33:46 92.0 20362575 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:34:46 92.2 21936943 194 88.2% 194.4 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:35:55 91.8 23618335 194 88.2% 194.4 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:36:56 92.3 25299168 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:37:58 92.6 26980905 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:39:02 92.4 28551583 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:40:06 92.8 30348365 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:41:06 92.6 31809583 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:42:08 92.8 33497044 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:43:10 92.8 35070149 194 88.2% 194.4 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:44:10 93.1 36757506 194 88.2% 194.3 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:45:12 93.1 38333350 194 88.2% 194.3 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:46:13 93.3 40024474 194 88.2% 194.2 0.2% 7.7% 0.0% 0.0% 4.0% 0.0% +May 03 03:47:13 93.1 41492700 194 88.2% 194.2 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:48:16 93.3 43187170 194 88.2% 194.1 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:49:24 92.9 44768436 194 88.2% 194.0 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:50:24 93.2 46452853 194 88.2% 194.0 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:51:24 93.4 48138687 194 88.2% 194.0 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:52:28 93.3 49713499 194 88.2% 194.0 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:53:29 93.5 51403033 194 88.2% 194.0 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:54:29 93.3 52868403 194 88.2% 194.0 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:55:29 93.5 54560924 194 88.2% 193.9 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:56:29 93.4 56026074 194 88.2% 193.9 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:57:30 93.5 57711677 194 88.2% 193.9 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:58:31 93.3 59173120 194 88.2% 193.9 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 03:59:35 93.6 60973404 194 88.2% 193.9 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 04:00:38 93.5 62550773 194 88.2% 193.9 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 04:01:39 93.6 64244236 194 88.2% 193.9 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +May 03 04:02:49 93.5 65937663 194 88.1% 193.8 0.2% 7.8% 0.0% 0.0% 4.0% 0.0% +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192398_1Log.std.out b/src/multiqc/rna-seq/data/SRR3192398_1Log.std.out new file mode 100644 index 00000000..51e6ef1e --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_1Log.std.out @@ -0,0 +1,4 @@ +May 03 03:15:50 ..... Started STAR run +May 03 03:15:51 ..... Loading genome +May 03 03:20:29 ..... Started mapping +May 03 04:03:15 ..... Finished successfully diff --git a/src/multiqc/rna-seq/data/SRR3192398_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192398_1_fastqc.html new file mode 100644 index 00000000..a6f68753 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192398_1.fastq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192398_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192398_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences68765938
Sequences flagged as poor quality0
Sequence length100
%GC47

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT7110091.0339552119539182No Hit
CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT5029400.7313795385151294No Hit
CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG3167690.460648119131306No Hit
GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC2347900.3414335742791729No Hit
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT2213760.32192682371321685No Hit
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG2210270.3214193050053356No Hit
CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA2109340.3067419803100773No Hit
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA2053710.29865221935895064No Hit
CACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCAT1739290.25292900098301574No Hit
CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT1457640.211971223311169No Hit
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1290780.18770630308278496No Hit
CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA1288780.18741546141637738No Hit
GGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAA1264890.1839413577111389No Hit
GCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1132950.16475453297823117No Hit
CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG1056540.15364292711312974No Hit
CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC928640.13504360254636533No Hit
GCCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATA874660.12719378597002487No Hit
GTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT827070.12027320851785663No Hit
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA818120.11897169206068273No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGTATAC704900.032.01159394
GTCTGGA904750.029.247261
CTCGCTA348200.027.4808126
GTCCGTT63450.027.3970661
GTCTCGC356550.026.8881684
ACAGCCC2854750.026.6792794
CGCTATG377350.025.4946638
TGGAGTC965450.024.6645154
CAGCCCA2135250.024.62600594
TCGCTAT394100.024.4121237
GCCCCTC429950.024.2806971
GGAGTCT989150.024.1353175
TATACCC603900.023.54596594
GAGTCTT1030750.023.2357446
GTGGGTA476850.023.1571521
GTCCGAT61050.022.6866821
TCTGGAG1103250.022.6470322
GTCTTGG1078950.022.2105588
AGTCTTG1082050.022.0262417
TACAGCC2934750.021.98554892-93
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192398_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192398_1_fastqc.zip new file mode 100644 index 00000000..f851864c Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192398_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192398_1_star_aligned.bam_counts.txt.summary b/src/multiqc/rna-seq/data/SRR3192398_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..88d1367f --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_1_star_aligned.bam_counts.txt.summary @@ -0,0 +1,12 @@ +Status SRR3192398_1_star_aligned.bam +Assigned 36507149 +Unassigned_Ambiguity 1752489 +Unassigned_MultiMapping 12867738 +Unassigned_NoFeatures 20643821 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_FragmentLength 0 +Unassigned_Chimera 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_Duplicate 0 diff --git a/src/multiqc/rna-seq/data/SRR3192398_1_val_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192398_1_val_1_fastqc.html new file mode 100644 index 00000000..34b05e01 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_1_val_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192398_1_val_1.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192398_1_val_1.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192398_1_val_1.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences66565696
Sequences flagged as poor quality0
Sequence length20-100
%GC47

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT6906221.0375043626074307No Hit
CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT4877460.7327287616732798No Hit
CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG3070880.46133071304474904No Hit
GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC2277030.3420725894610942No Hit
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT2145310.32228461939314806No Hit
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG2140130.3215064407949704No Hit
CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA2042930.30690432501449394No Hit
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA1997310.30005094515950076No Hit
CACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCAT1690000.2538845233436754No Hit
CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT1411580.21205817482926942No Hit
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1253300.18828016160155525No Hit
CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA1240960.1864263538985606No Hit
GGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAA1225910.18416542959304444No Hit
GCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1096350.1647019509868867No Hit
CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG1024960.153977207719724No Hit
CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC901270.13539556470648184No Hit
GCCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATA851380.12790071330434222No Hit
GTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT808610.12147548190587537No Hit
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA788690.11848294953604932No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGTATAC695200.052.37178894
ACAGCCC2696500.043.7534694
TATACCC583650.038.637394
GTCTGGA878800.028.5580431
GTCTCGC339600.028.0018224
CTCGCTA339100.027.9093676
GTCCGTT59000.027.5731221
CGCTATG368400.025.9113488
TACAGCC2777650.025.07245692-93
TCGCTAT384100.024.8176487
TGGAGTC942000.024.7700864
GTCCGAT54800.024.43291
GGAGTCT971300.024.0463565
GCCCCTC408800.023.6309951
GTGGGTA453300.023.3676821
GAGTCTT1007950.023.2767126
TCTGGAG1047450.023.0578542
ACCGGGT103150.022.81842494
GCGCACT2829950.022.53592586-87
GTCTTGG1049950.022.3967348
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192398_1_val_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192398_1_val_1_fastqc.zip new file mode 100644 index 00000000..aa0c980f Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192398_1_val_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192398_2.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192398_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..4873619b --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_2.fastq.gz_trimming_report.txt @@ -0,0 +1,157 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192398_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192398_2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1552.56 s (23 us/read; 2.66 M reads/minute). + +=== Summary === + +Total reads processed: 68,765,938 +Reads with adapters: 25,752,326 (37.4%) +Reads written (passing filters): 68,765,938 (100.0%) + +Total basepairs processed: 6,876,593,800 bp +Quality-trimmed: 282,522,512 bp (4.1%) +Total written (filtered): 6,533,246,681 bp (95.0%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25752326 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 32.5% + C: 29.4% + G: 21.1% + T: 16.9% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 16564140 17191484.5 0 16564140 +2 4962759 4297871.1 0 4962759 +3 1622779 1074467.8 0 1622779 +4 502960 268616.9 0 502960 +5 261263 67154.2 0 261263 +6 189650 16788.6 0 189650 +7 172380 4197.1 0 172380 +8 151946 1049.3 0 151946 +9 143312 262.3 0 141928 1384 +10 126353 65.6 1 121951 4402 +11 116318 16.4 1 112914 3404 +12 115082 4.1 1 111975 3107 +13 107501 1.0 1 104629 2872 +14 92108 1.0 1 89429 2679 +15 76639 1.0 1 74504 2135 +16 75434 1.0 1 73259 2175 +17 58571 1.0 1 56829 1742 +18 38866 1.0 1 37651 1215 +19 34770 1.0 1 33709 1061 +20 25685 1.0 1 24865 820 +21 22593 1.0 1 21898 695 +22 24593 1.0 1 23818 775 +23 28123 1.0 1 27213 910 +24 28200 1.0 1 27282 918 +25 19612 1.0 1 18980 632 +26 18924 1.0 1 18057 867 +27 18378 1.0 1 17789 589 +28 22029 1.0 1 21304 725 +29 14864 1.0 1 14337 527 +30 17938 1.0 1 17378 560 +31 6556 1.0 1 6309 247 +32 7698 1.0 1 7439 259 +33 6090 1.0 1 5885 205 +34 12855 1.0 1 12460 395 +35 6528 1.0 1 6305 223 +36 5619 1.0 1 5401 218 +37 5002 1.0 1 4788 214 +38 5565 1.0 1 5376 189 +39 4812 1.0 1 4645 167 +40 4447 1.0 1 4257 190 +41 3554 1.0 1 3361 193 +42 3080 1.0 1 2940 140 +43 1823 1.0 1 1719 104 +44 2075 1.0 1 1945 130 +45 2015 1.0 1 1909 106 +46 1509 1.0 1 1413 96 +47 1508 1.0 1 1398 110 +48 1165 1.0 1 1081 84 +49 1033 1.0 1 958 75 +50 854 1.0 1 772 82 +51 801 1.0 1 721 80 +52 382 1.0 1 305 77 +53 340 1.0 1 273 67 +54 380 1.0 1 310 70 +55 329 1.0 1 286 43 +56 301 1.0 1 250 51 +57 302 1.0 1 255 47 +58 392 1.0 1 306 86 +59 355 1.0 1 317 38 +60 332 1.0 1 253 79 +61 288 1.0 1 226 62 +62 455 1.0 1 337 118 +63 1175 1.0 1 917 258 +64 1889 1.0 1 1380 509 +65 3415 1.0 1 2455 960 +66 1487 1.0 1 1133 354 +67 213 1.0 1 159 54 +68 112 1.0 1 45 67 +69 70 1.0 1 15 55 +70 57 1.0 1 8 49 +71 54 1.0 1 5 49 +72 36 1.0 1 2 34 +73 45 1.0 1 2 43 +74 56 1.0 1 5 51 +75 46 1.0 1 3 43 +76 58 1.0 1 3 55 +77 40 1.0 1 3 37 +78 69 1.0 1 6 63 +79 48 1.0 1 9 39 +80 52 1.0 1 6 46 +81 50 1.0 1 7 43 +82 96 1.0 1 7 89 +83 70 1.0 1 10 60 +84 57 1.0 1 9 48 +85 70 1.0 1 7 63 +86 54 1.0 1 11 43 +87 36 1.0 1 8 28 +88 52 1.0 1 14 38 +89 42 1.0 1 10 32 +90 42 1.0 1 5 37 +91 76 1.0 1 11 65 +92 54 1.0 1 6 48 +93 62 1.0 1 4 58 +94 33 1.0 1 3 30 +95 78 1.0 1 7 71 +96 41 1.0 1 2 39 +97 112 1.0 1 9 103 +98 49 1.0 1 3 46 +99 44 1.0 1 3 41 +100 71 1.0 1 3 68 + + +RUN STATISTICS FOR INPUT FILE: SRR3192398_2.fastq.gz +============================================= +68765938 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 68765938 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2200242 (3.20%) diff --git a/src/multiqc/rna-seq/data/SRR3192398_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192398_2_fastqc.html new file mode 100644 index 00000000..e780d0ab --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192398_2.fastq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192398_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192398_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences68765938
Sequences flagged as poor quality0
Sequence length100
%GC47

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG2837110.41257490009079784No Hit
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG2672540.38864299357045057No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA1993400.28988188890843025No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA1892970.2752772746297738No Hit
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT1820520.2647415352641594No Hit
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT1719260.2500162216939439No Hit
GCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAG1315660.1913243734128952No Hit
GCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAG1250530.18185311454633252No Hit
GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG1214060.17654961675939038No Hit
GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT1059330.1540486512377683No Hit
GTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAG911670.13257581100689705No Hit
GTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAG866600.12602169405440236No Hit
CTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCC857660.12472163180556048No Hit
GTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGAT789100.1147515794811088No Hit
GTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGAT710470.10331713936629497No Hit
CCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCT700630.10188619836756971No Hit
CAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG698940.10164043715945531No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGCGATC196600.052.303072
CGGTGGC1168400.048.5791131
GGGCGAT211950.048.5595051
GCGGTGG599450.044.033311
GCGATCT254250.040.665243
CGATCTG275400.038.0676464
GGTGGCG1536150.036.781072
GGCGCGT1632350.034.4981355
TGGCGCG1635750.034.4371764
GTGGCGC1668850.033.7772833
GCGCGTG1742350.032.303126
CGCGTGC1859200.030.237497
TCACCCG249000.029.4567173
ACCCGGC252650.029.382415
GCGTGCC1961400.028.7338228
CGGCCCG266900.027.167468
CGTGCCT2093950.026.9912349
CACCCGG292950.025.99784
CCTGTAG2303300.021.05833612-13
TGTAGTC2388750.020.20220614-15
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192398_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192398_2_fastqc.zip new file mode 100644 index 00000000..97251999 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192398_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192398_2_val_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192398_2_val_2_fastqc.html new file mode 100644 index 00000000..f082fdd3 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192398_2_val_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192398_2_val_2.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192398_2_val_2.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192398_2_val_2.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences66565696
Sequences flagged as poor quality0
Sequence length20-100
%GC47

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG2746020.4125277981018932No Hit
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG2623830.3941714963815597No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA1916620.28792908587630484No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA1856230.27885684542380507No Hit
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT1787280.26849865732644035No Hit
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT1676250.2518188948253467No Hit
GCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAG1271600.19102932537504003No Hit
GCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAG1226210.18421049785162616No Hit
GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG1187880.17845227668016872No Hit
GTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAG893150.13417571717420337No Hit
CTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCC843980.12678902959265986No Hit
GTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAG841610.1264329903498643No Hit
GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT770150.11569773115569917No Hit
GTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGAT757130.11374176873325263No Hit
GTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGAT695480.10448024159470969No Hit
CAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG684360.10280971147661401No Hit
CCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCT678370.10190984858026572No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGCGATC186200.054.279152
GGGCGAT201300.050.117031
CGGTGGC1154150.046.760041
GCGGTGG580950.044.013821
GCGATCT245800.041.0802423
CGATCTG273450.037.389174
GGTGGCG1489000.036.1405262
GGCGCGT1596150.033.6726235
TGGCGCG1596350.033.663664
GTGGCGC1622000.033.151353
GCGATTT315700.032.35402794
GCGCGTG1704000.031.5643356
CGCGTGC1827850.029.4249387
ACCCGGC237000.028.976645
TCACCCG233550.028.9208133
CGGCCCG242550.028.1709928
GCGTGCC1915550.028.1181958
CGTGCCT2039300.026.5034319
CACCCGG272500.025.7873574
TTCGTTG129700.025.15091594
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192398_2_val_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192398_2_val_2_fastqc.zip new file mode 100644 index 00000000..bb3a5670 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192398_2_val_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192399_1.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192399_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..91fb0da6 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_1.fastq.gz_trimming_report.txt @@ -0,0 +1,154 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192399_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192399_1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1694.98 s (22 us/read; 2.72 M reads/minute). + +=== Summary === + +Total reads processed: 76,795,926 +Reads with adapters: 27,726,219 (36.1%) +Reads written (passing filters): 76,795,926 (100.0%) + +Total basepairs processed: 7,679,592,600 bp +Quality-trimmed: 306,342,809 bp (4.0%) +Total written (filtered): 7,304,196,164 bp (95.1%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 27726219 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 27.8% + C: 34.5% + G: 19.2% + T: 18.4% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 17707434 19198981.5 0 17707434 +2 5264485 4799745.4 0 5264485 +3 1673429 1199936.3 0 1673429 +4 526635 299984.1 0 526635 +5 328087 74996.0 0 328087 +6 234065 18749.0 0 234065 +7 209903 4687.3 0 209903 +8 185312 1171.8 0 185312 +9 169127 293.0 0 167166 1961 +10 151665 73.2 1 148352 3313 +11 139504 18.3 1 137096 2408 +12 139254 4.6 1 137219 2035 +13 129286 1.1 1 127327 1959 +14 115507 1.1 1 113611 1896 +15 113426 1.1 1 111464 1962 +16 84942 1.1 1 83503 1439 +17 56751 1.1 1 55720 1031 +18 41177 1.1 1 40447 730 +19 38382 1.1 1 37742 640 +20 37112 1.1 1 36424 688 +21 31177 1.1 1 30655 522 +22 28439 1.1 1 27906 533 +23 25904 1.1 1 25452 452 +24 25674 1.1 1 25179 495 +25 27693 1.1 1 27204 489 +26 25609 1.1 1 25115 494 +27 21939 1.1 1 21413 526 +28 18882 1.1 1 18459 423 +29 15849 1.1 1 15507 342 +30 14279 1.1 1 13931 348 +31 10469 1.1 1 10220 249 +32 10435 1.1 1 10194 241 +33 10337 1.1 1 10063 274 +34 19251 1.1 1 18764 487 +35 10273 1.1 1 9986 287 +36 7621 1.1 1 7416 205 +37 7093 1.1 1 6881 212 +38 7945 1.1 1 7685 260 +39 6605 1.1 1 6360 245 +40 5259 1.1 1 5065 194 +41 5005 1.1 1 4847 158 +42 3541 1.1 1 3444 97 +43 3133 1.1 1 3021 112 +44 2487 1.1 1 2388 99 +45 2358 1.1 1 2267 91 +46 2349 1.1 1 2228 121 +47 2143 1.1 1 2051 92 +48 1982 1.1 1 1854 128 +49 1694 1.1 1 1611 83 +50 1282 1.1 1 1200 82 +51 1228 1.1 1 1125 103 +52 947 1.1 1 838 109 +53 761 1.1 1 706 55 +54 515 1.1 1 462 53 +55 450 1.1 1 399 51 +56 655 1.1 1 558 97 +57 1012 1.1 1 910 102 +58 529 1.1 1 430 99 +59 390 1.1 1 294 96 +60 311 1.1 1 226 85 +61 310 1.1 1 187 123 +62 455 1.1 1 149 306 +63 743 1.1 1 297 446 +64 593 1.1 1 387 206 +65 410 1.1 1 195 215 +66 497 1.1 1 171 326 +67 976 1.1 1 333 643 +68 1636 1.1 1 516 1120 +69 4312 1.1 1 805 3507 +70 2834 1.1 1 1652 1182 +71 1634 1.1 1 709 925 +72 973 1.1 1 522 451 +73 409 1.1 1 315 94 +74 174 1.1 1 130 44 +75 50 1.1 1 26 24 +76 28 1.1 1 6 22 +77 33 1.1 1 5 28 +78 43 1.1 1 1 42 +79 37 1.1 1 3 34 +80 26 1.1 1 4 22 +81 60 1.1 1 2 58 +82 42 1.1 1 2 40 +83 51 1.1 1 2 49 +84 46 1.1 1 3 43 +85 46 1.1 1 6 40 +86 34 1.1 1 2 32 +87 32 1.1 1 3 29 +88 29 1.1 1 5 24 +89 44 1.1 1 6 38 +90 32 1.1 1 6 26 +91 55 1.1 1 7 48 +92 43 1.1 1 8 35 +93 36 1.1 1 4 32 +94 34 1.1 1 2 32 +95 49 1.1 1 12 37 +96 37 1.1 1 5 32 +97 53 1.1 1 11 42 +98 26 1.1 1 5 21 +99 43 1.1 1 2 41 +100 266 1.1 1 2 264 + + +RUN STATISTICS FOR INPUT FILE: SRR3192399_1.fastq.gz +============================================= +76795926 sequences processed in total + diff --git a/src/multiqc/rna-seq/data/SRR3192399_1Log.final.out b/src/multiqc/rna-seq/data/SRR3192399_1Log.final.out new file mode 100644 index 00000000..8e53f654 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_1Log.final.out @@ -0,0 +1,34 @@ + Started job on | May 03 03:04:08 + Started mapping on | May 03 03:08:41 + Finished on | May 03 03:57:42 + Mapping speed, Million of reads per hour | 90.99 + + Number of input reads | 74334517 + Average input read length | 194 + UNIQUE READS: + Uniquely mapped reads number | 65561303 + Uniquely mapped reads % | 88.20% + Average mapped length | 193.89 + Number of splices: Total | 29471296 + Number of splices: Annotated (sjdb) | 29139586 + Number of splices: GT/AG | 29142619 + Number of splices: GC/AG | 217680 + Number of splices: AT/AC | 27811 + Number of splices: Non-canonical | 83186 + Mismatch rate per base, % | 0.21% + Deletion rate per base | 0.01% + Deletion average length | 1.45 + Insertion rate per base | 0.01% + Insertion average length | 1.52 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 6039270 + % of reads mapped to multiple loci | 8.12% + Number of reads mapped to too many loci | 18574 + % of reads mapped to too many loci | 0.02% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 3.61% + % of reads unmapped: other | 0.04% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff --git a/src/multiqc/rna-seq/data/SRR3192399_1Log.out b/src/multiqc/rna-seq/data/SRR3192399_1Log.out new file mode 100644 index 00000000..96bb1828 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_1Log.out @@ -0,0 +1,408 @@ +STAR version=STAR_2.5.1b +STAR compilation time,server,dir=Tue Jan 26 13:48:00 CET 2016 milou-b.uppmax.uu.se:/sw/apps/bioinfo/star/2.5.1b/src/source +##### DEFAULT parameters: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 1 +runDirPerm User_RWX +runRNGseed 777 +genomeDir ./GenomeDir/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn Read1 Read2 +readFilesCommand - +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outTmpDir - +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +##### Command Line: +STAR --runThreadN 4 --outQSconversionAdd 0 --outSAMattributes Standard --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --readFilesIn SRR3192399_1_val_1.fq.gz SRR3192399_2_val_2.fq.gz --outFileNamePrefix SRR3192399_1 --outStd SAM +##### Initial USER parameters from Command Line: +outFileNamePrefix SRR3192399_1 +outStd SAM +###### All USER parameters from Command Line: +runThreadN 4 ~RE-DEFINED +outQSconversionAdd 0 ~RE-DEFINED +outSAMattributes Standard ~RE-DEFINED +genomeLoad NoSharedMemory ~RE-DEFINED +readFilesCommand zcat ~RE-DEFINED +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ~RE-DEFINED +readFilesIn SRR3192399_1_val_1.fq.gz SRR3192399_2_val_2.fq.gz ~RE-DEFINED +outFileNamePrefix SRR3192399_1 ~RE-DEFINED +outStd SAM ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runThreadN 4 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +readFilesIn SRR3192399_1_val_1.fq.gz SRR3192399_2_val_2.fq.gz +readFilesCommand zcat +outFileNamePrefix SRR3192399_1 +outStd SAM +outQSconversionAdd 0 +outSAMattributes Standard + +------------------------------- +##### Final effective command line: +STAR --runThreadN 4 --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --genomeLoad NoSharedMemory --readFilesIn SRR3192399_1_val_1.fq.gz SRR3192399_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix SRR3192399_1 --outStd SAM --outQSconversionAdd 0 --outSAMattributes Standard + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 4 +runDirPerm User_RWX +runRNGseed 777 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn SRR3192399_1_val_1.fq.gz SRR3192399_2_val_2.fq.gz +readFilesCommand zcat +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outFileNamePrefix SRR3192399_1 +outTmpDir - +outStd SAM +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +---------------------------------------- + + + Input read files for mate 1, from input string SRR3192399_1_val_1.fq.gz +-rw-rw-r-- 1 phil b2013064 5790522763 May 3 02:07 SRR3192399_1_val_1.fq.gz + + readsCommandsFile: +exec > "SRR3192399_1_STARtmp/tmp.fifo.read1" +echo FILE 0 +zcat "SRR3192399_1_val_1.fq.gz" + + + Input read files for mate 2, from input string SRR3192399_2_val_2.fq.gz +-rw-rw-r-- 1 phil b2013064 5768530319 May 3 02:07 SRR3192399_2_val_2.fq.gz + + readsCommandsFile: +exec > "SRR3192399_1_STARtmp/tmp.fifo.read2" +echo FILE 0 +zcat "SRR3192399_2_val_2.fq.gz" + +Finished loading and checking parameters +Reading genome generation parameters: +versionGenome 20201 ~RE-DEFINED +genomeFastaFiles genome.fa ~RE-DEFINED +genomeSAindexNbases 14 ~RE-DEFINED +genomeChrBinNbits 18 ~RE-DEFINED +genomeSAsparseD 1 ~RE-DEFINED +sjdbOverhang 100 ~RE-DEFINED +sjdbFileChrStartEnd - ~RE-DEFINED +sjdbGTFfile genes.gtf ~RE-DEFINED +sjdbGTFchrPrefix - ~RE-DEFINED +sjdbGTFfeatureExon exon ~RE-DEFINED +sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED +sjdbGTFtagExonParentGene gene_id ~RE-DEFINED +sjdbInsertSave Basic ~RE-DEFINED +Genome version is compatible with current STAR version +Number of real (reference) chromosmes= 25 +1 1 249250621 0 +2 2 243199373 249298944 +3 3 198022430 492568576 +4 4 191154276 690749440 +5 5 180915260 882114560 +6 6 171115067 1063256064 +7 7 159138663 1234436096 +8 8 146364022 1393819648 +9 9 141213431 1540358144 +10 10 135534747 1681653760 +11 11 135006516 1817444352 +12 12 133851895 1952710656 +13 13 115169878 2086666240 +14 14 107349540 2202009600 +15 15 102531392 2309488640 +16 16 90354753 2412249088 +17 17 81195210 2502688768 +18 18 78077248 2583953408 +19 19 59128983 2662072320 +20 20 63025520 2721316864 +21 21 48129895 2784493568 +22 22 51304566 2832728064 +23 X 155270560 2884108288 +24 Y 59373566 3039559680 +25 MT 16569 3099066368 +--sjdbOverhang = 100 taken from the generated genome +Started loading the genome: Tue May 3 03:04:09 2016 + +checking Genome sizefile size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +checking SA sizefile size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 +Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 +nGenome=3168538239; nSAbyte=24152204822 +GstrandBit=32 SA number of indices=5855079956 +Shared memory is not used for genomes. Allocated a private copy of the genome. +Genome file size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3168538239 bytes +SA file size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24152204822 bytes +Loading SAindex ... done: 1565873619 bytes +Finished loading the genome: Tue May 3 03:08:41 2016 + +Processing splice junctions database sjdbN=344327, sjdbOverhang=100 +alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 +Created thread # 1 +Created thread # 2 +Created thread # 3 +Starting to map file # 0 +mate 1: SRR3192399_1_val_1.fq.gz +mate 2: SRR3192399_2_val_2.fq.gz +Thread #3 end of input stream, nextChar=-1 +Completed: thread #1 +Completed: thread #3 +Completed: thread #2 +Completed: thread #0 +Joined thread # 1 +Joined thread # 2 +Joined thread # 3 +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192399_1Log.progress.out b/src/multiqc/rna-seq/data/SRR3192399_1Log.progress.out new file mode 100644 index 00000000..551e8e99 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_1Log.progress.out @@ -0,0 +1,50 @@ + Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped + M/hr number length unique length MMrate multi multi+ MM short other +May 03 03:09:41 76.0 1267361 195 88.2% 194.8 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:10:50 79.8 2860343 195 88.2% 194.8 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:11:51 84.4 4453577 195 88.2% 194.8 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:13:00 84.1 6047319 195 88.2% 194.8 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:14:02 85.7 7642071 195 88.2% 194.8 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:15:04 85.8 9123900 195 88.2% 194.7 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:16:04 87.0 10708539 194 88.2% 194.6 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:17:05 86.1 12058580 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:18:06 86.8 13630354 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:19:09 86.5 15086917 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:20:09 87.2 16657336 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:21:16 86.9 18228150 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:22:16 87.5 19799936 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:23:19 87.6 21373051 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:24:21 87.4 22834047 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:25:21 87.9 24408092 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:26:22 87.4 25754705 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:27:22 87.7 27321991 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:28:22 87.4 28667562 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:29:26 87.8 30349492 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:30:26 87.4 31695933 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:31:28 87.9 33380035 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:32:32 87.7 34841485 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:33:33 88.1 36527841 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:34:36 88.0 37990021 194 88.2% 194.5 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:35:36 88.4 39676765 194 88.2% 194.4 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:36:38 88.3 41139125 194 88.2% 194.4 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:37:38 88.8 42827862 194 88.2% 194.4 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:38:40 88.6 44294019 194 88.2% 194.3 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:39:40 89.1 45988009 194 88.2% 194.3 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:40:41 89.0 47456493 194 88.2% 194.2 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:41:43 89.3 49152565 194 88.2% 194.2 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:42:44 89.4 50729462 194 88.2% 194.1 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:43:48 89.6 52414416 194 88.2% 194.1 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:44:48 89.9 54100966 194 88.2% 194.1 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:45:48 89.8 55564050 194 88.2% 194.1 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:46:59 89.9 57366601 194 88.2% 194.1 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:48:03 90.2 59170745 194 88.2% 194.1 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:49:03 90.3 60750556 194 88.2% 194.0 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:50:04 90.4 62329688 194 88.2% 194.0 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:51:10 90.4 64015382 194 88.2% 194.0 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:52:10 90.7 65702158 194 88.2% 194.0 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:53:15 90.6 67277299 194 88.2% 194.0 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:54:19 90.8 69079093 194 88.2% 194.0 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:55:20 90.9 70658521 194 88.2% 194.0 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:56:21 91.1 72352298 194 88.2% 193.9 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +May 03 03:57:24 91.1 73933623 194 88.2% 193.9 0.2% 8.1% 0.0% 0.0% 3.6% 0.0% +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192399_1Log.std.out b/src/multiqc/rna-seq/data/SRR3192399_1Log.std.out new file mode 100644 index 00000000..845d28c0 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_1Log.std.out @@ -0,0 +1,4 @@ +May 03 03:04:08 ..... Started STAR run +May 03 03:04:09 ..... Loading genome +May 03 03:08:41 ..... Started mapping +May 03 03:57:42 ..... Finished successfully diff --git a/src/multiqc/rna-seq/data/SRR3192399_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192399_1_fastqc.html new file mode 100644 index 00000000..e8c35f01 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192399_1.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192399_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192399_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences76795926
Sequences flagged as poor quality0
Sequence length100
%GC47

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT8671021.1290989576712702No Hit
CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT6165940.8028993621354341No Hit
CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG3690190.48051897961358003No Hit
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG2847210.3707501358861146No Hit
GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC2662650.3467176110357729No Hit
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT2563460.33380156129636357No Hit
CACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCAT2169340.28248113057455676No Hit
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA2150340.280007040998503No Hit
CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA2119400.2759781814467606No Hit
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1531730.19945459085941616No Hit
GCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1335730.1739324036538084No Hit
CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT1332030.17345060726268213No Hit
CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA1279800.16664946523335106No Hit
GGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAA1199510.156194483545911No Hit
GCCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATA1104700.1438487765614025No Hit
GTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT970870.1264220708791245No Hit
CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC909360.11841253141475239No Hit
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA838820.1092271483255505No Hit
CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG797880.10389613636535876No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGTATAC783650.032.6863394
CTCGCTA394900.029.28936
GTCCGTT74100.028.8018111
CGCTATG402400.028.7312168
GTCTGGA1048350.028.5998421
GTCTCGC406700.028.5990894
ACAGCCC3268150.028.33692494
TCGCTAT422900.027.4176987
CAGCCCA2388400.027.08990194
GTGGGTA513250.025.9499551
GCCCCTC517950.024.9504131
TGGAGTC1084600.024.9490034
GGAGTCT1124900.024.2599035
GAGTCTT1161750.023.500296
TACAGCC3382950.023.26420892-93
GTCCGAT67950.023.1577721
GCGCACT3458500.022.85005686-87
TAGCGCA3516400.022.49920784-85
GCACTAC3546400.022.28452188-89
AGTCTTG1228500.022.2127027
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192399_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192399_1_fastqc.zip new file mode 100644 index 00000000..dfd3c839 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192399_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192399_1_star_aligned.bam_counts.txt.summary b/src/multiqc/rna-seq/data/SRR3192399_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..55a98aeb --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_1_star_aligned.bam_counts.txt.summary @@ -0,0 +1,12 @@ +Status SRR3192399_1_star_aligned.bam +Assigned 42336127 +Unassigned_Ambiguity 2090852 +Unassigned_MultiMapping 15109829 +Unassigned_NoFeatures 21382636 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_FragmentLength 0 +Unassigned_Chimera 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_Duplicate 0 diff --git a/src/multiqc/rna-seq/data/SRR3192399_1_val_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192399_1_val_1_fastqc.html new file mode 100644 index 00000000..13fb436e --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_1_val_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192399_1_val_1.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192399_1_val_1.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192399_1_val_1.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences74334517
Sequences flagged as poor quality0
Sequence length20-100
%GC47

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT8407001.1309685378059293No Hit
CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATT5973310.8035715090474053No Hit
CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG3573180.4806892066037101No Hit
GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG2753710.37044836115636565No Hit
GTCTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACC2579190.3469707081032086No Hit
CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT2481490.33382741963602186No Hit
CACCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCAT2107850.2835627491868953No Hit
GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA2089220.28105651106874074No Hit
CTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGA2049990.2757790166309953No Hit
GCCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1483900.199624623914621No Hit
GCTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGAT1290360.17358826721104542No Hit
CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT1284230.1727636166654584No Hit
CCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCA1237930.16653501629666875No Hit
GGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAA1160140.1560701605150673No Hit
GCCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATA1073190.1443730373602885No Hit
GTGGGTATAATACTAAGTTGAGATGATATCATTTACGGGGGAAGGCGCTT948880.12764998526862023No Hit
CTCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATC880890.11850349414391163No Hit
GGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCA807670.10865342677884085No Hit
CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG773350.10403645993959978No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGTATAC745900.053.75395294
ACAGCCC3095600.047.2138794
TATACCC604800.035.17076594
CTCGCTA375700.028.9955836
GTCTCGC378950.028.9630154
GTCTGGA1000150.028.3111521
CGCTATG384850.028.2936468
GTCCGTT68700.028.129031
TCGCTAT399800.027.2594247
TACAGCC3204250.026.92094292-93
GTGGGTA496350.025.3481921
GCCCCTC492950.024.7630831
ACCGGGT115450.024.64273894
TGGAGTC1051400.024.559994
GGAGTCT1080050.024.0140445
GCGCACT3308500.023.83339786-87
GCACTAC3376400.023.54573688-89
TAGCGCA3337150.023.46605384-85
GAGTCTT1126150.022.9544626
GTCCGAT63150.022.4263951
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192399_1_val_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192399_1_val_1_fastqc.zip new file mode 100644 index 00000000..7edab1c2 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192399_1_val_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192399_2.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192399_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..ebe557a1 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_2.fastq.gz_trimming_report.txt @@ -0,0 +1,157 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192399_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192399_2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1693.72 s (22 us/read; 2.72 M reads/minute). + +=== Summary === + +Total reads processed: 76,795,926 +Reads with adapters: 28,921,721 (37.7%) +Reads written (passing filters): 76,795,926 (100.0%) + +Total basepairs processed: 7,679,592,600 bp +Quality-trimmed: 314,228,271 bp (4.1%) +Total written (filtered): 7,294,474,633 bp (95.0%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 28921721 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 32.3% + C: 29.8% + G: 21.4% + T: 16.6% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 18364094 19198981.5 0 18364094 +2 5573442 4799745.4 0 5573442 +3 1839567 1199936.3 0 1839567 +4 586513 299984.1 0 586513 +5 311512 74996.0 0 311512 +6 231259 18749.0 0 231259 +7 211269 4687.3 0 211269 +8 185719 1171.8 0 185719 +9 174550 293.0 0 172950 1600 +10 154985 73.2 1 149922 5063 +11 142105 18.3 1 138230 3875 +12 142397 4.6 1 139031 3366 +13 135460 1.1 1 132182 3278 +14 123946 1.1 1 120845 3101 +15 108713 1.1 1 105979 2734 +16 85595 1.1 1 83358 2237 +17 59538 1.1 1 57791 1747 +18 37746 1.1 1 36576 1170 +19 40443 1.1 1 39278 1165 +20 35097 1.1 1 34063 1034 +21 29645 1.1 1 28792 853 +22 27714 1.1 1 26896 818 +23 26823 1.1 1 26006 817 +24 30372 1.1 1 29461 911 +25 27023 1.1 1 26202 821 +26 25668 1.1 1 24811 857 +27 22605 1.1 1 21883 722 +28 20460 1.1 1 19824 636 +29 16473 1.1 1 15974 499 +30 21981 1.1 1 21299 682 +31 7451 1.1 1 7216 235 +32 9399 1.1 1 9122 277 +33 8200 1.1 1 7941 259 +34 16270 1.1 1 15857 413 +35 9141 1.1 1 8839 302 +36 7140 1.1 1 6880 260 +37 6626 1.1 1 6412 214 +38 7222 1.1 1 6992 230 +39 6259 1.1 1 6023 236 +40 5123 1.1 1 4946 177 +41 4731 1.1 1 4513 218 +42 4934 1.1 1 4739 195 +43 3012 1.1 1 2857 155 +44 2781 1.1 1 2625 156 +45 2728 1.1 1 2582 146 +46 1860 1.1 1 1756 104 +47 2073 1.1 1 1968 105 +48 1820 1.1 1 1731 89 +49 1549 1.1 1 1468 81 +50 1481 1.1 1 1389 92 +51 1432 1.1 1 1312 120 +52 678 1.1 1 596 82 +53 525 1.1 1 473 52 +54 555 1.1 1 480 75 +55 506 1.1 1 439 67 +56 617 1.1 1 542 75 +57 1017 1.1 1 942 75 +58 618 1.1 1 525 93 +59 422 1.1 1 364 58 +60 462 1.1 1 375 87 +61 388 1.1 1 304 84 +62 529 1.1 1 406 123 +63 1300 1.1 1 1004 296 +64 2261 1.1 1 1647 614 +65 3841 1.1 1 2884 957 +66 1656 1.1 1 1234 422 +67 212 1.1 1 159 53 +68 116 1.1 1 56 60 +69 103 1.1 1 20 83 +70 68 1.1 1 16 52 +71 72 1.1 1 8 64 +72 40 1.1 1 6 34 +73 65 1.1 1 7 58 +74 55 1.1 1 4 51 +75 54 1.1 1 5 49 +76 73 1.1 1 6 67 +77 42 1.1 1 2 40 +78 62 1.1 1 6 56 +79 49 1.1 1 10 39 +80 74 1.1 1 6 68 +81 29 1.1 1 5 24 +82 96 1.1 1 8 88 +83 79 1.1 1 5 74 +84 63 1.1 1 8 55 +85 89 1.1 1 20 69 +86 56 1.1 1 10 46 +87 61 1.1 1 14 47 +88 53 1.1 1 8 45 +89 34 1.1 1 8 26 +90 47 1.1 1 4 43 +91 91 1.1 1 8 83 +92 53 1.1 1 2 51 +93 58 1.1 1 7 51 +94 44 1.1 1 8 36 +95 103 1.1 1 8 95 +96 45 1.1 1 10 35 +97 135 1.1 1 10 125 +98 60 1.1 1 9 51 +99 49 1.1 1 2 47 +100 70 1.1 1 6 64 + + +RUN STATISTICS FOR INPUT FILE: SRR3192399_2.fastq.gz +============================================= +76795926 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 76795926 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2461409 (3.21%) diff --git a/src/multiqc/rna-seq/data/SRR3192399_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192399_2_fastqc.html new file mode 100644 index 00000000..f56a8a90 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192399_2.fastq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192399_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192399_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences76795926
Sequences flagged as poor quality0
Sequence length100
%GC47

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG3147230.4098173124444128No Hit
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG2971570.386943703237591No Hit
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT2010930.26185373427231023No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA1889810.2460820643011714No Hit
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT1886440.24564323893952397No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA1756910.2287764587928792No Hit
GCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAG1612720.21000072321544766No Hit
GCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAG1561220.2032946383119334No Hit
GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG1516530.1974753191985731No Hit
GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT1370710.17848733277856432No Hit
GTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAG1083700.1411142565036588No Hit
GTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAG1017270.1324640580543296No Hit
CTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCC922670.12014569627039852No Hit
AGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGT906530.11804402228316122No Hit
CAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG831340.10825313832403037No Hit
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCT822900.10715412169129909No Hit
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT797650.10386618685996442No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGCGATC248700.055.355332
GGGCGAT256500.053.7636681
CGGTGGC1365950.046.9818651
GCGATCT310600.044.519953
GCGGTGG729650.044.0376971
CGATCTG341450.041.0020644
GGTGGCG1681550.037.948822
GGCGCGT1743750.036.413375
TGGCGCG1767450.035.985434
GTGGCGC1804600.035.3218773
GCGCGTG1868200.034.0310756
CGCGTGC2017450.031.450347
GCGTGCC2126750.029.9356588
CGTGCCT2231400.028.6138449
CCTGTAG2519000.020.12236412-13
TGTAGTC2616750.019.27154414-15
TAGTCCC2637600.019.0590216-17
TGCCTGT2754150.018.4949310-11
GTGCCTG2627950.018.4451910-11
GCTGCGA445850.018.4081810-11
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192399_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192399_2_fastqc.zip new file mode 100644 index 00000000..110291db Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192399_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192399_2_val_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192399_2_val_2_fastqc.html new file mode 100644 index 00000000..072e499b --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192399_2_val_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192399_2_val_2.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192399_2_val_2.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192399_2_val_2.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences74334517
Sequences flagged as poor quality0
Sequence length20-100
%GC47

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGG3048050.4100450400451246No Hit
CGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGG2917030.3924193117445022No Hit
CCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTT1973870.26553882094908887No Hit
CCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTT1840200.24755659608308211No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGA1816630.244385794556249No Hit
GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGA1722300.23169586209862642No Hit
GCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAG1557220.20948814398027232No Hit
GCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAG1530850.20594066683718412No Hit
GTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGG1484760.1997403171396136No Hit
GTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAG1061790.14283942949410702No Hit
GGGCGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATT996010.13399024305222834No Hit
GTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAG987790.13288443106450804No Hit
CTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCC907440.12207518614804479No Hit
AGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGT889660.11968329598482491No Hit
CAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG815060.1096475813517427No Hit
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCT804700.10825388157159883No Hit
CGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCT768660.1034055282823725No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGCGATC234350.056.5538982
GGGCGAT239800.055.287571
CGGTGGC1310250.045.0370181
GCGATCT295550.044.8119623
GCGGTGG701000.043.7361341
CGATCTG330500.040.5247964
GGTGGCG1622350.036.1625372
GGCGCGT1702350.034.4089475
TGGCGCG1724050.033.994864
GTGGCGC1759250.033.3067473
GCGCGTG1823750.032.1476866
CGCGTGC1967550.029.788217
GCGTGCC2069650.028.3384888
CGTGCCT2175450.027.0042139
TTCGTTG145350.022.68707894
CGCGCAC71550.020.38271594
CCTGTAG2441050.019.55069412-13
ACGCACG190300.019.07385494
TGTAGTC2557600.018.61469514-15
TAGTCCC2578200.018.41659416-17
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192399_2_val_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192399_2_val_2_fastqc.zip new file mode 100644 index 00000000..3a2f4b18 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192399_2_val_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192400_1.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192400_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..e2b28981 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_1.fastq.gz_trimming_report.txt @@ -0,0 +1,154 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192400_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA SRR3192400_1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2263.99 s (24 us/read; 2.54 M reads/minute). + +=== Summary === + +Total reads processed: 95,791,942 +Reads with adapters: 37,358,468 (39.0%) +Reads written (passing filters): 95,791,942 (100.0%) + +Total basepairs processed: 9,579,194,200 bp +Quality-trimmed: 276,282,222 bp (2.9%) +Total written (filtered): 9,074,213,717 bp (94.7%) + +=== Adapter 1 === + +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 37358468 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 18.9% + C: 32.4% + G: 24.1% + T: 24.6% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 19443457 23947985.5 0 19443457 +2 6046907 5986996.4 0 6046907 +3 2370672 1496749.1 0 2370672 +4 768377 374187.3 0 768377 +5 487131 93546.8 0 487131 +6 424806 23386.7 0 424806 +7 381765 5846.7 0 381765 +8 408266 1461.7 0 408266 +9 437348 365.4 0 434441 2907 +10 394207 91.4 1 388627 5580 +11 401807 22.8 1 397126 4681 +12 394721 5.7 1 390592 4129 +13 359216 5.7 1 355660 3556 +14 335536 5.7 1 332152 3384 +15 266079 5.7 1 263091 2988 +16 239415 5.7 1 236521 2894 +17 206383 5.7 1 203718 2665 +18 171799 5.7 1 169319 2480 +19 179108 5.7 1 176432 2676 +20 177893 5.7 1 174896 2997 +21 195992 5.7 1 192476 3516 +22 153730 5.7 1 151462 2268 +23 134133 5.7 1 132439 1694 +24 121405 5.7 1 120258 1147 +25 118861 5.7 1 117150 1711 +26 111181 5.7 1 109861 1320 +27 120698 5.7 1 119112 1586 +28 108377 5.7 1 106888 1489 +29 127454 5.7 1 125162 2292 +30 114164 5.7 1 112013 2151 +31 105654 5.7 1 104141 1513 +32 100293 5.7 1 97753 2540 +33 91596 5.7 1 82531 9065 +34 100498 5.7 1 90864 9634 +35 160143 5.7 1 149754 10389 +36 96720 5.7 1 86965 9755 +37 68447 5.7 1 61094 7353 +38 73226 5.7 1 66182 7044 +39 74660 5.7 1 67273 7387 +40 81015 5.7 1 73126 7889 +41 80911 5.7 1 73202 7709 +42 85555 5.7 1 77788 7767 +43 101626 5.7 1 93188 8438 +44 76771 5.7 1 70044 6727 +45 48496 5.7 1 47574 922 +46 46731 5.7 1 45599 1132 +47 48585 5.7 1 47671 914 +48 48937 5.7 1 47950 987 +49 44410 5.7 1 43355 1055 +50 44314 5.7 1 43222 1092 +51 48031 5.7 1 46799 1232 +52 44964 5.7 1 43801 1163 +53 49469 5.7 1 48145 1324 +54 51131 5.7 1 49826 1305 +55 48030 5.7 1 46882 1148 +56 33355 5.7 1 32430 925 +57 29892 5.7 1 28728 1164 +58 29993 5.7 1 29234 759 +59 30616 5.7 1 29667 949 +60 26844 5.7 1 26029 815 +61 30479 5.7 1 29631 848 +62 26354 5.7 1 25240 1114 +63 22806 5.7 1 21946 860 +64 20993 5.7 1 20258 735 +65 16107 5.7 1 15276 831 +66 10012 5.7 1 9360 652 +67 7056 5.7 1 5931 1125 +68 4740 5.7 1 3879 861 +69 4118 5.7 1 3297 821 +70 4428 5.7 1 3815 613 +71 5433 5.7 1 4580 853 +72 7038 5.7 1 5664 1374 +73 4908 5.7 1 4082 826 +74 5862 5.7 1 1358 4504 +75 969 5.7 1 191 778 +76 420 5.7 1 63 357 +77 1178 5.7 1 55 1123 +78 297 5.7 1 8 289 +79 942 5.7 1 6 936 +80 312 5.7 1 8 304 +81 406 5.7 1 2 404 +82 881 5.7 1 5 876 +83 293 5.7 1 0 293 +84 2615 5.7 1 4 2611 +85 438 5.7 1 4 434 +86 340 5.7 1 1 339 +87 930 5.7 1 0 930 +88 310 5.7 1 1 309 +89 352 5.7 1 0 352 +90 509 5.7 1 6 503 +91 479 5.7 1 2 477 +92 1860 5.7 1 2 1858 +93 168 5.7 1 1 167 +94 309 5.7 1 1 308 +95 130 5.7 1 0 130 +96 230 5.7 1 0 230 +97 1179 5.7 1 3 1176 +98 310 5.7 1 0 310 +99 386 5.7 1 0 386 +100 90 5.7 1 0 90 + + +RUN STATISTICS FOR INPUT FILE: SRR3192400_1.fastq.gz +============================================= +95791942 sequences processed in total + diff --git a/src/multiqc/rna-seq/data/SRR3192400_1Log.final.out b/src/multiqc/rna-seq/data/SRR3192400_1Log.final.out new file mode 100644 index 00000000..4b155675 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_1Log.final.out @@ -0,0 +1,34 @@ + Started job on | May 03 03:08:08 + Started mapping on | May 03 03:12:49 + Finished on | May 03 04:17:53 + Mapping speed, Million of reads per hour | 87.53 + + Number of input reads | 94925479 + Average input read length | 188 + UNIQUE READS: + Uniquely mapped reads number | 73365420 + Uniquely mapped reads % | 77.29% + Average mapped length | 187.76 + Number of splices: Total | 53195453 + Number of splices: Annotated (sjdb) | 52360485 + Number of splices: GT/AG | 52445037 + Number of splices: GC/AG | 356334 + Number of splices: AT/AC | 31990 + Number of splices: Non-canonical | 362092 + Mismatch rate per base, % | 0.32% + Deletion rate per base | 0.01% + Deletion average length | 1.59 + Insertion rate per base | 0.01% + Insertion average length | 1.55 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 5519843 + % of reads mapped to multiple loci | 5.81% + Number of reads mapped to too many loci | 118450 + % of reads mapped to too many loci | 0.12% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 16.76% + % of reads unmapped: other | 0.01% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff --git a/src/multiqc/rna-seq/data/SRR3192400_1Log.out b/src/multiqc/rna-seq/data/SRR3192400_1Log.out new file mode 100644 index 00000000..e43bfa39 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_1Log.out @@ -0,0 +1,408 @@ +STAR version=STAR_2.5.1b +STAR compilation time,server,dir=Tue Jan 26 13:48:00 CET 2016 milou-b.uppmax.uu.se:/sw/apps/bioinfo/star/2.5.1b/src/source +##### DEFAULT parameters: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 1 +runDirPerm User_RWX +runRNGseed 777 +genomeDir ./GenomeDir/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn Read1 Read2 +readFilesCommand - +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outTmpDir - +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +##### Command Line: +STAR --runThreadN 4 --outQSconversionAdd 0 --outSAMattributes Standard --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --readFilesIn SRR3192400_1_val_1.fq.gz SRR3192400_2_val_2.fq.gz --outFileNamePrefix SRR3192400_1 --outStd SAM +##### Initial USER parameters from Command Line: +outFileNamePrefix SRR3192400_1 +outStd SAM +###### All USER parameters from Command Line: +runThreadN 4 ~RE-DEFINED +outQSconversionAdd 0 ~RE-DEFINED +outSAMattributes Standard ~RE-DEFINED +genomeLoad NoSharedMemory ~RE-DEFINED +readFilesCommand zcat ~RE-DEFINED +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ~RE-DEFINED +readFilesIn SRR3192400_1_val_1.fq.gz SRR3192400_2_val_2.fq.gz ~RE-DEFINED +outFileNamePrefix SRR3192400_1 ~RE-DEFINED +outStd SAM ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runThreadN 4 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +readFilesIn SRR3192400_1_val_1.fq.gz SRR3192400_2_val_2.fq.gz +readFilesCommand zcat +outFileNamePrefix SRR3192400_1 +outStd SAM +outQSconversionAdd 0 +outSAMattributes Standard + +------------------------------- +##### Final effective command line: +STAR --runThreadN 4 --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --genomeLoad NoSharedMemory --readFilesIn SRR3192400_1_val_1.fq.gz SRR3192400_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix SRR3192400_1 --outStd SAM --outQSconversionAdd 0 --outSAMattributes Standard + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 4 +runDirPerm User_RWX +runRNGseed 777 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn SRR3192400_1_val_1.fq.gz SRR3192400_2_val_2.fq.gz +readFilesCommand zcat +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outFileNamePrefix SRR3192400_1 +outTmpDir - +outStd SAM +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +---------------------------------------- + + + Input read files for mate 1, from input string SRR3192400_1_val_1.fq.gz +-rw-rw-r-- 1 phil b2013064 8219540458 May 3 02:22 SRR3192400_1_val_1.fq.gz + + readsCommandsFile: +exec > "SRR3192400_1_STARtmp/tmp.fifo.read1" +echo FILE 0 +zcat "SRR3192400_1_val_1.fq.gz" + + + Input read files for mate 2, from input string SRR3192400_2_val_2.fq.gz +-rw-rw-r-- 1 phil b2013064 8412108504 May 3 02:22 SRR3192400_2_val_2.fq.gz + + readsCommandsFile: +exec > "SRR3192400_1_STARtmp/tmp.fifo.read2" +echo FILE 0 +zcat "SRR3192400_2_val_2.fq.gz" + +Finished loading and checking parameters +Reading genome generation parameters: +versionGenome 20201 ~RE-DEFINED +genomeFastaFiles genome.fa ~RE-DEFINED +genomeSAindexNbases 14 ~RE-DEFINED +genomeChrBinNbits 18 ~RE-DEFINED +genomeSAsparseD 1 ~RE-DEFINED +sjdbOverhang 100 ~RE-DEFINED +sjdbFileChrStartEnd - ~RE-DEFINED +sjdbGTFfile genes.gtf ~RE-DEFINED +sjdbGTFchrPrefix - ~RE-DEFINED +sjdbGTFfeatureExon exon ~RE-DEFINED +sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED +sjdbGTFtagExonParentGene gene_id ~RE-DEFINED +sjdbInsertSave Basic ~RE-DEFINED +Genome version is compatible with current STAR version +Number of real (reference) chromosmes= 25 +1 1 249250621 0 +2 2 243199373 249298944 +3 3 198022430 492568576 +4 4 191154276 690749440 +5 5 180915260 882114560 +6 6 171115067 1063256064 +7 7 159138663 1234436096 +8 8 146364022 1393819648 +9 9 141213431 1540358144 +10 10 135534747 1681653760 +11 11 135006516 1817444352 +12 12 133851895 1952710656 +13 13 115169878 2086666240 +14 14 107349540 2202009600 +15 15 102531392 2309488640 +16 16 90354753 2412249088 +17 17 81195210 2502688768 +18 18 78077248 2583953408 +19 19 59128983 2662072320 +20 20 63025520 2721316864 +21 21 48129895 2784493568 +22 22 51304566 2832728064 +23 X 155270560 2884108288 +24 Y 59373566 3039559680 +25 MT 16569 3099066368 +--sjdbOverhang = 100 taken from the generated genome +Started loading the genome: Tue May 3 03:08:08 2016 + +checking Genome sizefile size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +checking SA sizefile size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 +Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 +nGenome=3168538239; nSAbyte=24152204822 +GstrandBit=32 SA number of indices=5855079956 +Shared memory is not used for genomes. Allocated a private copy of the genome. +Genome file size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3168538239 bytes +SA file size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24152204822 bytes +Loading SAindex ... done: 1565873619 bytes +Finished loading the genome: Tue May 3 03:12:49 2016 + +Processing splice junctions database sjdbN=344327, sjdbOverhang=100 +alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 +Created thread # 1 +Created thread # 2 +Created thread # 3 +Starting to map file # 0 +mate 1: SRR3192400_1_val_1.fq.gz +mate 2: SRR3192400_2_val_2.fq.gz +Thread #1 end of input stream, nextChar=-1 +Completed: thread #3 +Completed: thread #2 +Completed: thread #1 +Completed: thread #0 +Joined thread # 1 +Joined thread # 2 +Joined thread # 3 +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192400_1Log.progress.out b/src/multiqc/rna-seq/data/SRR3192400_1Log.progress.out new file mode 100644 index 00000000..599b5df1 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_1Log.progress.out @@ -0,0 +1,65 @@ + Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped + M/hr number length unique length MMrate multi multi+ MM short other +May 03 03:13:50 69.2 1171761 190 77.8% 189.2 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:14:51 75.5 2558037 190 77.7% 189.3 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:15:53 77.2 3946647 189 77.6% 188.9 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:16:53 78.6 5329603 190 77.7% 189.2 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:17:58 79.6 6830478 190 77.7% 189.3 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:19:03 80.2 8333618 190 77.7% 189.2 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:20:03 80.6 9718356 190 77.7% 189.3 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:21:05 81.3 11201735 190 77.6% 189.3 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:22:07 81.8 12681860 190 77.7% 189.2 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:23:12 81.8 14162164 190 77.7% 189.2 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:24:12 81.8 15528515 189 77.6% 189.1 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:25:15 82.1 17006047 190 77.6% 189.1 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:26:16 82.5 18487637 189 77.6% 189.1 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:27:16 82.9 19969806 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:28:16 83.3 21451641 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:29:16 84.1 23046131 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:30:18 84.6 24637815 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:31:21 84.9 26234011 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:32:24 85.3 27825866 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:33:26 85.6 29421822 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:34:30 85.5 30900854 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:35:33 85.8 32493424 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:36:36 86.0 34088734 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:37:41 86.1 35681611 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.7% 0.0% +May 03 03:38:44 86.0 37163855 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:39:48 86.2 38758943 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:40:48 86.5 40355596 189 77.6% 189.0 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:41:48 86.6 41838144 189 77.6% 188.9 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:42:53 86.7 43433310 189 77.6% 188.9 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:43:59 86.7 45034033 189 77.6% 188.9 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:45:01 86.9 46640528 189 77.6% 188.8 0.3% 5.5% 0.1% 0.0% 16.8% 0.0% +May 03 03:46:05 87.0 48249676 189 77.6% 188.8 0.3% 5.6% 0.1% 0.0% 16.7% 0.0% +May 03 03:47:09 87.1 49860592 189 77.5% 188.7 0.3% 5.6% 0.1% 0.0% 16.7% 0.0% +May 03 03:48:13 87.2 51468967 189 77.5% 188.6 0.3% 5.6% 0.1% 0.0% 16.7% 0.0% +May 03 03:49:16 87.4 53078966 189 77.5% 188.6 0.3% 5.6% 0.1% 0.0% 16.7% 0.0% +May 03 03:50:17 87.4 54575919 189 77.5% 188.5 0.3% 5.6% 0.1% 0.0% 16.7% 0.0% +May 03 03:51:21 87.5 56183920 189 77.5% 188.5 0.3% 5.6% 0.1% 0.0% 16.7% 0.0% +May 03 03:52:23 87.6 57795291 189 77.5% 188.4 0.3% 5.6% 0.1% 0.0% 16.7% 0.0% +May 03 03:53:24 87.5 59175176 189 77.5% 188.4 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 03:54:24 87.2 60437901 189 77.5% 188.4 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 03:55:25 87.2 61932994 189 77.4% 188.3 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 03:56:25 87.3 63427576 189 77.4% 188.3 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 03:57:25 87.3 64920737 189 77.4% 188.2 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 03:58:29 87.4 66532528 188 77.4% 188.2 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 03:59:29 87.5 68029312 188 77.4% 188.2 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 04:00:33 87.7 69751584 188 77.4% 188.1 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 04:01:35 87.7 71247379 188 77.4% 188.1 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 04:02:37 87.8 72858721 188 77.4% 188.1 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 04:03:37 87.8 74351740 188 77.4% 188.1 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 04:04:40 87.9 75962104 188 77.4% 188.0 0.3% 5.7% 0.1% 0.0% 16.7% 0.0% +May 03 04:05:45 87.9 77572613 188 77.4% 188.0 0.3% 5.8% 0.1% 0.0% 16.7% 0.0% +May 03 04:06:50 88.0 79180897 188 77.4% 188.0 0.3% 5.8% 0.1% 0.0% 16.7% 0.0% +May 03 04:07:52 88.1 80792599 188 77.4% 188.0 0.3% 5.8% 0.1% 0.0% 16.7% 0.0% +May 03 04:08:55 88.0 82287081 188 77.3% 187.9 0.3% 5.8% 0.1% 0.0% 16.7% 0.0% +May 03 04:09:57 88.0 83781802 188 77.3% 187.9 0.3% 5.8% 0.1% 0.0% 16.7% 0.0% +May 03 04:10:58 88.0 85278711 188 77.3% 187.9 0.3% 5.8% 0.1% 0.0% 16.7% 0.0% +May 03 04:12:02 87.8 86660594 188 77.3% 187.9 0.3% 5.8% 0.1% 0.0% 16.7% 0.0% +May 03 04:13:06 87.6 88040937 188 77.3% 187.9 0.3% 5.8% 0.1% 0.0% 16.8% 0.0% +May 03 04:14:09 87.5 89423850 188 77.3% 187.8 0.3% 5.8% 0.1% 0.0% 16.8% 0.0% +May 03 04:15:12 87.4 90922174 188 77.3% 187.8 0.3% 5.8% 0.1% 0.0% 16.8% 0.0% +May 03 04:16:12 87.5 92415617 188 77.3% 187.8 0.3% 5.8% 0.1% 0.0% 16.8% 0.0% +May 03 04:17:15 87.6 94027460 188 77.3% 187.8 0.3% 5.8% 0.1% 0.0% 16.8% 0.0% +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192400_1Log.std.out b/src/multiqc/rna-seq/data/SRR3192400_1Log.std.out new file mode 100644 index 00000000..174cc88f --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_1Log.std.out @@ -0,0 +1,4 @@ +May 03 03:08:08 ..... Started STAR run +May 03 03:08:08 ..... Loading genome +May 03 03:12:49 ..... Started mapping +May 03 04:17:53 ..... Finished successfully diff --git a/src/multiqc/rna-seq/data/SRR3192400_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192400_1_fastqc.html new file mode 100644 index 00000000..384732d4 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192400_1.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192400_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192400_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences95791942
Sequences flagged as poor quality0
Sequence length100
%GC45

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1851890.19332419422084585No Hit
GGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1686740.1760837044101267No Hit
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1210910.12641042395820726No Hit
GCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCAGCTCGTCAGCGC962120.10043851078830826No Hit

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGTATCA1180000.049.4709781
GTATCAA1950200.037.606921
GAGTACA2315100.034.891271
GTACATG3612700.033.4880941
TACATGG3681200.032.368642
AGTACAT2443250.032.1875042
CAACGCA2323000.030.8214055
ATCAACG2345500.030.398383
ACATGGG3918550.029.84543
CTAGTAC399000.029.2228953
TCAACGC2473400.029.1484994
AACGCAG2521000.028.6472726
CTAACGC156050.028.6388663
TATCAAC2561650.028.2620242
TAACGCC155150.028.1709694
CATGGGG3152050.027.3788764
CTGTGCG423300.026.9608769
TCTAACG169450.025.9324422
TAGTACT522350.024.3668824
CCTAGTA485100.023.7470342
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192400_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192400_1_fastqc.zip new file mode 100644 index 00000000..6fca77d5 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192400_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192400_1_star_aligned.bam_counts.txt.summary b/src/multiqc/rna-seq/data/SRR3192400_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..27ad816e --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_1_star_aligned.bam_counts.txt.summary @@ -0,0 +1,12 @@ +Status SRR3192400_1_star_aligned.bam +Assigned 63437308 +Unassigned_Ambiguity 4527006 +Unassigned_MultiMapping 15248435 +Unassigned_NoFeatures 6994629 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_FragmentLength 0 +Unassigned_Chimera 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_Duplicate 0 diff --git a/src/multiqc/rna-seq/data/SRR3192400_1_val_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192400_1_val_1_fastqc.html new file mode 100644 index 00000000..f8b9989e --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_1_val_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192400_1_val_1.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192400_1_val_1.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192400_1_val_1.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences94925479
Sequences flagged as poor quality0
Sequence length20-100
%GC45

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[OK]Overrepresented sequences

No overrepresented sequences

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGTATCA1179050.047.4648251
GTATCAA1957000.035.708871
GAGTACA2295150.032.9183651
GTACATG3577550.031.6660251
TACATGG3642950.030.625632
AGTACAT2415000.030.518522
CAACGCA2318950.029.3048525
ATCAACG2352350.028.8166123
ACATGGG3866000.028.2653263
TCAACGC2464750.027.7935644
CTAGTAC389600.027.6816223
CTAACGC152900.027.518683
AACGCAG2518900.027.222776
TATCAAC2550550.027.0020032
TAACGCC151850.026.9214214
CATGGGG3088700.025.9947244
GTACTAG291200.025.9072251
CTGTGCG420900.025.6141459
TCTAACG165550.024.8282472
TCGACGG160500.023.28146794
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192400_1_val_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192400_1_val_1_fastqc.zip new file mode 100644 index 00000000..c07d052b Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192400_1_val_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192400_2.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192400_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..ff0d52d6 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_2.fastq.gz_trimming_report.txt @@ -0,0 +1,157 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192400_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA SRR3192400_2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2198.06 s (23 us/read; 2.61 M reads/minute). + +=== Summary === + +Total reads processed: 95,791,942 +Reads with adapters: 36,966,867 (38.6%) +Reads written (passing filters): 95,791,942 (100.0%) + +Total basepairs processed: 9,579,194,200 bp +Quality-trimmed: 459,057,679 bp (4.8%) +Total written (filtered): 8,893,887,057 bp (92.8%) + +=== Adapter 1 === + +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 36966867 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 19.0% + C: 32.4% + G: 24.0% + T: 24.6% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 19223579 23947985.5 0 19223579 +2 5928936 5986996.4 0 5928936 +3 2345857 1496749.1 0 2345857 +4 771017 374187.3 0 771017 +5 492222 93546.8 0 492222 +6 425050 23386.7 0 425050 +7 381856 5846.7 0 381856 +8 406812 1461.7 0 406812 +9 446449 365.4 0 443507 2942 +10 386155 91.4 1 381466 4689 +11 395176 22.8 1 391286 3890 +12 387150 5.7 1 384113 3037 +13 346829 5.7 1 344319 2510 +14 338762 5.7 1 336107 2655 +15 261955 5.7 1 259778 2177 +16 240099 5.7 1 237878 2221 +17 204167 5.7 1 202277 1890 +18 166340 5.7 1 164723 1617 +19 180625 5.7 1 178600 2025 +20 165988 5.7 1 164217 1771 +21 159350 5.7 1 157754 1596 +22 162796 5.7 1 160834 1962 +23 133784 5.7 1 132320 1464 +24 141625 5.7 1 140203 1422 +25 129943 5.7 1 128101 1842 +26 115900 5.7 1 114194 1706 +27 115919 5.7 1 114337 1582 +28 143758 5.7 1 141697 2061 +29 147927 5.7 1 145993 1934 +30 90487 5.7 1 88917 1570 +31 106596 5.7 1 105175 1421 +32 113111 5.7 1 110962 2149 +33 97734 5.7 1 96224 1510 +34 94392 5.7 1 93117 1275 +35 142349 5.7 1 140657 1692 +36 88319 5.7 1 86671 1648 +37 92268 5.7 1 90496 1772 +38 77211 5.7 1 76084 1127 +39 97240 5.7 1 95708 1532 +40 59252 5.7 1 58194 1058 +41 79530 5.7 1 78068 1462 +42 227324 5.7 1 224144 3180 +43 14087 5.7 1 13556 531 +44 52570 5.7 1 51364 1206 +45 28034 5.7 1 27359 675 +46 34384 5.7 1 33409 975 +47 42698 5.7 1 41884 814 +48 41544 5.7 1 40849 695 +49 45470 5.7 1 44608 862 +50 41237 5.7 1 40424 813 +51 46203 5.7 1 45329 874 +52 45479 5.7 1 44297 1182 +53 50707 5.7 1 49408 1299 +54 85236 5.7 1 83320 1916 +55 23527 5.7 1 22683 844 +56 39957 5.7 1 38762 1195 +57 51866 5.7 1 50252 1614 +58 18044 5.7 1 17475 569 +59 19367 5.7 1 18598 769 +60 18528 5.7 1 17825 703 +61 20929 5.7 1 20304 625 +62 25842 5.7 1 24811 1031 +63 28351 5.7 1 27556 795 +64 12310 5.7 1 11804 506 +65 6907 5.7 1 6440 467 +66 6151 5.7 1 5707 444 +67 5948 5.7 1 5064 884 +68 3820 5.7 1 3399 421 +69 3615 5.7 1 3088 527 +70 3972 5.7 1 3664 308 +71 4429 5.7 1 4084 345 +72 5681 5.7 1 4956 725 +73 5463 5.7 1 5029 434 +74 6081 5.7 1 2341 3740 +75 1266 5.7 1 539 727 +76 775 5.7 1 405 370 +77 1556 5.7 1 457 1099 +78 489 5.7 1 185 304 +79 938 5.7 1 110 828 +80 350 5.7 1 33 317 +81 410 5.7 1 5 405 +82 811 5.7 1 9 802 +83 324 5.7 1 1 323 +84 2192 5.7 1 6 2186 +85 408 5.7 1 3 405 +86 331 5.7 1 0 331 +87 854 5.7 1 0 854 +88 290 5.7 1 1 289 +89 319 5.7 1 0 319 +90 450 5.7 1 4 446 +91 489 5.7 1 0 489 +92 1646 5.7 1 5 1641 +93 182 5.7 1 1 181 +94 313 5.7 1 0 313 +95 109 5.7 1 1 108 +96 232 5.7 1 1 231 +97 1053 5.7 1 2 1051 +98 327 5.7 1 0 327 +99 368 5.7 1 0 368 +100 109 5.7 1 0 109 + + +RUN STATISTICS FOR INPUT FILE: SRR3192400_2.fastq.gz +============================================= +95791942 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 95791942 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 866463 (0.90%) diff --git a/src/multiqc/rna-seq/data/SRR3192400_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192400_2_fastqc.html new file mode 100644 index 00000000..6ab1334f --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192400_2.fastq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192400_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192400_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences95791942
Sequences flagged as poor quality0
Sequence length100
%GC45

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1954950.20408292797738664No Hit
GGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1626230.169766889160677No Hit
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1080860.11283412544240935No Hit

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGTATCA1133250.048.859551
GTATCAA1964350.040.090251
GTACATG3610150.036.0546461
GAGTACA2205000.035.8745961
TACATGG3677650.034.840132
CAACGCA2248000.034.109495
ATCAACG2301900.033.300373
AGTACAT2334800.033.0673452
ACATGGG3929950.032.1042823
TCAACGC2419400.031.8630164
AACGCAG2422450.031.8493236
TATCAAC2503250.031.0391222
CTAACGC174400.030.0738493
CATGGGG3147150.029.7281364
CTAGTAC403350.029.6503093
TAACGCC172150.029.6444874
GTACTAG293500.029.1037651
CTGTGCG409500.028.1449349
TCTAACG183450.027.2856222
ACGCAGA2809750.027.0492657
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192400_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192400_2_fastqc.zip new file mode 100644 index 00000000..d2499dd8 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192400_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192400_2_val_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192400_2_val_2_fastqc.html new file mode 100644 index 00000000..6da6ee22 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192400_2_val_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192400_2_val_2.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192400_2_val_2.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192400_2_val_2.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences94925479
Sequences flagged as poor quality0
Sequence length20-100
%GC45

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[OK]Overrepresented sequences

No overrepresented sequences

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGTATCA1108750.046.2097051
GTATCAA1929800.037.484291
GTACATG3579900.033.3841441
GAGTACA2198150.033.149061
TACATGG3653650.032.281932
CAACGCA2208750.031.7837435
ATCAACG2266550.031.0129453
AGTACAT2324700.030.4542522
TCAACGC2372950.029.8670044
ACATGGG3885650.029.8482973
AACGCAG2368600.029.8115356
CTAGTAC388150.029.1813893
TATCAAC2456650.029.0161932
CTAACGC158250.028.9728373
TAACGCC156750.028.6040764
CATGGGG3100600.027.7123684
CTGTGCG399000.027.4580869
GTACTAG293200.026.5473961
TCTAACG170600.026.3118252
ACGCAGA2780700.025.0563837
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192400_2_val_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192400_2_val_2_fastqc.zip new file mode 100644 index 00000000..ea4d3f37 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192400_2_val_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192401_1.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192401_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..782739a5 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_1.fastq.gz_trimming_report.txt @@ -0,0 +1,154 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192401_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA SRR3192401_1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2121.80 s (22 us/read; 2.71 M reads/minute). + +=== Summary === + +Total reads processed: 95,735,344 +Reads with adapters: 37,721,932 (39.4%) +Reads written (passing filters): 95,735,344 (100.0%) + +Total basepairs processed: 9,573,534,400 bp +Quality-trimmed: 325,568,713 bp (3.4%) +Total written (filtered): 8,984,320,742 bp (93.8%) + +=== Adapter 1 === + +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 37721932 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 18.6% + C: 32.8% + G: 24.3% + T: 24.3% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 18858835 23933836.0 0 18858835 +2 5848235 5983459.0 0 5848235 +3 2337808 1495864.8 0 2337808 +4 732193 373966.2 0 732193 +5 468842 93491.5 0 468842 +6 410061 23372.9 0 410061 +7 369412 5843.2 0 369412 +8 403648 1460.8 0 403648 +9 428873 365.2 0 426235 2638 +10 386106 91.3 1 380116 5990 +11 399408 22.8 1 393870 5538 +12 397945 5.7 1 392782 5163 +13 343813 5.7 1 339592 4221 +14 314038 5.7 1 309988 4050 +15 280496 5.7 1 276661 3835 +16 264568 5.7 1 260595 3973 +17 247940 5.7 1 244181 3759 +18 245633 5.7 1 241939 3694 +19 261461 5.7 1 257418 4043 +20 253541 5.7 1 249130 4411 +21 294858 5.7 1 289367 5491 +22 214473 5.7 1 211344 3129 +23 179194 5.7 1 176920 2274 +24 166056 5.7 1 164378 1678 +25 154611 5.7 1 152557 2054 +26 151634 5.7 1 150061 1573 +27 163157 5.7 1 161100 2057 +28 147009 5.7 1 145082 1927 +29 178843 5.7 1 175751 3092 +30 147535 5.7 1 144941 2594 +31 126476 5.7 1 124700 1776 +32 112796 5.7 1 110178 2618 +33 118319 5.7 1 107605 10714 +34 132450 5.7 1 121727 10723 +35 155605 5.7 1 144748 10857 +36 138894 5.7 1 127741 11153 +37 126679 5.7 1 116071 10608 +38 118989 5.7 1 108894 10095 +39 142270 5.7 1 131406 10864 +40 126020 5.7 1 116799 9221 +41 129692 5.7 1 120684 9008 +42 124729 5.7 1 116322 8407 +43 150744 5.7 1 141781 8963 +44 81789 5.7 1 75493 6296 +45 52862 5.7 1 51873 989 +46 48877 5.7 1 47670 1207 +47 68220 5.7 1 67068 1152 +48 79736 5.7 1 78334 1402 +49 54934 5.7 1 53811 1123 +50 47493 5.7 1 46361 1132 +51 50978 5.7 1 49696 1282 +52 45164 5.7 1 44033 1131 +53 46714 5.7 1 45428 1286 +54 59991 5.7 1 58505 1486 +55 51196 5.7 1 50014 1182 +56 27059 5.7 1 26273 786 +57 23470 5.7 1 22435 1035 +58 25974 5.7 1 25317 657 +59 30101 5.7 1 29228 873 +60 22739 5.7 1 22005 734 +61 25971 5.7 1 25242 729 +62 19628 5.7 1 18688 940 +63 15686 5.7 1 14977 709 +64 13933 5.7 1 13299 634 +65 12655 5.7 1 11921 734 +66 7224 5.7 1 6638 586 +67 5153 5.7 1 3982 1171 +68 3661 5.7 1 2929 732 +69 3764 5.7 1 2930 834 +70 4086 5.7 1 3516 570 +71 5135 5.7 1 4422 713 +72 6547 5.7 1 5210 1337 +73 4508 5.7 1 3807 701 +74 6199 5.7 1 1201 4998 +75 983 5.7 1 133 850 +76 418 5.7 1 57 361 +77 1176 5.7 1 37 1139 +78 301 5.7 1 13 288 +79 913 5.7 1 1 912 +80 317 5.7 1 3 314 +81 395 5.7 1 1 394 +82 877 5.7 1 2 875 +83 334 5.7 1 0 334 +84 2718 5.7 1 4 2714 +85 455 5.7 1 0 455 +86 331 5.7 1 2 329 +87 1055 5.7 1 3 1052 +88 293 5.7 1 2 291 +89 328 5.7 1 2 326 +90 447 5.7 1 4 443 +91 488 5.7 1 1 487 +92 1934 5.7 1 8 1926 +93 163 5.7 1 0 163 +94 334 5.7 1 1 333 +95 124 5.7 1 0 124 +96 200 5.7 1 2 198 +97 1207 5.7 1 2 1205 +98 277 5.7 1 0 277 +99 445 5.7 1 1 444 +100 83 5.7 1 0 83 + + +RUN STATISTICS FOR INPUT FILE: SRR3192401_1.fastq.gz +============================================= +95735344 sequences processed in total + diff --git a/src/multiqc/rna-seq/data/SRR3192401_1Log.final.out b/src/multiqc/rna-seq/data/SRR3192401_1Log.final.out new file mode 100644 index 00000000..d2747399 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_1Log.final.out @@ -0,0 +1,34 @@ + Started job on | May 03 03:00:08 + Started mapping on | May 03 03:04:35 + Finished on | May 03 04:16:46 + Mapping speed, Million of reads per hour | 79.16 + + Number of input reads | 95236637 + Average input read length | 188 + UNIQUE READS: + Uniquely mapped reads number | 72790825 + Uniquely mapped reads % | 76.43% + Average mapped length | 187.50 + Number of splices: Total | 54102890 + Number of splices: Annotated (sjdb) | 53255851 + Number of splices: GT/AG | 53330650 + Number of splices: GC/AG | 362038 + Number of splices: AT/AC | 32302 + Number of splices: Non-canonical | 377900 + Mismatch rate per base, % | 0.31% + Deletion rate per base | 0.01% + Deletion average length | 1.59 + Insertion rate per base | 0.01% + Insertion average length | 1.54 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 5513851 + % of reads mapped to multiple loci | 5.79% + Number of reads mapped to too many loci | 172094 + % of reads mapped to too many loci | 0.18% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 17.59% + % of reads unmapped: other | 0.01% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff --git a/src/multiqc/rna-seq/data/SRR3192401_1Log.out b/src/multiqc/rna-seq/data/SRR3192401_1Log.out new file mode 100644 index 00000000..ac9a0ff9 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_1Log.out @@ -0,0 +1,408 @@ +STAR version=STAR_2.5.1b +STAR compilation time,server,dir=Tue Jan 26 13:48:00 CET 2016 milou-b.uppmax.uu.se:/sw/apps/bioinfo/star/2.5.1b/src/source +##### DEFAULT parameters: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 1 +runDirPerm User_RWX +runRNGseed 777 +genomeDir ./GenomeDir/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn Read1 Read2 +readFilesCommand - +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outTmpDir - +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +##### Command Line: +STAR --runThreadN 4 --outQSconversionAdd 0 --outSAMattributes Standard --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --readFilesIn SRR3192401_1_val_1.fq.gz SRR3192401_2_val_2.fq.gz --outFileNamePrefix SRR3192401_1 --outStd SAM +##### Initial USER parameters from Command Line: +outFileNamePrefix SRR3192401_1 +outStd SAM +###### All USER parameters from Command Line: +runThreadN 4 ~RE-DEFINED +outQSconversionAdd 0 ~RE-DEFINED +outSAMattributes Standard ~RE-DEFINED +genomeLoad NoSharedMemory ~RE-DEFINED +readFilesCommand zcat ~RE-DEFINED +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ~RE-DEFINED +readFilesIn SRR3192401_1_val_1.fq.gz SRR3192401_2_val_2.fq.gz ~RE-DEFINED +outFileNamePrefix SRR3192401_1 ~RE-DEFINED +outStd SAM ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runThreadN 4 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +readFilesIn SRR3192401_1_val_1.fq.gz SRR3192401_2_val_2.fq.gz +readFilesCommand zcat +outFileNamePrefix SRR3192401_1 +outStd SAM +outQSconversionAdd 0 +outSAMattributes Standard + +------------------------------- +##### Final effective command line: +STAR --runThreadN 4 --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --genomeLoad NoSharedMemory --readFilesIn SRR3192401_1_val_1.fq.gz SRR3192401_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix SRR3192401_1 --outStd SAM --outQSconversionAdd 0 --outSAMattributes Standard + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 4 +runDirPerm User_RWX +runRNGseed 777 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn SRR3192401_1_val_1.fq.gz SRR3192401_2_val_2.fq.gz +readFilesCommand zcat +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outFileNamePrefix SRR3192401_1 +outTmpDir - +outStd SAM +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +---------------------------------------- + + + Input read files for mate 1, from input string SRR3192401_1_val_1.fq.gz +-rw-rw-r-- 1 phil b2013064 8425165702 May 3 02:00 SRR3192401_1_val_1.fq.gz + + readsCommandsFile: +exec > "SRR3192401_1_STARtmp/tmp.fifo.read1" +echo FILE 0 +zcat "SRR3192401_1_val_1.fq.gz" + + + Input read files for mate 2, from input string SRR3192401_2_val_2.fq.gz +-rw-rw-r-- 1 phil b2013064 8231020529 May 3 02:00 SRR3192401_2_val_2.fq.gz + + readsCommandsFile: +exec > "SRR3192401_1_STARtmp/tmp.fifo.read2" +echo FILE 0 +zcat "SRR3192401_2_val_2.fq.gz" + +Finished loading and checking parameters +Reading genome generation parameters: +versionGenome 20201 ~RE-DEFINED +genomeFastaFiles genome.fa ~RE-DEFINED +genomeSAindexNbases 14 ~RE-DEFINED +genomeChrBinNbits 18 ~RE-DEFINED +genomeSAsparseD 1 ~RE-DEFINED +sjdbOverhang 100 ~RE-DEFINED +sjdbFileChrStartEnd - ~RE-DEFINED +sjdbGTFfile genes.gtf ~RE-DEFINED +sjdbGTFchrPrefix - ~RE-DEFINED +sjdbGTFfeatureExon exon ~RE-DEFINED +sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED +sjdbGTFtagExonParentGene gene_id ~RE-DEFINED +sjdbInsertSave Basic ~RE-DEFINED +Genome version is compatible with current STAR version +Number of real (reference) chromosmes= 25 +1 1 249250621 0 +2 2 243199373 249298944 +3 3 198022430 492568576 +4 4 191154276 690749440 +5 5 180915260 882114560 +6 6 171115067 1063256064 +7 7 159138663 1234436096 +8 8 146364022 1393819648 +9 9 141213431 1540358144 +10 10 135534747 1681653760 +11 11 135006516 1817444352 +12 12 133851895 1952710656 +13 13 115169878 2086666240 +14 14 107349540 2202009600 +15 15 102531392 2309488640 +16 16 90354753 2412249088 +17 17 81195210 2502688768 +18 18 78077248 2583953408 +19 19 59128983 2662072320 +20 20 63025520 2721316864 +21 21 48129895 2784493568 +22 22 51304566 2832728064 +23 X 155270560 2884108288 +24 Y 59373566 3039559680 +25 MT 16569 3099066368 +--sjdbOverhang = 100 taken from the generated genome +Started loading the genome: Tue May 3 03:00:08 2016 + +checking Genome sizefile size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +checking SA sizefile size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 +Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 +nGenome=3168538239; nSAbyte=24152204822 +GstrandBit=32 SA number of indices=5855079956 +Shared memory is not used for genomes. Allocated a private copy of the genome. +Genome file size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3168538239 bytes +SA file size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24152204822 bytes +Loading SAindex ... done: 1565873619 bytes +Finished loading the genome: Tue May 3 03:04:35 2016 + +Processing splice junctions database sjdbN=344327, sjdbOverhang=100 +alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 +Created thread # 1 +Created thread # 2 +Created thread # 3 +Starting to map file # 0 +mate 1: SRR3192401_1_val_1.fq.gz +mate 2: SRR3192401_2_val_2.fq.gz +Thread #0 end of input stream, nextChar=-1 +Completed: thread #1 +Completed: thread #3 +Completed: thread #0 +Joined thread # 1 +Completed: thread #2 +Joined thread # 2 +Joined thread # 3 +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192401_1Log.progress.out b/src/multiqc/rna-seq/data/SRR3192401_1Log.progress.out new file mode 100644 index 00000000..5875ff7a --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_1Log.progress.out @@ -0,0 +1,72 @@ + Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped + M/hr number length unique length MMrate multi multi+ MM short other +May 03 03:05:35 63.8 1063912 188 76.8% 188.1 0.3% 5.5% 0.2% 0.0% 17.5% 0.0% +May 03 03:06:39 71.3 2456376 189 76.8% 188.4 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:07:41 72.3 3737781 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:08:45 73.9 5129237 189 76.7% 188.4 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:09:50 74.5 6520825 189 76.7% 188.5 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:10:56 74.8 7917823 189 76.7% 188.4 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:12:00 75.3 9311897 189 76.7% 188.4 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:13:01 76.1 10694205 189 76.7% 188.4 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:14:06 76.1 12071374 189 76.7% 188.3 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:15:07 76.6 13444927 189 76.7% 188.3 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:16:10 76.2 14708280 188 76.7% 188.3 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:17:13 76.4 16080479 189 76.7% 188.3 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:18:15 76.6 17453561 189 76.7% 188.3 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:19:20 77.1 18948076 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:20:23 77.2 20323203 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:21:27 77.2 21702592 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:22:28 77.4 23074153 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:23:29 77.6 24446506 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:24:30 77.8 25823031 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:25:32 77.9 27195953 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:26:34 78.0 28570366 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:27:36 78.1 29947041 188 76.7% 188.2 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:28:37 78.2 31319395 188 76.7% 188.2 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:29:37 78.4 32694101 188 76.7% 188.2 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:30:37 78.8 34183224 188 76.7% 188.2 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:31:41 78.7 35558258 188 76.7% 188.2 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:32:43 78.8 36938093 188 76.7% 188.1 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:33:44 78.9 38313214 188 76.7% 188.1 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:34:47 78.9 39692013 188 76.7% 188.1 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:35:49 78.9 41070940 188 76.7% 188.1 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:36:51 78.9 42446496 188 76.7% 188.1 0.3% 5.5% 0.2% 0.0% 17.6% 0.0% +May 03 03:37:54 78.9 43827243 188 76.7% 188.1 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:38:54 79.0 45207557 188 76.7% 188.0 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:39:56 79.1 46589332 188 76.7% 188.0 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:40:59 79.1 47974537 188 76.6% 188.0 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:42:01 79.1 49357663 188 76.6% 188.0 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:43:04 79.3 50854976 188 76.6% 187.9 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:44:04 79.4 52239561 188 76.6% 187.9 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:45:06 79.4 53624691 188 76.6% 187.9 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:46:10 79.4 55006576 188 76.6% 187.9 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:47:11 79.4 56391279 188 76.6% 187.9 0.3% 5.6% 0.2% 0.0% 17.6% 0.0% +May 03 03:48:16 79.4 57776894 188 76.6% 187.8 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:49:25 79.2 59157569 188 76.6% 187.8 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:50:26 79.2 60540293 188 76.6% 187.8 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:51:26 79.2 61809731 188 76.5% 187.8 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:52:27 79.2 63191990 188 76.5% 187.8 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:53:27 79.3 64575979 188 76.5% 187.8 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:54:31 79.3 65962363 188 76.5% 187.7 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:55:34 79.3 67346642 188 76.5% 187.7 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:56:34 79.3 68727396 188 76.5% 187.7 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:57:34 79.4 70110605 188 76.5% 187.7 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:58:38 79.4 71497907 188 76.5% 187.7 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 03:59:39 79.5 72994639 188 76.5% 187.7 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 04:00:40 79.6 74376991 188 76.5% 187.7 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 04:01:43 79.6 75761323 188 76.5% 187.7 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 04:02:44 79.6 77145682 188 76.5% 187.6 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 04:03:44 79.7 78527364 188 76.5% 187.6 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 04:04:47 79.6 79911796 188 76.5% 187.6 0.3% 5.7% 0.2% 0.0% 17.6% 0.0% +May 03 04:05:47 79.7 81298141 188 76.5% 187.6 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:06:50 79.6 82564979 188 76.5% 187.6 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:07:50 79.5 83833770 188 76.5% 187.6 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:08:52 79.5 85219600 188 76.5% 187.6 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:09:56 79.4 86490235 188 76.5% 187.6 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:10:59 79.3 87758929 188 76.5% 187.6 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:12:02 79.2 89029843 188 76.5% 187.6 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:13:06 79.2 90417646 188 76.4% 187.5 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:14:08 79.2 91800222 188 76.4% 187.5 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:15:10 79.2 93184160 188 76.4% 187.5 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +May 03 04:16:18 79.2 94686574 188 76.4% 187.5 0.3% 5.8% 0.2% 0.0% 17.6% 0.0% +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192401_1Log.std.out b/src/multiqc/rna-seq/data/SRR3192401_1Log.std.out new file mode 100644 index 00000000..52550f53 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_1Log.std.out @@ -0,0 +1,4 @@ +May 03 03:00:08 ..... Started STAR run +May 03 03:00:08 ..... Loading genome +May 03 03:04:35 ..... Started mapping +May 03 04:16:46 ..... Finished successfully diff --git a/src/multiqc/rna-seq/data/SRR3192401_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192401_1_fastqc.html new file mode 100644 index 00000000..5ba27266 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192401_1.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192401_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192401_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences95735344
Sequences flagged as poor quality0
Sequence length100
%GC45

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT2084790.21776596948353788No Hit
GGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1964500.20520112195972262No Hit
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1465160.15304274667880233No Hit

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGTATCA1237650.051.3406031
GTATCAA2049600.037.4606551
GAGTACA2335550.034.667241
AGTACAT2457550.032.1466752
GTACATG3546000.032.0129281
TACATGG3626750.030.8745352
CAACGCA2489900.030.1834225
ATCAACG2512900.029.7380983
TCAACGC2649950.028.5377164
ACATGGG3875500.028.3761333
AACGCAG2713950.027.9810816
TATCAAC2728850.027.829932
CTAACGC159050.026.0894183
CTAGTAC383350.025.97363
CATGGGG3119000.025.7071194
TAACGCC160900.025.2073334
GTACTAG289600.025.006331
CTGTGCG403250.024.5249129
GTGGTAT461150.023.9519351
TCTAACG169350.023.7012062
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192401_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192401_1_fastqc.zip new file mode 100644 index 00000000..3e1d6bb5 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192401_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192401_1_star_aligned.bam_counts.txt.summary b/src/multiqc/rna-seq/data/SRR3192401_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..19c6e2fa --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_1_star_aligned.bam_counts.txt.summary @@ -0,0 +1,12 @@ +Status SRR3192401_1_star_aligned.bam +Assigned 63800363 +Unassigned_Ambiguity 4557129 +Unassigned_MultiMapping 15309144 +Unassigned_NoFeatures 5926031 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_FragmentLength 0 +Unassigned_Chimera 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_Duplicate 0 diff --git a/src/multiqc/rna-seq/data/SRR3192401_1_val_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192401_1_val_1_fastqc.html new file mode 100644 index 00000000..dd3e8889 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_1_val_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192401_1_val_1.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192401_1_val_1.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192401_1_val_1.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences95236637
Sequences flagged as poor quality0
Sequence length20-100
%GC45

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[OK]Overrepresented sequences

No overrepresented sequences

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGTATCA1229050.048.2719761
GTATCAA2015700.034.796451
GAGTACA2310300.032.495091
AGTACAT2428600.030.214772
GTACATG3515150.030.1931441
TACATGG3600600.029.080312
CAACGCA2464000.027.8370275
ATCAACG2487850.027.46043
ACATGGG3851800.026.6723923
TCAACGC2630000.026.2627264
TATCAAC2678700.025.8922122
AACGCAG2679300.025.8696846
GTACTAG277950.025.335371
CTAGTAC372050.025.1536673
CTAACGC151850.025.1307093
CATGGGG3089150.024.5433714
TAACGCC154700.024.5261384
CTGTGCG390950.023.598019
TCTAACG162350.022.912252
TCGACGG169150.022.81936894
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192401_1_val_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192401_1_val_1_fastqc.zip new file mode 100644 index 00000000..fc39cca6 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192401_1_val_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192401_2.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192401_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..becd737b --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_2.fastq.gz_trimming_report.txt @@ -0,0 +1,157 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192401_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA SRR3192401_2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2151.00 s (22 us/read; 2.67 M reads/minute). + +=== Summary === + +Total reads processed: 95,735,344 +Reads with adapters: 38,037,448 (39.7%) +Reads written (passing filters): 95,735,344 (100.0%) + +Total basepairs processed: 9,573,534,400 bp +Quality-trimmed: 328,931,711 bp (3.4%) +Total written (filtered): 8,974,093,171 bp (93.7%) + +=== Adapter 1 === + +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38037448 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 18.7% + C: 32.6% + G: 24.0% + T: 24.7% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 18994292 23933836.0 0 18994292 +2 5857733 5983459.0 0 5857733 +3 2296990 1495864.8 0 2296990 +4 758450 373966.2 0 758450 +5 495196 93491.5 0 495196 +6 423881 23372.9 0 423881 +7 385943 5843.2 0 385943 +8 412898 1460.8 0 412898 +9 445517 365.2 0 442559 2958 +10 395118 91.3 1 390548 4570 +11 399678 22.8 1 395958 3720 +12 395485 5.7 1 392574 2911 +13 341547 5.7 1 339210 2337 +14 323004 5.7 1 320444 2560 +15 282795 5.7 1 280436 2359 +16 266409 5.7 1 264066 2343 +17 243983 5.7 1 241975 2008 +18 239757 5.7 1 237715 2042 +19 261017 5.7 1 258589 2428 +20 227818 5.7 1 225600 2218 +21 232894 5.7 1 231013 1881 +22 230583 5.7 1 228083 2500 +23 187494 5.7 1 185692 1802 +24 198719 5.7 1 196943 1776 +25 175321 5.7 1 173048 2273 +26 165554 5.7 1 163498 2056 +27 164063 5.7 1 162153 1910 +28 197382 5.7 1 194871 2511 +29 202125 5.7 1 199801 2324 +30 122210 5.7 1 120172 2038 +31 142664 5.7 1 141005 1659 +32 136400 5.7 1 133915 2485 +33 117967 5.7 1 116185 1782 +34 151714 5.7 1 149898 1816 +35 128081 5.7 1 126545 1536 +36 123745 5.7 1 121822 1923 +37 90063 5.7 1 88228 1835 +38 86248 5.7 1 85108 1140 +39 91962 5.7 1 90577 1385 +40 112038 5.7 1 110416 1622 +41 101085 5.7 1 99421 1664 +42 135220 5.7 1 133295 1925 +43 90993 5.7 1 89770 1223 +44 101064 5.7 1 99304 1760 +45 75598 5.7 1 74423 1175 +46 74472 5.7 1 72938 1534 +47 69362 5.7 1 68274 1088 +48 71036 5.7 1 70024 1012 +49 80279 5.7 1 79084 1195 +50 62878 5.7 1 61861 1017 +51 63598 5.7 1 62486 1112 +52 61750 5.7 1 60294 1456 +53 60872 5.7 1 59363 1509 +54 88690 5.7 1 86625 2065 +55 35845 5.7 1 34833 1012 +56 48906 5.7 1 47684 1222 +57 55573 5.7 1 53831 1742 +58 25399 5.7 1 24673 726 +59 27121 5.7 1 26242 879 +60 24099 5.7 1 23306 793 +61 25352 5.7 1 24593 759 +62 30033 5.7 1 28891 1142 +63 28567 5.7 1 27649 918 +64 13684 5.7 1 13149 535 +65 7743 5.7 1 7288 455 +66 6835 5.7 1 6407 428 +67 6827 5.7 1 5825 1002 +68 4746 5.7 1 4324 422 +69 4905 5.7 1 4284 621 +70 5418 5.7 1 5087 331 +71 5876 5.7 1 5498 378 +72 7118 5.7 1 6293 825 +73 6673 5.7 1 6215 458 +74 7018 5.7 1 2679 4339 +75 1435 5.7 1 584 851 +76 836 5.7 1 456 380 +77 1819 5.7 1 578 1241 +78 565 5.7 1 258 307 +79 1085 5.7 1 118 967 +80 358 5.7 1 43 315 +81 417 5.7 1 4 413 +82 927 5.7 1 8 919 +83 350 5.7 1 2 348 +84 2557 5.7 1 5 2552 +85 449 5.7 1 4 445 +86 337 5.7 1 1 336 +87 965 5.7 1 0 965 +88 286 5.7 1 2 284 +89 370 5.7 1 0 370 +90 421 5.7 1 5 416 +91 448 5.7 1 3 445 +92 1701 5.7 1 5 1696 +93 204 5.7 1 0 204 +94 322 5.7 1 0 322 +95 118 5.7 1 0 118 +96 183 5.7 1 0 183 +97 1077 5.7 1 1 1076 +98 340 5.7 1 0 340 +99 408 5.7 1 0 408 +100 97 5.7 1 0 97 + + +RUN STATISTICS FOR INPUT FILE: SRR3192401_2.fastq.gz +============================================= +95735344 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 95735344 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 498707 (0.52%) diff --git a/src/multiqc/rna-seq/data/SRR3192401_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192401_2_fastqc.html new file mode 100644 index 00000000..e1a53fd2 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192401_2.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192401_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192401_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences95735344
Sequences flagged as poor quality0
Sequence length100
%GC45

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT2294510.23967219462855852No Hit
GGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1865250.19483399986529532No Hit
TATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1310120.13684810073905412No Hit

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGTATCA1148800.049.708021
GTATCAA2003500.039.723881
GTACATG3611900.035.6390531
GAGTACA2226350.035.387081
TACATGG3684050.034.4664272
CAACGCA2277400.033.980775
ATCAACG2337100.033.1289373
AGTACAT2361950.032.6361922
ACATGGG3921300.031.89663
AACGCAG2457950.031.6759916
TCAACGC2465500.031.6359044
TATCAAC2560950.030.7527372
CTAGTAC392850.030.2548983
CTAACGC176000.030.2453883
CATGGGG3126000.029.5279674
TAACGCC176050.029.4866624
GTACTAG303750.028.793271
CTGTGCG404300.028.5532259
TCTAACG186650.027.7910442
ACGCAGA2854100.026.935697
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192401_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192401_2_fastqc.zip new file mode 100644 index 00000000..0c12c50a Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192401_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192401_2_val_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192401_2_val_2_fastqc.html new file mode 100644 index 00000000..e35d2e16 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192401_2_val_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192401_2_val_2.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192401_2_val_2.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192401_2_val_2.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences95236637
Sequences flagged as poor quality0
Sequence length20-100
%GC45

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[WARN]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT1007470.10578596974187571No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGTATCA1134250.046.8027531
GTATCAA1969500.037.278031
GTACATG3558100.033.7964481
GAGTACA2190250.032.8698231
TACATGG3624550.032.648032
CAACGCA2251400.031.6785325
ATCAACG2303800.030.9837063
AGTACAT2317550.030.3390882
ACATGGG3850550.030.243163
TCAACGC2425050.029.644934
AACGCAG2431350.029.5483676
CTAACGC164650.029.1869133
TAACGCC163850.028.896024
TATCAAC2505750.028.8841082
CTAGTAC373050.028.0997183
CATGGGG3062900.027.959344
GTACTAG299500.027.7731931
CTGTGCG389450.026.7368769
TCTAACG176000.026.7301542
ACGCAGA2834600.025.0027567
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192401_2_val_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192401_2_val_2_fastqc.zip new file mode 100644 index 00000000..70659623 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192401_2_val_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192657_1.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192657_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..e3c44e33 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_1.fastq.gz_trimming_report.txt @@ -0,0 +1,155 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192657_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192657_1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 2001.07 s (21 us/read; 2.81 M reads/minute). + +=== Summary === + +Total reads processed: 93,555,584 +Reads with adapters: 28,666,140 (30.6%) +Reads written (passing filters): 93,555,584 (100.0%) + +Total basepairs processed: 9,449,113,984 bp +Quality-trimmed: 146,347,194 bp (1.5%) +Total written (filtered): 9,262,914,510 bp (98.0%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 28666140 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 28.6% + C: 35.1% + G: 19.4% + T: 16.8% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 20311079 23388896.0 0 20311079 +2 6515303 5847224.0 0 6515303 +3 1395339 1461806.0 0 1395339 +4 324932 365451.5 0 324932 +5 78104 91362.9 0 78104 +6 15473 22840.7 0 15473 +7 2580 5710.2 0 2580 +8 1644 1427.5 0 1644 +9 2470 356.9 0 1518 952 +10 3304 89.2 1 1237 2067 +11 2370 22.3 1 1116 1254 +12 1457 5.6 1 1291 166 +13 968 1.4 1 915 53 +14 1046 1.4 1 1026 20 +15 757 1.4 1 739 18 +16 759 1.4 1 729 30 +17 688 1.4 1 635 53 +18 545 1.4 1 465 80 +19 277 1.4 1 219 58 +20 241 1.4 1 191 50 +21 198 1.4 1 182 16 +22 176 1.4 1 135 41 +23 207 1.4 1 163 44 +24 202 1.4 1 134 68 +25 159 1.4 1 130 29 +26 130 1.4 1 95 35 +27 144 1.4 1 113 31 +28 173 1.4 1 126 47 +29 197 1.4 1 150 47 +30 151 1.4 1 110 41 +31 104 1.4 1 80 24 +32 117 1.4 1 85 32 +33 212 1.4 1 191 21 +34 224 1.4 1 184 40 +35 403 1.4 1 300 103 +36 173 1.4 1 124 49 +37 264 1.4 1 217 47 +38 134 1.4 1 102 32 +39 103 1.4 1 77 26 +40 92 1.4 1 67 25 +41 89 1.4 1 66 23 +42 67 1.4 1 49 18 +43 80 1.4 1 35 45 +44 70 1.4 1 32 38 +45 62 1.4 1 41 21 +46 81 1.4 1 32 49 +47 88 1.4 1 21 67 +48 116 1.4 1 27 89 +49 53 1.4 1 15 38 +50 38 1.4 1 12 26 +51 56 1.4 1 19 37 +52 43 1.4 1 13 30 +53 58 1.4 1 9 49 +54 57 1.4 1 7 50 +55 70 1.4 1 5 65 +56 63 1.4 1 6 57 +57 36 1.4 1 9 27 +58 53 1.4 1 7 46 +59 42 1.4 1 18 24 +60 58 1.4 1 13 45 +61 51 1.4 1 13 38 +62 33 1.4 1 2 31 +63 58 1.4 1 8 50 +64 34 1.4 1 10 24 +65 24 1.4 1 10 14 +66 44 1.4 1 15 29 +67 40 1.4 1 21 19 +68 31 1.4 1 7 24 +69 54 1.4 1 9 45 +70 107 1.4 1 18 89 +71 66 1.4 1 4 62 +72 62 1.4 1 1 61 +73 38 1.4 1 0 38 +74 51 1.4 1 1 50 +75 57 1.4 1 1 56 +76 48 1.4 1 0 48 +77 32 1.4 1 0 32 +78 42 1.4 1 0 42 +79 57 1.4 1 0 57 +80 57 1.4 1 0 57 +81 53 1.4 1 0 53 +82 58 1.4 1 0 58 +83 64 1.4 1 1 63 +84 78 1.4 1 0 78 +85 47 1.4 1 0 47 +86 68 1.4 1 0 68 +87 47 1.4 1 0 47 +88 54 1.4 1 0 54 +89 32 1.4 1 0 32 +90 58 1.4 1 0 58 +91 37 1.4 1 0 37 +92 64 1.4 1 0 64 +93 30 1.4 1 0 30 +94 34 1.4 1 0 34 +95 41 1.4 1 0 41 +96 39 1.4 1 0 39 +97 34 1.4 1 0 34 +98 71 1.4 1 1 70 +99 16 1.4 1 0 16 +100 19 1.4 1 0 19 +101 31 1.4 1 0 31 + + +RUN STATISTICS FOR INPUT FILE: SRR3192657_1.fastq.gz +============================================= +93555584 sequences processed in total + diff --git a/src/multiqc/rna-seq/data/SRR3192657_1Log.final.out b/src/multiqc/rna-seq/data/SRR3192657_1Log.final.out new file mode 100644 index 00000000..23c0f248 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_1Log.final.out @@ -0,0 +1,34 @@ + Started job on | May 03 01:21:22 + Started mapping on | May 03 01:25:48 + Finished on | May 03 02:27:45 + Mapping speed, Million of reads per hour | 90.21 + + Number of input reads | 93144645 + Average input read length | 197 + UNIQUE READS: + Uniquely mapped reads number | 84960909 + Uniquely mapped reads % | 91.21% + Average mapped length | 196.51 + Number of splices: Total | 58736628 + Number of splices: Annotated (sjdb) | 58053182 + Number of splices: GT/AG | 58152586 + Number of splices: GC/AG | 397045 + Number of splices: AT/AC | 62651 + Number of splices: Non-canonical | 124346 + Mismatch rate per base, % | 0.27% + Deletion rate per base | 0.01% + Deletion average length | 1.75 + Insertion rate per base | 0.01% + Insertion average length | 1.71 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 2709580 + % of reads mapped to multiple loci | 2.91% + Number of reads mapped to too many loci | 21883 + % of reads mapped to too many loci | 0.02% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 5.84% + % of reads unmapped: other | 0.02% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff --git a/src/multiqc/rna-seq/data/SRR3192657_1Log.out b/src/multiqc/rna-seq/data/SRR3192657_1Log.out new file mode 100644 index 00000000..3f6d02de --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_1Log.out @@ -0,0 +1,408 @@ +STAR version=STAR_2.5.1b +STAR compilation time,server,dir=Tue Jan 26 13:48:00 CET 2016 milou-b.uppmax.uu.se:/sw/apps/bioinfo/star/2.5.1b/src/source +##### DEFAULT parameters: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 1 +runDirPerm User_RWX +runRNGseed 777 +genomeDir ./GenomeDir/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn Read1 Read2 +readFilesCommand - +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outTmpDir - +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +##### Command Line: +STAR --runThreadN 4 --outQSconversionAdd 0 --outSAMattributes Standard --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --readFilesIn SRR3192657_1_val_1.fq.gz SRR3192657_2_val_2.fq.gz --outFileNamePrefix SRR3192657_1 --outStd SAM +##### Initial USER parameters from Command Line: +outFileNamePrefix SRR3192657_1 +outStd SAM +###### All USER parameters from Command Line: +runThreadN 4 ~RE-DEFINED +outQSconversionAdd 0 ~RE-DEFINED +outSAMattributes Standard ~RE-DEFINED +genomeLoad NoSharedMemory ~RE-DEFINED +readFilesCommand zcat ~RE-DEFINED +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ~RE-DEFINED +readFilesIn SRR3192657_1_val_1.fq.gz SRR3192657_2_val_2.fq.gz ~RE-DEFINED +outFileNamePrefix SRR3192657_1 ~RE-DEFINED +outStd SAM ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runThreadN 4 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +readFilesIn SRR3192657_1_val_1.fq.gz SRR3192657_2_val_2.fq.gz +readFilesCommand zcat +outFileNamePrefix SRR3192657_1 +outStd SAM +outQSconversionAdd 0 +outSAMattributes Standard + +------------------------------- +##### Final effective command line: +STAR --runThreadN 4 --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --genomeLoad NoSharedMemory --readFilesIn SRR3192657_1_val_1.fq.gz SRR3192657_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix SRR3192657_1 --outStd SAM --outQSconversionAdd 0 --outSAMattributes Standard + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 4 +runDirPerm User_RWX +runRNGseed 777 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn SRR3192657_1_val_1.fq.gz SRR3192657_2_val_2.fq.gz +readFilesCommand zcat +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outFileNamePrefix SRR3192657_1 +outTmpDir - +outStd SAM +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +---------------------------------------- + + + Input read files for mate 1, from input string SRR3192657_1_val_1.fq.gz +-rw-rw-r-- 1 phil b2013064 7744404240 May 3 00:26 SRR3192657_1_val_1.fq.gz + + readsCommandsFile: +exec > "SRR3192657_1_STARtmp/tmp.fifo.read1" +echo FILE 0 +zcat "SRR3192657_1_val_1.fq.gz" + + + Input read files for mate 2, from input string SRR3192657_2_val_2.fq.gz +-rw-rw-r-- 1 phil b2013064 7899165644 May 3 00:26 SRR3192657_2_val_2.fq.gz + + readsCommandsFile: +exec > "SRR3192657_1_STARtmp/tmp.fifo.read2" +echo FILE 0 +zcat "SRR3192657_2_val_2.fq.gz" + +Finished loading and checking parameters +Reading genome generation parameters: +versionGenome 20201 ~RE-DEFINED +genomeFastaFiles genome.fa ~RE-DEFINED +genomeSAindexNbases 14 ~RE-DEFINED +genomeChrBinNbits 18 ~RE-DEFINED +genomeSAsparseD 1 ~RE-DEFINED +sjdbOverhang 100 ~RE-DEFINED +sjdbFileChrStartEnd - ~RE-DEFINED +sjdbGTFfile genes.gtf ~RE-DEFINED +sjdbGTFchrPrefix - ~RE-DEFINED +sjdbGTFfeatureExon exon ~RE-DEFINED +sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED +sjdbGTFtagExonParentGene gene_id ~RE-DEFINED +sjdbInsertSave Basic ~RE-DEFINED +Genome version is compatible with current STAR version +Number of real (reference) chromosmes= 25 +1 1 249250621 0 +2 2 243199373 249298944 +3 3 198022430 492568576 +4 4 191154276 690749440 +5 5 180915260 882114560 +6 6 171115067 1063256064 +7 7 159138663 1234436096 +8 8 146364022 1393819648 +9 9 141213431 1540358144 +10 10 135534747 1681653760 +11 11 135006516 1817444352 +12 12 133851895 1952710656 +13 13 115169878 2086666240 +14 14 107349540 2202009600 +15 15 102531392 2309488640 +16 16 90354753 2412249088 +17 17 81195210 2502688768 +18 18 78077248 2583953408 +19 19 59128983 2662072320 +20 20 63025520 2721316864 +21 21 48129895 2784493568 +22 22 51304566 2832728064 +23 X 155270560 2884108288 +24 Y 59373566 3039559680 +25 MT 16569 3099066368 +--sjdbOverhang = 100 taken from the generated genome +Started loading the genome: Tue May 3 01:21:22 2016 + +checking Genome sizefile size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +checking SA sizefile size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 +Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 +nGenome=3168538239; nSAbyte=24152204822 +GstrandBit=32 SA number of indices=5855079956 +Shared memory is not used for genomes. Allocated a private copy of the genome. +Genome file size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3168538239 bytes +SA file size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24152204822 bytes +Loading SAindex ... done: 1565873619 bytes +Finished loading the genome: Tue May 3 01:25:48 2016 + +Processing splice junctions database sjdbN=344327, sjdbOverhang=100 +alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 +Created thread # 1 +Created thread # 2 +Created thread # 3 +Starting to map file # 0 +mate 1: SRR3192657_1_val_1.fq.gz +mate 2: SRR3192657_2_val_2.fq.gz +Thread #0 end of input stream, nextChar=-1 +Completed: thread #3 +Completed: thread #1 +Completed: thread #2 +Completed: thread #0 +Joined thread # 1 +Joined thread # 2 +Joined thread # 3 +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192657_1Log.progress.out b/src/multiqc/rna-seq/data/SRR3192657_1Log.progress.out new file mode 100644 index 00000000..042a7675 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_1Log.progress.out @@ -0,0 +1,63 @@ + Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped + M/hr number length unique length MMrate multi multi+ MM short other +May 03 01:26:50 72.8 1254170 196 91.2% 196.2 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:27:53 78.2 2716015 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:28:53 83.5 4290301 197 91.2% 196.8 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:29:53 82.9 5640743 197 91.2% 196.8 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:30:54 84.9 7217646 197 91.2% 196.8 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:31:55 86.3 8795591 197 91.2% 196.7 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:32:56 86.3 10254519 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:33:57 86.9 11806274 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:35:00 87.8 13469291 197 91.2% 196.7 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:36:03 88.6 15133769 197 91.2% 196.7 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:37:06 87.4 16466323 197 91.2% 196.7 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:38:10 88.0 18132888 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:39:10 88.4 19686148 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:40:12 89.0 21349441 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:41:14 88.6 22791646 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:42:16 89.1 24456794 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:43:16 89.4 26012079 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:44:16 89.6 27565732 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:45:18 89.9 29228219 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:46:20 90.3 30891475 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:47:20 90.4 32445586 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:48:20 90.5 34001426 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:49:22 90.5 35558738 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:50:28 90.5 37222125 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:51:29 90.6 38773571 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:52:31 90.8 40437078 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:53:35 90.9 42102048 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:54:37 90.7 43546287 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:55:37 90.8 45101295 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:56:44 90.7 46764652 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:57:44 90.8 48316853 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:58:44 90.7 49759214 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 01:59:44 90.3 51091429 197 91.2% 196.6 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:00:45 90.4 52646534 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:01:49 90.5 54311811 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:02:52 90.6 55974218 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:03:52 90.7 57526841 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:04:53 90.7 59081342 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:05:54 90.4 60413973 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:06:54 90.5 61965929 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:07:54 90.5 63518265 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:08:55 90.6 65072138 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:09:56 90.6 66628016 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:10:57 90.5 68070539 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:11:58 90.3 69512089 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:12:59 90.2 70954673 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:13:59 90.0 72287756 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:15:02 90.1 73953146 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:16:05 90.2 75615713 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:17:06 90.4 77279905 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:18:07 90.4 78835784 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:19:08 90.4 80391726 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:20:08 90.5 81943617 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:21:13 90.5 83607040 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:22:14 90.4 85050217 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:23:16 90.4 86606161 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:24:17 90.4 88159024 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:25:23 90.3 89711327 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:26:26 90.3 91265209 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +May 03 02:27:26 90.4 92820339 197 91.2% 196.5 0.3% 2.9% 0.0% 0.0% 5.8% 0.0% +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192657_1Log.std.out b/src/multiqc/rna-seq/data/SRR3192657_1Log.std.out new file mode 100644 index 00000000..28ba4aab --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_1Log.std.out @@ -0,0 +1,4 @@ +May 03 01:21:22 ..... Started STAR run +May 03 01:21:22 ..... Loading genome +May 03 01:25:48 ..... Started mapping +May 03 02:27:45 ..... Finished successfully diff --git a/src/multiqc/rna-seq/data/SRR3192657_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192657_1_fastqc.html new file mode 100644 index 00000000..70f19bbb --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192657_1.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192657_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192657_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences93555584
Sequences flagged as poor quality0
Sequence length101
%GC50

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[OK]Overrepresented sequences

No overrepresented sequences

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CCGAACG118350.018.739783
TACCGCG178050.018.0111161
CGGGTGT327000.017.8387951
GTCCGAA145950.017.2128431
CGAACGG109150.016.925514
AACGGTA107350.016.8996326
TGCGTCG319950.015.8082359
CGGTATA193500.015.0451134
TAGATCG123700.015.011468
GCGGTGT450850.014.9140682
CGGGGGA640000.014.8017841
CGGGGTT581150.014.67143251
ACGTACG78850.014.51553736-37
GCGGGTT214350.014.4504141
ACTATCG146450.014.34078358-59
GTGCGTC397650.013.86586958
CGTACGA81350.013.86512736-37
CGCATTC417200.013.37087194-95
CGGTGTG496100.013.3542933
TGAGCGT643950.012.685058
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192657_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192657_1_fastqc.zip new file mode 100644 index 00000000..de18b146 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192657_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192657_1_star_aligned.bam_counts.txt.summary b/src/multiqc/rna-seq/data/SRR3192657_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..bb70c458 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_1_star_aligned.bam_counts.txt.summary @@ -0,0 +1,12 @@ +Status SRR3192657_1_star_aligned.bam +Assigned 67122403 +Unassigned_Ambiguity 4205720 +Unassigned_MultiMapping 6547971 +Unassigned_NoFeatures 13887904 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_FragmentLength 0 +Unassigned_Chimera 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_Duplicate 0 diff --git a/src/multiqc/rna-seq/data/SRR3192657_1_val_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192657_1_val_1_fastqc.html new file mode 100644 index 00000000..50b3e090 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_1_val_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192657_1_val_1.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192657_1_val_1.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192657_1_val_1.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences93144645
Sequences flagged as poor quality0
Sequence length20-101
%GC50

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[OK]Overrepresented sequences

No overrepresented sequences

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGCATTC416850.018.88296594-95
CGGGTGT309400.017.99671
TACCGCG177950.017.4273971
TGCGTCG314700.016.2982449
CCGAACG112350.016.1150823
GTCCGAA138250.016.022761
CGGTATA197300.015.7817434
CGGGGGA574400.015.1984831
GCGGGTT208650.015.1984521
CGGGGTT542050.015.1935831
CTATACC324150.015.113461594-95
CGAACGG102600.014.9246614
AACGGTA101800.014.7676276
GTGCGTC390350.014.5227578
TCGCATT444000.014.35563194-95
GCGGTGT446750.014.3025262
ACTATCG145450.013.90216158-59
TAGATCG105850.013.7628828
CGGGGGG718700.013.60691451
CGGGCTA88050.013.5057811
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192657_1_val_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192657_1_val_1_fastqc.zip new file mode 100644 index 00000000..e54b5f09 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192657_1_val_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192657_2.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192657_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..462bbdd0 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_2.fastq.gz_trimming_report.txt @@ -0,0 +1,157 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192657_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192657_2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1986.06 s (21 us/read; 2.83 M reads/minute). + +=== Summary === + +Total reads processed: 93,555,584 +Reads with adapters: 30,516,092 (32.6%) +Reads written (passing filters): 93,555,584 (100.0%) + +Total basepairs processed: 9,449,113,984 bp +Quality-trimmed: 247,487,419 bp (2.6%) +Total written (filtered): 9,157,670,096 bp (96.9%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 30516092 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 32.5% + C: 30.4% + G: 22.3% + T: 14.8% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 20709985 23388896.0 0 20709985 +2 7337450 5847224.0 0 7337450 +3 1932874 1461806.0 0 1932874 +4 393575 365451.5 0 393575 +5 93056 91362.9 0 93056 +6 15073 22840.7 0 15073 +7 4869 5710.2 0 4869 +8 1687 1427.5 0 1687 +9 3798 356.9 0 1549 2249 +10 3911 89.2 1 1262 2649 +11 4890 22.3 1 1038 3852 +12 1908 5.6 1 1265 643 +13 1075 1.4 1 960 115 +14 1220 1.4 1 1161 59 +15 758 1.4 1 631 127 +16 757 1.4 1 684 73 +17 861 1.4 1 757 104 +18 281 1.4 1 242 39 +19 271 1.4 1 237 34 +20 212 1.4 1 152 60 +21 142 1.4 1 92 50 +22 169 1.4 1 120 49 +23 219 1.4 1 129 90 +24 294 1.4 1 224 70 +25 183 1.4 1 106 77 +26 222 1.4 1 114 108 +27 189 1.4 1 121 68 +28 228 1.4 1 165 63 +29 260 1.4 1 130 130 +30 406 1.4 1 326 80 +31 51 1.4 1 15 36 +32 113 1.4 1 73 40 +33 119 1.4 1 88 31 +34 183 1.4 1 95 88 +35 256 1.4 1 175 81 +36 140 1.4 1 92 48 +37 234 1.4 1 176 58 +38 104 1.4 1 69 35 +39 103 1.4 1 72 31 +40 131 1.4 1 80 51 +41 148 1.4 1 100 48 +42 165 1.4 1 103 62 +43 67 1.4 1 16 51 +44 126 1.4 1 43 83 +45 152 1.4 1 72 80 +46 73 1.4 1 12 61 +47 111 1.4 1 14 97 +48 78 1.4 1 15 63 +49 53 1.4 1 14 39 +50 64 1.4 1 20 44 +51 65 1.4 1 24 41 +52 55 1.4 1 11 44 +53 57 1.4 1 2 55 +54 80 1.4 1 15 65 +55 51 1.4 1 7 44 +56 48 1.4 1 3 45 +57 89 1.4 1 9 80 +58 62 1.4 1 7 55 +59 46 1.4 1 18 28 +60 74 1.4 1 14 60 +61 79 1.4 1 3 76 +62 92 1.4 1 12 80 +63 77 1.4 1 36 41 +64 65 1.4 1 31 34 +65 96 1.4 1 37 59 +66 70 1.4 1 11 59 +67 42 1.4 1 2 40 +68 63 1.4 1 0 63 +69 94 1.4 1 1 93 +70 83 1.4 1 0 83 +71 45 1.4 1 0 45 +72 73 1.4 1 1 72 +73 73 1.4 1 11 62 +74 67 1.4 1 0 67 +75 14 1.4 1 0 14 +76 67 1.4 1 0 67 +77 61 1.4 1 0 61 +78 56 1.4 1 1 55 +79 30 1.4 1 0 30 +80 55 1.4 1 0 55 +81 38 1.4 1 0 38 +82 39 1.4 1 0 39 +83 34 1.4 1 0 34 +84 69 1.4 1 0 69 +85 22 1.4 1 0 22 +86 28 1.4 1 0 28 +87 44 1.4 1 0 44 +88 72 1.4 1 0 72 +89 50 1.4 1 0 50 +90 40 1.4 1 0 40 +91 26 1.4 1 0 26 +92 151 1.4 1 0 151 +93 40 1.4 1 0 40 +94 36 1.4 1 0 36 +95 31 1.4 1 0 31 +97 1 1.4 1 0 1 +98 56 1.4 1 0 56 +99 18 1.4 1 0 18 +100 42 1.4 1 0 42 +101 32 1.4 1 0 32 + + +RUN STATISTICS FOR INPUT FILE: SRR3192657_2.fastq.gz +============================================= +93555584 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 93555584 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 410939 (0.44%) diff --git a/src/multiqc/rna-seq/data/SRR3192657_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192657_2_fastqc.html new file mode 100644 index 00000000..eebc8f08 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192657_2.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192657_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192657_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences93555584
Sequences flagged as poor quality0
Sequence length101
%GC51

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[WARN]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[OK]Overrepresented sequences

No overrepresented sequences

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TAGGTCG101400.023.8385477
TAACACG160750.020.0594377
TAGTGCG189700.019.1411178-79
GTCTAAC172700.019.0272644
AACACGT183550.017.800648
GGCGCGT336700.017.5586225
GTACTCG292350.016.40631928-29
TACGCAC270050.015.87444950-51
TATGCCG250200.014.89912786-87
AGCGCTC357700.014.5115879
TCGTAAG111650.014.4191546
CGCGTGC436750.013.6026767
CCAGTAG411350.013.4024735
CGGTACA332450.013.382359560-61
ATCGCAC395250.013.31062268-69
TCTCCGG661000.013.2626116
TAGCATA437550.013.1874949
TGGCGCG438350.013.1727114
CGATCGC406100.013.10158566-67
TGCGAAT332250.013.04459374-75
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192657_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192657_2_fastqc.zip new file mode 100644 index 00000000..76ed23a9 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192657_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192657_2_val_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192657_2_val_2_fastqc.html new file mode 100644 index 00000000..eccba4c1 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192657_2_val_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192657_2_val_2.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192657_2_val_2.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192657_2_val_2.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences93144645
Sequences flagged as poor quality0
Sequence length20-101
%GC51

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[OK]Overrepresented sequences

No overrepresented sequences

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TAGGTCG96300.022.0311137
TAACACG156600.019.821127
TAGTGCG185450.018.8709778-79
GGCGCGT316700.018.6541885
GTCTAAC168850.017.9721134
AACACGT181350.016.8363918
GTACTCG286950.016.42323328-29
TACGCAC268700.015.45311850-51
TATGCCG243350.014.61156686-87
CGCGTGC412000.014.5753387
AGCGCTC345100.014.52790459
TGGCGCG412250.013.8495084
CGGTACA323300.013.43345660-61
TGCGAAT326100.013.11550974-75
CACTGCG399600.013.0068985
CCAGTAG401950.012.9882215
ACCCGAT367950.012.95510876-77
CGATCGG212150.012.93898992-93
CGCACGG324900.012.90327652-53
TCGTAAG106050.012.8731486
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192657_2_val_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192657_2_val_2_fastqc.zip new file mode 100644 index 00000000..f7ade59e Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192657_2_val_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192658_1.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192658_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..39cd2377 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_1.fastq.gz_trimming_report.txt @@ -0,0 +1,155 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192658_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192658_1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1951.56 s (20 us/read; 3.00 M reads/minute). + +=== Summary === + +Total reads processed: 97,548,052 +Reads with adapters: 28,796,974 (29.5%) +Reads written (passing filters): 97,548,052 (100.0%) + +Total basepairs processed: 9,852,353,252 bp +Quality-trimmed: 176,076,813 bp (1.8%) +Total written (filtered): 9,636,205,578 bp (97.8%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 28796974 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 27.4% + C: 36.0% + G: 20.2% + T: 16.4% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 20288104 24387013.0 0 20288104 +2 6684234 6096753.2 0 6684234 +3 1398486 1524188.3 0 1398486 +4 311360 381047.1 0 311360 +5 78753 95261.8 0 78753 +6 15151 23815.4 0 15151 +7 1911 5953.9 0 1911 +8 1063 1488.5 0 1063 +9 1828 372.1 0 912 916 +10 2535 93.0 1 727 1808 +11 2068 23.3 1 735 1333 +12 810 5.8 1 677 133 +13 637 1.5 1 592 45 +14 599 1.5 1 563 36 +15 522 1.5 1 497 25 +16 483 1.5 1 451 32 +17 429 1.5 1 372 57 +18 307 1.5 1 256 51 +19 211 1.5 1 168 43 +20 235 1.5 1 218 17 +21 267 1.5 1 234 33 +22 214 1.5 1 177 37 +23 315 1.5 1 253 62 +24 264 1.5 1 239 25 +25 201 1.5 1 180 21 +26 206 1.5 1 169 37 +27 207 1.5 1 175 32 +28 220 1.5 1 191 29 +29 261 1.5 1 229 32 +30 191 1.5 1 169 22 +31 236 1.5 1 180 56 +32 181 1.5 1 143 38 +33 208 1.5 1 187 21 +34 164 1.5 1 124 40 +35 268 1.5 1 201 67 +36 173 1.5 1 144 29 +37 214 1.5 1 170 44 +38 116 1.5 1 87 29 +39 148 1.5 1 104 44 +40 83 1.5 1 65 18 +41 119 1.5 1 90 29 +42 60 1.5 1 47 13 +43 59 1.5 1 24 35 +44 75 1.5 1 18 57 +45 65 1.5 1 21 44 +46 54 1.5 1 22 32 +47 92 1.5 1 21 71 +48 89 1.5 1 10 79 +49 56 1.5 1 15 41 +50 59 1.5 1 13 46 +51 29 1.5 1 10 19 +52 33 1.5 1 12 21 +53 33 1.5 1 4 29 +54 22 1.5 1 7 15 +55 21 1.5 1 1 20 +56 35 1.5 1 4 31 +57 43 1.5 1 2 41 +58 39 1.5 1 3 36 +59 41 1.5 1 4 37 +60 29 1.5 1 5 24 +61 45 1.5 1 8 37 +62 23 1.5 1 4 19 +63 17 1.5 1 4 13 +64 43 1.5 1 7 36 +65 29 1.5 1 12 17 +66 43 1.5 1 20 23 +67 81 1.5 1 14 67 +68 58 1.5 1 13 45 +69 45 1.5 1 12 33 +70 104 1.5 1 20 84 +71 91 1.5 1 5 86 +72 49 1.5 1 1 48 +73 37 1.5 1 1 36 +74 39 1.5 1 0 39 +75 41 1.5 1 2 39 +76 30 1.5 1 0 30 +77 41 1.5 1 0 41 +78 59 1.5 1 0 59 +79 81 1.5 1 0 81 +80 44 1.5 1 0 44 +81 89 1.5 1 0 89 +82 66 1.5 1 0 66 +83 66 1.5 1 0 66 +84 61 1.5 1 0 61 +85 48 1.5 1 0 48 +86 60 1.5 1 0 60 +87 62 1.5 1 0 62 +88 77 1.5 1 0 77 +89 32 1.5 1 0 32 +90 64 1.5 1 0 64 +91 56 1.5 1 0 56 +92 38 1.5 1 0 38 +93 27 1.5 1 0 27 +94 29 1.5 1 0 29 +95 76 1.5 1 0 76 +96 16 1.5 1 0 16 +97 50 1.5 1 0 50 +98 35 1.5 1 0 35 +99 8 1.5 1 0 8 +100 15 1.5 1 1 14 +101 83 1.5 1 0 83 + + +RUN STATISTICS FOR INPUT FILE: SRR3192658_1.fastq.gz +============================================= +97548052 sequences processed in total + diff --git a/src/multiqc/rna-seq/data/SRR3192658_1Log.final.out b/src/multiqc/rna-seq/data/SRR3192658_1Log.final.out new file mode 100644 index 00000000..87a01735 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_1Log.final.out @@ -0,0 +1,34 @@ + Started job on | May 03 01:29:21 + Started mapping on | May 03 01:33:40 + Finished on | May 03 02:39:29 + Mapping speed, Million of reads per hour | 88.49 + + Number of input reads | 97071168 + Average input read length | 196 + UNIQUE READS: + Uniquely mapped reads number | 87107290 + Uniquely mapped reads % | 89.74% + Average mapped length | 195.63 + Number of splices: Total | 58190696 + Number of splices: Annotated (sjdb) | 57513306 + Number of splices: GT/AG | 57610842 + Number of splices: GC/AG | 383072 + Number of splices: AT/AC | 63200 + Number of splices: Non-canonical | 133582 + Mismatch rate per base, % | 0.35% + Deletion rate per base | 0.01% + Deletion average length | 1.76 + Insertion rate per base | 0.01% + Insertion average length | 1.74 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 2712251 + % of reads mapped to multiple loci | 2.79% + Number of reads mapped to too many loci | 22014 + % of reads mapped to too many loci | 0.02% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 7.43% + % of reads unmapped: other | 0.02% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff --git a/src/multiqc/rna-seq/data/SRR3192658_1Log.out b/src/multiqc/rna-seq/data/SRR3192658_1Log.out new file mode 100644 index 00000000..76b24b44 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_1Log.out @@ -0,0 +1,408 @@ +STAR version=STAR_2.5.1b +STAR compilation time,server,dir=Tue Jan 26 13:48:00 CET 2016 milou-b.uppmax.uu.se:/sw/apps/bioinfo/star/2.5.1b/src/source +##### DEFAULT parameters: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 1 +runDirPerm User_RWX +runRNGseed 777 +genomeDir ./GenomeDir/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn Read1 Read2 +readFilesCommand - +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outTmpDir - +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +##### Command Line: +STAR --runThreadN 4 --outQSconversionAdd 0 --outSAMattributes Standard --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --readFilesIn SRR3192658_1_val_1.fq.gz SRR3192658_2_val_2.fq.gz --outFileNamePrefix SRR3192658_1 --outStd SAM +##### Initial USER parameters from Command Line: +outFileNamePrefix SRR3192658_1 +outStd SAM +###### All USER parameters from Command Line: +runThreadN 4 ~RE-DEFINED +outQSconversionAdd 0 ~RE-DEFINED +outSAMattributes Standard ~RE-DEFINED +genomeLoad NoSharedMemory ~RE-DEFINED +readFilesCommand zcat ~RE-DEFINED +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ ~RE-DEFINED +readFilesIn SRR3192658_1_val_1.fq.gz SRR3192658_2_val_2.fq.gz ~RE-DEFINED +outFileNamePrefix SRR3192658_1 ~RE-DEFINED +outStd SAM ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runThreadN 4 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +readFilesIn SRR3192658_1_val_1.fq.gz SRR3192658_2_val_2.fq.gz +readFilesCommand zcat +outFileNamePrefix SRR3192658_1 +outStd SAM +outQSconversionAdd 0 +outSAMattributes Standard + +------------------------------- +##### Final effective command line: +STAR --runThreadN 4 --genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ --genomeLoad NoSharedMemory --readFilesIn SRR3192658_1_val_1.fq.gz SRR3192658_2_val_2.fq.gz --readFilesCommand zcat --outFileNamePrefix SRR3192658_1 --outStd SAM --outQSconversionAdd 0 --outSAMattributes Standard + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode alignReads +runThreadN 4 +runDirPerm User_RWX +runRNGseed 777 +genomeDir /sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/ +genomeLoad NoSharedMemory +genomeFastaFiles - +genomeSAindexNbases 14 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeSuffixLengthMax 18446744073709551615 +readFilesIn SRR3192658_1_val_1.fq.gz SRR3192658_2_val_2.fq.gz +readFilesCommand zcat +readMatesLengthsIn NotEqual +readMapNumber 18446744073709551615 +readNameSeparator / +inputBAMfile - +bamRemoveDuplicatesType - +bamRemoveDuplicatesMate2basesN 0 +limitGenomeGenerateRAM 31000000000 +limitIObufferSize 150000000 +limitOutSAMoneReadBytes 100000 +limitOutSJcollapsed 1000000 +limitOutSJoneRead 1000 +limitBAMsortRAM 0 +limitSjdbInsertNsj 1000000 +outFileNamePrefix SRR3192658_1 +outTmpDir - +outStd SAM +outReadsUnmapped None +outQSconversionAdd 0 +outMultimapperOrder Old_2.4 +outSAMtype SAM +outSAMmode Full +outSAMstrandField None +outSAMattributes Standard +outSAMunmapped None +outSAMorder Paired +outSAMprimaryFlag OneBestScore +outSAMreadID Standard +outSAMmapqUnique 255 +outSAMflagOR 0 +outSAMflagAND 65535 +outSAMattrRGline - +outSAMheaderHD - +outSAMheaderPG - +outSAMheaderCommentFile - +outBAMcompression 1 +outBAMsortingThreadN 0 +outSAMfilter None +outSAMmultNmax 18446744073709551615 +outSAMattrIHstart 1 +outSJfilterReads All +outSJfilterCountUniqueMin 3 1 1 1 +outSJfilterCountTotalMin 3 1 1 1 +outSJfilterOverhangMin 30 12 12 12 +outSJfilterDistToOtherSJmin 10 0 5 10 +outSJfilterIntronMaxVsReadN 50000 100000 200000 +outWigType None +outWigStrand Stranded +outWigReferencesPrefix - +outWigNorm RPM +outFilterType Normal +outFilterMultimapNmax 10 +outFilterMultimapScoreRange 1 +outFilterScoreMin 0 +outFilterScoreMinOverLread 0.66 +outFilterMatchNmin 0 +outFilterMatchNminOverLread 0.66 +outFilterMismatchNmax 10 +outFilterMismatchNoverLmax 0.3 +outFilterMismatchNoverReadLmax 1 +outFilterIntronMotifs None +clip5pNbases 0 +clip3pNbases 0 +clip3pAfterAdapterNbases 0 +clip3pAdapterSeq - +clip3pAdapterMMp 0.1 +winBinNbits 16 +winAnchorDistNbins 9 +winFlankNbins 4 +winAnchorMultimapNmax 50 +scoreGap 0 +scoreGapNoncan -8 +scoreGapGCAG -4 +scoreGapATAC -8 +scoreStitchSJshift 1 +scoreGenomicLengthLog2scale -0.25 +scoreDelBase -2 +scoreDelOpen -2 +scoreInsOpen -2 +scoreInsBase -2 +seedSearchLmax 0 +seedSearchStartLmax 50 +seedSearchStartLmaxOverLread 1 +seedPerReadNmax 1000 +seedPerWindowNmax 50 +seedNoneLociPerWindow 10 +seedMultimapNmax 10000 +alignIntronMin 21 +alignIntronMax 0 +alignMatesGapMax 0 +alignTranscriptsPerReadNmax 10000 +alignSJoverhangMin 5 +alignSJDBoverhangMin 3 +alignSJstitchMismatchNmax 0 -1 0 0 +alignSplicedMateMapLmin 0 +alignSplicedMateMapLminOverLmate 0.66 +alignWindowsPerReadNmax 10000 +alignTranscriptsPerWindowNmax 100 +alignEndsType Local +alignSoftClipAtReferenceEnds Yes +chimSegmentMin 0 +chimScoreMin 0 +chimScoreDropMax 20 +chimScoreSeparation 10 +chimScoreJunctionNonGTAG -1 +chimJunctionOverhangMin 20 +chimOutType SeparateSAMold +chimFilter banGenomicN +chimSegmentReadGapMax 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbOverhang 100 +sjdbScore 2 +sjdbInsertSave Basic +quantMode - +quantTranscriptomeBAMcompression 1 +quantTranscriptomeBan IndelSoftclipSingleend +twopass1readsN 18446744073709551615 +twopassMode None +---------------------------------------- + + + Input read files for mate 1, from input string SRR3192658_1_val_1.fq.gz +-rw-rw-r-- 1 phil b2013064 8067809665 May 3 00:34 SRR3192658_1_val_1.fq.gz + + readsCommandsFile: +exec > "SRR3192658_1_STARtmp/tmp.fifo.read1" +echo FILE 0 +zcat "SRR3192658_1_val_1.fq.gz" + + + Input read files for mate 2, from input string SRR3192658_2_val_2.fq.gz +-rw-rw-r-- 1 phil b2013064 8225727237 May 3 00:34 SRR3192658_2_val_2.fq.gz + + readsCommandsFile: +exec > "SRR3192658_1_STARtmp/tmp.fifo.read2" +echo FILE 0 +zcat "SRR3192658_2_val_2.fq.gz" + +Finished loading and checking parameters +Reading genome generation parameters: +versionGenome 20201 ~RE-DEFINED +genomeFastaFiles genome.fa ~RE-DEFINED +genomeSAindexNbases 14 ~RE-DEFINED +genomeChrBinNbits 18 ~RE-DEFINED +genomeSAsparseD 1 ~RE-DEFINED +sjdbOverhang 100 ~RE-DEFINED +sjdbFileChrStartEnd - ~RE-DEFINED +sjdbGTFfile genes.gtf ~RE-DEFINED +sjdbGTFchrPrefix - ~RE-DEFINED +sjdbGTFfeatureExon exon ~RE-DEFINED +sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED +sjdbGTFtagExonParentGene gene_id ~RE-DEFINED +sjdbInsertSave Basic ~RE-DEFINED +Genome version is compatible with current STAR version +Number of real (reference) chromosmes= 25 +1 1 249250621 0 +2 2 243199373 249298944 +3 3 198022430 492568576 +4 4 191154276 690749440 +5 5 180915260 882114560 +6 6 171115067 1063256064 +7 7 159138663 1234436096 +8 8 146364022 1393819648 +9 9 141213431 1540358144 +10 10 135534747 1681653760 +11 11 135006516 1817444352 +12 12 133851895 1952710656 +13 13 115169878 2086666240 +14 14 107349540 2202009600 +15 15 102531392 2309488640 +16 16 90354753 2412249088 +17 17 81195210 2502688768 +18 18 78077248 2583953408 +19 19 59128983 2662072320 +20 20 63025520 2721316864 +21 21 48129895 2784493568 +22 22 51304566 2832728064 +23 X 155270560 2884108288 +24 Y 59373566 3039559680 +25 MT 16569 3099066368 +--sjdbOverhang = 100 taken from the generated genome +Started loading the genome: Tue May 3 01:29:21 2016 + +checking Genome sizefile size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +checking SA sizefile size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0 +Read from SAindex: genomeSAindexNbases=14 nSAi=357913940 +nGenome=3168538239; nSAbyte=24152204822 +GstrandBit=32 SA number of indices=5855079956 +Shared memory is not used for genomes. Allocated a private copy of the genome. +Genome file size: 3168538239 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3168538239 bytes +SA file size: 24152204822 bytes; state: good=1 eof=0 fail=0 bad=0 +Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24152204822 bytes +Loading SAindex ... done: 1565873619 bytes +Finished loading the genome: Tue May 3 01:33:40 2016 + +Processing splice junctions database sjdbN=344327, sjdbOverhang=100 +alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 +Created thread # 1 +Created thread # 2 +Created thread # 3 +Starting to map file # 0 +mate 1: SRR3192658_1_val_1.fq.gz +mate 2: SRR3192658_2_val_2.fq.gz +Thread #3 end of input stream, nextChar=-1 +Completed: thread #1 +Completed: thread #0 +Joined thread # 1 +Completed: thread #2 +Joined thread # 2 +Completed: thread #3 +Joined thread # 3 +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192658_1Log.progress.out b/src/multiqc/rna-seq/data/SRR3192658_1Log.progress.out new file mode 100644 index 00000000..d74f5a4a --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_1Log.progress.out @@ -0,0 +1,67 @@ + Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped + M/hr number length unique length MMrate multi multi+ MM short other +May 03 01:34:40 68.6 1143917 196 89.8% 195.1 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:35:42 77.0 2608223 196 89.8% 195.5 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:36:43 73.5 3734229 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:37:45 78.0 5311114 197 89.8% 195.8 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:38:46 79.7 6776456 197 89.8% 195.9 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:39:47 80.9 8243456 197 89.8% 195.8 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:40:49 81.5 9711327 197 89.7% 195.8 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:41:50 82.8 11271347 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:42:50 84.0 12825898 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:43:51 84.7 14379606 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:44:51 85.5 15934755 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:45:54 85.8 17491290 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:46:59 85.8 19048674 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:48:01 86.2 20607546 196 89.7% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:49:01 86.6 22163843 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:50:02 87.0 23718809 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:51:04 87.2 25274156 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:52:05 87.4 26830329 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:53:07 87.9 28499360 196 89.8% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:54:11 88.2 30169794 196 89.7% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:55:14 88.3 31724711 196 89.8% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:56:15 88.4 33278298 196 89.7% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:57:17 88.5 34832342 196 89.7% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:58:20 88.0 36165972 196 89.7% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 01:59:24 88.0 37723362 196 89.7% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:00:25 87.6 39059590 196 89.7% 195.7 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:01:27 87.7 40619560 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:02:27 87.9 42174825 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:03:30 87.9 43728216 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:04:30 87.9 45171265 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:05:31 87.8 46615261 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:06:33 87.9 48172162 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:07:35 88.0 49730579 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:08:38 88.0 51288428 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:09:40 88.1 52843519 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:10:43 88.1 54397723 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:11:44 88.2 55952900 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:12:46 88.2 57508889 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:13:46 88.2 58954267 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:14:48 88.3 60513435 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:15:50 88.3 62068843 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:16:52 88.4 63622374 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:17:53 88.3 65066582 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:18:57 88.4 66735201 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:19:57 88.5 68290051 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:21:00 88.5 69844062 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:22:01 88.5 71288632 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:23:04 88.3 72735563 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:24:04 88.4 74291586 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:25:06 88.3 75735214 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:26:09 88.4 77291744 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:27:09 88.5 78849887 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:28:12 88.6 80514921 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:29:12 88.7 82069237 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:30:15 88.7 83626152 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:31:15 88.8 85185434 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:32:15 88.7 86628405 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:33:15 88.7 88071553 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:34:15 88.5 89405126 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:35:17 88.6 90963462 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:36:21 88.6 92518720 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:37:21 88.6 94073053 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:38:22 88.7 95629299 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +May 03 02:39:22 88.6 97071168 196 89.7% 195.6 0.3% 2.8% 0.0% 0.0% 7.4% 0.0% +ALL DONE! diff --git a/src/multiqc/rna-seq/data/SRR3192658_1Log.std.out b/src/multiqc/rna-seq/data/SRR3192658_1Log.std.out new file mode 100644 index 00000000..c1a05ff0 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_1Log.std.out @@ -0,0 +1,4 @@ +May 03 01:29:21 ..... Started STAR run +May 03 01:29:21 ..... Loading genome +May 03 01:33:40 ..... Started mapping +May 03 02:39:29 ..... Finished successfully diff --git a/src/multiqc/rna-seq/data/SRR3192658_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192658_1_fastqc.html new file mode 100644 index 00000000..2188d5d6 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192658_1.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192658_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192658_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences97548052
Sequences flagged as poor quality0
Sequence length101
%GC52

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GGTCTGATGAGCGTCGGCATCGGGCGCCTTAACCCGGCGTTCGGTTCATC984300.10090411646559584No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CTACGAA320550.023.6300561
TAGATCG165050.021.667028
TACCGCG219700.017.4984151
TGCGTCG503750.016.9226829
CGGGTGT331300.016.5443041
ACGAACG337800.016.14991228-29
GTGCGTC571650.015.6852548
GCGGGTT209150.015.1052411
ACGTACG142850.015.01060436-37
TACGAAT508650.014.975452
CGGTATA173950.014.9342254
CGTACGA159250.014.71730936-37
TACGTAC162500.014.58367434-35
GCGGTGT565750.014.5811082
TTTAGCG375050.014.53692210-11
GTCCGAA139900.014.45402051
ACTATCG227600.014.27947658-59
CTATACC458300.013.897367594-95
GAACGTG404300.013.80841230-31
CCGAACG119400.013.5236643
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192658_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192658_1_fastqc.zip new file mode 100644 index 00000000..5e4c6920 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192658_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192658_1_star_aligned.bam_counts.txt.summary b/src/multiqc/rna-seq/data/SRR3192658_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..d43b3bff --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_1_star_aligned.bam_counts.txt.summary @@ -0,0 +1,12 @@ +Status SRR3192658_1_star_aligned.bam +Assigned 66903054 +Unassigned_Ambiguity 4441287 +Unassigned_MultiMapping 6569070 +Unassigned_NoFeatures 16087416 +Unassigned_Unmapped 0 +Unassigned_MappingQuality 0 +Unassigned_FragmentLength 0 +Unassigned_Chimera 0 +Unassigned_Secondary 0 +Unassigned_Nonjunction 0 +Unassigned_Duplicate 0 diff --git a/src/multiqc/rna-seq/data/SRR3192658_1_val_1_fastqc.html b/src/multiqc/rna-seq/data/SRR3192658_1_val_1_fastqc.html new file mode 100644 index 00000000..fe0990e8 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_1_val_1_fastqc.html @@ -0,0 +1,187 @@ +SRR3192658_1_val_1.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192658_1_val_1.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192658_1_val_1.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences97071168
Sequences flagged as poor quality0
Sequence length20-101
%GC52

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GGTCTGATGAGCGTCGGCATCGGGCGCCTTAACCCGGCGTTCGGTTCATC975540.10049740001068083No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CTACGAA302000.024.028961
TAGATCG149850.020.3570658
CTATACC449750.018.51805794-95
CGGGTGT318450.017.1930331
TGCGTCG495350.016.7314139
TACCGCG219100.016.6665081
ACGAACG319750.016.38136728-29
CGCATTC577950.015.99353994-95
GTGCGTC560450.015.6329738
GTCCGAA134600.015.6210671
GCGGGTT206550.015.5171281
CGGTATA172700.015.3783684
TACGAAT482000.015.19998552
TTTAGCG351900.014.86341110-11
ACGTACG127750.014.602653536-37
CGTACGA141350.014.47111836-37
ACTATCG226250.014.4129558-59
TACGTAC145650.014.20878534-35
GCGGTGT555550.014.1660492
CCTATAC498600.014.05813694-95
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192658_1_val_1_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192658_1_val_1_fastqc.zip new file mode 100644 index 00000000..ae039fd6 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192658_1_val_1_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192658_2.fastq.gz_trimming_report.txt b/src/multiqc/rna-seq/data/SRR3192658_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..86b73e98 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_2.fastq.gz_trimming_report.txt @@ -0,0 +1,158 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: SRR3192658_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.9.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file will be GZIP compressed + + +This is cutadapt 1.9.1 with Python 2.7.6 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192658_2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1971.98 s (20 us/read; 2.97 M reads/minute). + +=== Summary === + +Total reads processed: 97,548,052 +Reads with adapters: 30,622,375 (31.4%) +Reads written (passing filters): 97,548,052 (100.0%) + +Total basepairs processed: 9,852,353,252 bp +Quality-trimmed: 287,989,645 bp (2.9%) +Total written (filtered): 9,520,194,936 bp (96.6%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 30622375 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 31.5% + C: 31.2% + G: 23.1% + T: 14.3% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 20624337 24387013.0 0 20624337 +2 7568536 6096753.2 0 7568536 +3 1899525 1524188.3 0 1899525 +4 388085 381047.1 0 388085 +5 96465 95261.8 0 96465 +6 15464 23815.4 0 15464 +7 4786 5953.9 0 4786 +8 1171 1488.5 0 1171 +9 2846 372.1 0 896 1950 +10 3353 93.0 1 762 2591 +11 4399 23.3 1 717 3682 +12 1353 5.8 1 710 643 +13 703 1.5 1 631 72 +14 803 1.5 1 728 75 +15 560 1.5 1 423 137 +16 528 1.5 1 434 94 +17 510 1.5 1 450 60 +18 222 1.5 1 146 76 +19 266 1.5 1 207 59 +20 298 1.5 1 200 98 +21 215 1.5 1 127 88 +22 196 1.5 1 152 44 +23 322 1.5 1 234 88 +24 396 1.5 1 342 54 +25 240 1.5 1 175 65 +26 319 1.5 1 184 135 +27 235 1.5 1 161 74 +28 270 1.5 1 212 58 +29 376 1.5 1 200 176 +30 528 1.5 1 438 90 +31 104 1.5 1 38 66 +32 190 1.5 1 133 57 +33 151 1.5 1 74 77 +34 169 1.5 1 72 97 +35 243 1.5 1 146 97 +36 175 1.5 1 116 59 +37 209 1.5 1 142 67 +38 142 1.5 1 72 70 +39 170 1.5 1 97 73 +40 109 1.5 1 71 38 +41 117 1.5 1 62 55 +42 139 1.5 1 69 70 +43 105 1.5 1 16 89 +44 124 1.5 1 39 85 +45 120 1.5 1 41 79 +46 60 1.5 1 13 47 +47 112 1.5 1 12 100 +48 82 1.5 1 5 77 +49 181 1.5 1 6 175 +50 82 1.5 1 13 69 +51 32 1.5 1 12 20 +52 41 1.5 1 5 36 +53 89 1.5 1 8 81 +54 64 1.5 1 3 61 +55 69 1.5 1 3 66 +56 57 1.5 1 2 55 +57 93 1.5 1 0 93 +58 37 1.5 1 6 31 +59 30 1.5 1 6 24 +60 43 1.5 1 11 32 +61 69 1.5 1 12 57 +62 51 1.5 1 10 41 +63 96 1.5 1 30 66 +64 90 1.5 1 43 47 +65 91 1.5 1 23 68 +66 36 1.5 1 15 21 +67 56 1.5 1 2 54 +68 44 1.5 1 2 42 +69 64 1.5 1 0 64 +70 57 1.5 1 0 57 +71 56 1.5 1 0 56 +72 61 1.5 1 0 61 +73 50 1.5 1 0 50 +74 58 1.5 1 0 58 +75 17 1.5 1 0 17 +76 44 1.5 1 0 44 +77 63 1.5 1 0 63 +78 34 1.5 1 0 34 +79 23 1.5 1 0 23 +80 55 1.5 1 0 55 +81 53 1.5 1 0 53 +82 26 1.5 1 0 26 +83 47 1.5 1 0 47 +84 38 1.5 1 0 38 +85 41 1.5 1 0 41 +86 19 1.5 1 1 18 +87 36 1.5 1 0 36 +88 20 1.5 1 0 20 +89 32 1.5 1 0 32 +90 16 1.5 1 0 16 +91 16 1.5 1 0 16 +92 54 1.5 1 0 54 +93 32 1.5 1 0 32 +94 17 1.5 1 0 17 +95 17 1.5 1 0 17 +96 33 1.5 1 0 33 +97 38 1.5 1 0 38 +98 30 1.5 1 0 30 +99 10 1.5 1 0 10 +100 25 1.5 1 0 25 +101 14 1.5 1 0 14 + + +RUN STATISTICS FOR INPUT FILE: SRR3192658_2.fastq.gz +============================================= +97548052 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 97548052 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 476884 (0.49%) diff --git a/src/multiqc/rna-seq/data/SRR3192658_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192658_2_fastqc.html new file mode 100644 index 00000000..6b841f43 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192658_2.fastq.gz FastQC Report
FastQCFastQC Report
Mon 2 May 2016
SRR3192658_2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192658_2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences97548052
Sequences flagged as poor quality0
Sequence length101
%GC53

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[WARN]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GCCCCTCTCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCTTTGGTGACT1891000.19385317914908234No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TAACACG191950.022.2418177
GTCTAAC192800.021.920664
TCTCCGG1015750.020.5526816
AACACGT212550.019.9522028
AGCGCTC415100.018.7401089
CTCTCCG1130400.018.5888585
TTATCCG447200.017.2564748
TAGGTCG80750.016.8786647
TCCGGCC1251400.016.7849988
AGTCTAA275150.015.8777263
TATCCGG490750.015.7641939
GTACTCG300400.015.59522828-29
ACGTCTC293000.015.502707520-21
GAGTCTA299050.015.3070322
ATCGCAC866300.015.09897768-69
CTCCGGC1426500.014.9509917
CGATCGC898500.014.76444866-67
CTAACAC295500.014.7209426
CCCCTCT1450500.014.5221722
CGACCCA830600.014.44970592-93
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192658_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192658_2_fastqc.zip new file mode 100644 index 00000000..78e796f1 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192658_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/SRR3192658_2_val_2_fastqc.html b/src/multiqc/rna-seq/data/SRR3192658_2_val_2_fastqc.html new file mode 100644 index 00000000..9525e0e7 --- /dev/null +++ b/src/multiqc/rna-seq/data/SRR3192658_2_val_2_fastqc.html @@ -0,0 +1,187 @@ +SRR3192658_2_val_2.fq.gz FastQC Report
FastQCFastQC Report
Tue 3 May 2016
SRR3192658_2_val_2.fq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameSRR3192658_2_val_2.fq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences97071168
Sequences flagged as poor quality0
Sequence length20-101
%GC52

[OK]Per base sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[OK]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[WARN]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GCCCCTCTCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCTTTGGTGACT1760340.1813452991520613No Hit

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GTCTAAC187700.022.148424
TAACACG190150.022.106357
AACACGT209950.019.7587188
TCTCCGG974500.019.6845046
AGCGCTC402050.018.600379
CTCTCCG1082300.017.9395265
TTATCCG445150.016.829958
TAGGTCG76350.016.564987
TCCGGCC1189050.016.492458
AGTCTAA273050.015.6126243
TATCCGG490350.015.3540739
GTACTCG296500.015.17654528-29
ACGTCTC289050.015.02397820-21
GAGTCTA295800.014.9867722
CTCCGGC1350200.014.7079377
ATCGCAC791750.014.65037768-69
ACCCATT757950.014.48074294-95
CGCAGTT547500.014.4805041
CTAACAC294650.014.3909866
CGATCGC817900.014.2529766-67
Produced by FastQC (version 0.11.2)
\ No newline at end of file diff --git a/src/multiqc/rna-seq/data/SRR3192658_2_val_2_fastqc.zip b/src/multiqc/rna-seq/data/SRR3192658_2_val_2_fastqc.zip new file mode 100644 index 00000000..ed983500 Binary files /dev/null and b/src/multiqc/rna-seq/data/SRR3192658_2_val_2_fastqc.zip differ diff --git a/src/multiqc/rna-seq/data/fastqc_theoretical_gc_hg38_txome.txt b/src/multiqc/rna-seq/data/fastqc_theoretical_gc_hg38_txome.txt new file mode 100644 index 00000000..b2fbc90e --- /dev/null +++ b/src/multiqc/rna-seq/data/fastqc_theoretical_gc_hg38_txome.txt @@ -0,0 +1,102 @@ +# FastQC theoretical GC content curve: Human Transcriptome (UCSC hg38) +0 0 +1 0 +2 0 +3 0 +4 0 +5 0 +6 0 +7 0 +8 0 +9 0.001 +10 0.001 +11 0.001 +12 0.002 +13 0.002 +14 0.003 +15 0.005 +16 0.011 +17 0.018 +18 0.03 +19 0.046 +20 0.078 +21 0.116 +22 0.167 +23 0.23 +24 0.305 +25 0.395 +26 0.507 +27 0.612 +28 0.729 +29 0.858 +30 1.001 +31 1.136 +32 1.267 +33 1.444 +34 1.578 +35 1.766 +36 1.922 +37 2.129 +38 2.311 +39 2.4 +40 2.576 +41 2.667 +42 2.736 +43 2.807 +44 2.827 +45 2.852 +46 2.872 +47 2.886 +48 2.915 +49 2.911 +50 2.893 +51 2.866 +52 2.896 +53 2.862 +54 2.877 +55 2.865 +56 2.834 +57 2.795 +58 2.756 +59 2.686 +60 2.569 +61 2.444 +62 2.269 +63 2.102 +64 1.926 +65 1.754 +66 1.538 +67 1.328 +68 1.169 +69 0.976 +70 0.799 +71 0.663 +72 0.558 +73 0.463 +74 0.378 +75 0.318 +76 0.263 +77 0.226 +78 0.178 +79 0.145 +80 0.119 +81 0.097 +82 0.076 +83 0.058 +84 0.042 +85 0.032 +86 0.018 +87 0.015 +88 0.009 +89 0.005 +90 0.004 +91 0.002 +92 0.001 +93 0.001 +94 0 +95 0 +96 0 +97 0 +98 0 +99 0 +100 0 diff --git a/src/multiqc/script.sh b/src/multiqc/script.sh index 7360588b..9ced97de 100644 --- a/src/multiqc/script.sh +++ b/src/multiqc/script.sh @@ -1,24 +1,87 @@ #!/bin/bash +# disable flags +[[ "$par_ignore_symlinks" == "false" ]] && unset ignore_symlinks +[[ "$par_dirs" == "false" ]] && unset par_dirs +[[ "$par_full_names" == "false" ]] && unset par_full_names +[[ "$par_fn_as_s_name" == "false" ]] && unset par_fn_as_s_name +[[ "$par_profile_runtime" == "false" ]] && unset par_profile_runtime +[[ "$par_verbose" == "false" ]] && unset par_verbose +[[ "$par_quiet" == "false" ]] && unset par_quiet +[[ "$par_strict" == "false" ]] && unset par_strict +[[ "$par_development" == "false" ]] && unset par_development +[[ "$par_require_logs" == "false" ]] && unset par_require_logs +[[ "$par_no_megaqc_upload" == "false" ]] && unset par_no_megaqc_upload +[[ "$par_no_ansi" == "false" ]] && unset par_no_ansi +[[ "$par_flat" == "false" ]] && unset par_flat +[[ "$par_interactive" == "false" ]] && unset par_interactive +[[ "$par_static_plot_export" == "false" ]] && unset par_static_plot_export +[[ "$par_data_dir" == "false" ]] && unset par_data_dir +[[ "$par_no_data_dir" == "false" ]] && unset par_no_data_dir +[[ "$par_zip_data_dir" == "false" ]] && unset par_zip_data_dir +[[ "$par_pdf" == "false" ]] && unset par_pdf + + +# handle inputs +out_dir=$(dirname "$par_output_report") +output_report_file=$(basename "$par_output_report") +report_name="${output_report_file%.*}" + +# echo ============ +# echo $out_dir +# echo $output_report_file +# echo $report_name +# echo ============ + +# handle outputs +[[ -z "$par_output_report" ]] && no_report=true +[[ -z "$par_output_data" ]] && no_data_dir=true +[[ ! -z "$par_output_data" ]] && data_dir=true +[[ ! -z "$par_output_plots" ]] && export=true + +# echo =========== +# echo par_output_data: $par_output_data +# echo data_dir: $data_dir +# echo no_data_dir: $no_data_dir +# echo par_output_report: $par_output_report +# echo no_report: $no_report +# echo =========== + +# allow for multiple inputs if [[ -n "$par_input" ]]; then IFS=":" read -ra inputs <<< $par_input unset IFS fi + +# run multiqc multiqc \ - --filename "$par_output_report" \ + ${par_output_report:+--filename "$report_name"} \ + ${out_dir:+--outdir "$out_dir"} \ + ${no_report:+--no-report} \ + ${export:+--export} \ + ${par_data_format:+--data-format "$par_data_format"} \ + ${par_zip_data_dir:+--zip-data-dir} \ + ${par_pdf:+--pdf} \ + ${par_interactive:+--interactive} \ + ${par_flat:+--flat} \ + ${par_verbose:+--verbose} \ + ${par_quiet:+--quiet} \ + ${par_strict:+--strict} \ + ${par_no_megaqc_upload:+--no-megaqc-upload} \ + ${par_no_ansi:+--no-ansi} \ + ${par_profile_runtime:+--profile-runtime} \ + ${par_require_logs:+--require-logs} \ + ${par_development:+--development} \ --force \ "${inputs[@]}" -# if [[ -n "$par_output_report" ]]; then -# mv multiqc_report.html "$par_output_report" -# fi - -# if [[ -n "$par_output_data" ]]; then -# mv "data" "$par_output_data" -# fi +# handle output files +if [[ -n "$par_output_data" ]]; then + mv "${out_dir}/${report_name}_data" "$par_output_data" +fi -# if [[ -n "$par_output_plots" ]]; then -# mv "plots" "$par_output_data" -# fi \ No newline at end of file +if [[ -n "$par_output_plots" ]]; then + mv "${out_dir}/${report_name}_plots" "$par_output_plots" +fi \ No newline at end of file diff --git a/src/multiqc/test_data2/a.txt b/src/multiqc/test_data2/a.txt new file mode 100644 index 00000000..1be51d70 --- /dev/null +++ b/src/multiqc/test_data2/a.txt @@ -0,0 +1,1504 @@ +# This file was produced by samtools stats (1.3+htslib-1.3) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats mapped/a.bam +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK db35d7d5 ec933459 1f587026 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 21838387 +SN filtered sequences: 0 +SN sequences: 21838387 +SN is sorted: 1 +SN 1st fragments: 21838387 +SN last fragments: 0 +SN reads mapped: 21231961 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 606426 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 0 # paired-end technology bit set +SN reads duplicated: 3096782 # PCR or optical duplicate bit set +SN reads MQ0: 4882153 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 1090509989 # ignores clipping +SN bases mapped: 1060219802 # ignores clipping +SN bases mapped (cigar): 1060219787 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 154717551 +SN mismatches: 6032903 # from NM fields +SN error rate: 5.690238e-03 # mismatches / bases mapped (cigar) +SN average length: 49 +SN maximum length: 50 +SN average quality: 37.0 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 51315 0 0 0 0 0 0 0 0 0 0 0 0 382312 0 0 0 0 0 0 178198 0 0 0 0 1338772 0 0 0 0 0 19887790 0 0 0 0 0 0 0 0 +FFQ 2 0 0 5115 0 0 0 0 0 0 0 0 0 0 0 0 275192 0 0 0 0 0 0 147400 0 0 0 0 1284560 0 0 0 0 0 20126120 0 0 0 0 0 0 0 0 +FFQ 3 0 0 5128 0 0 0 0 0 0 0 0 0 0 0 0 191502 0 0 0 0 0 0 150841 0 0 0 0 1285815 0 0 0 0 0 20205101 0 0 0 0 0 0 0 0 +FFQ 4 0 0 5145 0 0 0 0 0 0 0 0 0 0 0 0 146549 0 0 0 0 0 0 39295 0 0 0 0 471059 0 0 0 0 0 1708658 0 0 0 19467681 0 0 0 0 +FFQ 5 0 0 5171 0 0 0 0 0 0 0 0 0 0 0 0 182896 0 0 0 0 0 0 41859 0 0 0 0 541845 0 0 0 0 0 1799240 0 0 0 19267376 0 0 0 0 +FFQ 6 0 0 5207 0 0 0 4751 0 0 0 0 0 0 0 0 177726 0 0 0 0 0 0 50754 0 0 0 0 533328 0 0 0 0 0 1789862 0 0 0 19276759 0 0 0 0 +FFQ 7 0 0 5265 0 0 0 5303 0 0 0 0 0 0 0 0 189482 0 0 0 0 0 0 50374 0 0 0 0 545491 0 0 0 0 0 1801670 0 0 0 19240802 0 0 0 0 +FFQ 8 0 0 5321 0 0 0 5251 0 0 0 0 0 0 0 0 189946 0 0 0 0 0 0 50759 0 0 0 0 544729 0 0 0 0 0 1805074 0 0 0 19237307 0 0 0 0 +FFQ 9 0 0 5412 0 0 0 5572 0 0 0 0 0 0 0 0 194980 0 0 0 0 0 0 50487 0 0 0 0 546813 0 0 0 0 0 1809993 0 0 0 19225130 0 0 0 0 +FFQ 10 0 0 5522 0 0 0 5109 0 0 0 0 0 0 0 0 187331 0 0 0 0 0 0 52119 0 0 0 0 547170 0 0 0 0 0 1806426 0 0 0 19234710 0 0 0 0 +FFQ 11 0 0 5659 0 0 0 5437 0 0 0 0 0 0 0 0 188095 0 0 0 0 0 0 53798 0 0 0 0 550305 0 0 0 0 0 1815355 0 0 0 19219738 0 0 0 0 +FFQ 12 0 0 5842 0 0 0 5812 0 0 0 0 0 0 0 0 191987 0 0 0 0 0 0 54137 0 0 0 0 551697 0 0 0 0 0 1820134 0 0 0 19208778 0 0 0 0 +FFQ 13 0 0 6054 0 0 0 5991 0 0 0 0 0 0 0 0 190425 0 0 0 0 0 0 55749 0 0 0 0 554090 0 0 0 0 0 1824863 0 0 0 19201215 0 0 0 0 +FFQ 14 0 0 6305 0 0 0 6562 0 0 0 0 0 0 0 0 194459 0 0 0 0 0 0 56577 0 0 0 0 553776 0 0 0 0 0 1736245 0 0 0 6044499 0 0 13239964 0 +FFQ 15 0 0 6575 0 0 0 6948 0 0 0 0 0 0 0 0 200015 0 0 0 0 0 0 58113 0 0 0 0 558164 0 0 0 0 0 1741159 0 0 0 6049860 0 0 13217553 0 +FFQ 16 0 0 6884 0 0 0 7121 0 0 0 0 0 0 0 0 201645 0 0 0 0 0 0 59457 0 0 0 0 560449 0 0 0 0 0 1751983 0 0 0 6029168 0 0 13221680 0 +FFQ 17 0 0 7255 0 0 0 7367 0 0 0 0 0 0 0 0 199780 0 0 0 0 0 0 63085 0 0 0 0 565569 0 0 0 0 0 1761217 0 0 0 6046012 0 0 13188102 0 +FFQ 18 0 0 7720 0 0 0 8336 0 0 0 0 0 0 0 0 200938 0 0 0 0 0 0 65311 0 0 0 0 558465 0 0 0 0 0 1759662 0 0 0 6058023 0 0 13179932 0 +FFQ 19 0 0 8413 0 0 0 8308 0 0 0 0 0 0 0 0 201721 0 0 0 0 0 0 69098 0 0 0 0 563047 0 0 0 0 0 1769492 0 0 0 5699288 0 0 13519020 0 +FFQ 20 0 0 8973 0 0 0 9516 0 0 0 0 0 0 0 0 201161 0 0 0 0 0 0 74284 0 0 0 0 562610 0 0 0 0 0 1778241 0 0 0 5767457 0 0 13436145 0 +FFQ 21 0 0 9857 0 0 0 10500 0 0 0 0 0 0 0 0 200349 0 0 0 0 0 0 80072 0 0 0 0 557657 0 0 0 0 0 1780395 0 0 0 5847132 0 0 13352425 0 +FFQ 22 0 0 11063 0 0 0 12270 0 0 0 0 0 0 0 0 204602 0 0 0 0 0 0 89896 0 0 0 0 558198 0 0 0 0 0 1791483 0 0 0 5932912 0 0 13237963 0 +FFQ 23 0 0 12768 0 0 0 14297 0 0 0 0 0 0 0 0 207883 0 0 0 0 0 0 99992 0 0 0 0 556435 0 0 0 0 0 1802873 0 0 0 6033565 0 0 13110574 0 +FFQ 24 0 0 14914 0 0 0 16397 0 0 0 0 0 0 0 0 207240 0 0 0 0 0 0 111512 0 0 0 0 545672 0 0 0 0 0 1806750 0 0 0 6007638 0 0 13128264 0 +FFQ 25 0 0 17715 0 0 0 20138 0 0 0 0 0 0 0 0 214768 0 0 0 0 0 0 129032 0 0 0 0 540112 0 0 0 0 0 1819460 0 0 0 6047119 0 0 13050043 0 +FFQ 26 0 0 21240 0 0 0 34290 0 0 0 0 0 0 0 0 249730 0 0 0 0 0 0 144422 0 0 0 0 520807 0 0 0 0 0 1809886 0 0 0 6058279 0 0 12999733 0 +FFQ 27 0 0 24829 0 0 0 43086 0 0 0 0 0 0 0 0 259480 0 0 0 0 0 0 161601 0 0 0 0 518294 0 0 0 0 0 1824722 0 0 0 6047197 0 0 12959178 0 +FFQ 28 0 0 28496 0 0 0 52585 0 0 0 0 0 0 0 0 260264 0 0 0 0 0 0 176084 0 0 0 0 509295 0 0 0 0 0 1839906 0 0 0 6068273 0 0 12903484 0 +FFQ 29 0 0 32506 0 0 0 62389 0 0 0 0 0 0 0 0 254623 0 0 0 0 0 0 189495 0 0 0 0 499599 0 0 0 0 0 1852205 0 0 0 6080516 0 0 12867054 0 +FFQ 30 0 0 36854 0 0 0 73580 0 0 0 0 0 0 0 0 247860 0 0 0 0 0 0 200625 0 0 0 0 495018 0 0 0 0 0 1863132 0 0 0 6112314 0 0 12809004 0 +FFQ 31 0 0 41323 0 0 0 87468 0 0 0 0 0 0 0 0 242078 0 0 0 0 0 0 209555 0 0 0 0 491444 0 0 0 0 0 1867737 0 0 0 6132089 0 0 12766610 0 +FFQ 32 0 0 46286 0 0 0 98002 0 0 0 0 0 0 0 0 232699 0 0 0 0 0 0 213564 0 0 0 0 491302 0 0 0 0 0 1878843 0 0 0 6142018 0 0 12735496 0 +FFQ 33 0 0 51663 0 0 0 106786 0 0 0 0 0 0 0 0 221792 0 0 0 0 0 0 218240 0 0 0 0 491145 0 0 0 0 0 1877911 0 0 0 6158285 0 0 12712271 0 +FFQ 34 0 0 57443 0 0 0 119491 0 0 0 0 0 0 0 0 216326 0 0 0 0 0 0 222138 0 0 0 0 487486 0 0 0 0 0 1875659 0 0 0 6153206 0 0 12706214 0 +FFQ 35 0 0 63864 0 0 0 122385 0 0 0 0 0 0 0 0 210969 0 0 0 0 0 0 227897 0 0 0 0 488945 0 0 0 0 0 1888985 0 0 0 6136699 0 0 12698075 0 +FFQ 36 0 0 70925 0 0 0 127772 0 0 0 0 0 0 0 0 204278 0 0 0 0 0 0 232925 0 0 0 0 489984 0 0 0 0 0 1893912 0 0 0 6147628 0 0 12670239 0 +FFQ 37 0 0 78443 0 0 0 130513 0 0 0 0 0 0 0 0 201817 0 0 0 0 0 0 237205 0 0 0 0 489393 0 0 0 0 0 1901072 0 0 0 6157060 0 0 12641982 0 +FFQ 38 0 0 86727 0 0 0 134572 0 0 0 0 0 0 0 0 201643 0 0 0 0 0 0 245851 0 0 0 0 493135 0 0 0 0 0 1911564 0 0 0 6168370 0 0 12595418 0 +FFQ 39 0 0 96199 0 0 0 136517 0 0 0 0 0 0 0 0 202556 0 0 0 0 0 0 253424 0 0 0 0 496159 0 0 0 0 0 1926927 0 0 0 6191376 0 0 12533859 0 +FFQ 40 0 0 106625 0 0 0 141535 0 0 0 0 0 0 0 0 207572 0 0 0 0 0 0 263379 0 0 0 0 494281 0 0 0 0 0 1936713 0 0 0 6212472 0 0 12474092 0 +FFQ 41 0 0 118435 0 0 0 134585 0 0 0 0 0 0 0 0 207617 0 0 0 0 0 0 271430 0 0 0 0 497097 0 0 0 0 0 1952887 0 0 0 6236465 0 0 12417628 0 +FFQ 42 0 0 132662 0 0 0 134133 0 0 0 0 0 0 0 0 204434 0 0 0 0 0 0 279354 0 0 0 0 498810 0 0 0 0 0 1968372 0 0 0 6267796 0 0 12349794 0 +FFQ 43 0 0 147587 0 0 0 131817 0 0 0 0 0 0 0 0 204674 0 0 0 0 0 0 288492 0 0 0 0 497849 0 0 0 0 0 1975284 0 0 0 6290454 0 0 12298484 0 +FFQ 44 0 0 166442 0 0 0 128205 0 0 0 0 0 0 0 0 201990 0 0 0 0 0 0 298737 0 0 0 0 496519 0 0 0 0 0 1988815 0 0 0 6294537 0 0 12258940 0 +FFQ 45 0 0 190003 0 0 0 124333 0 0 0 0 0 0 0 0 196796 0 0 0 0 0 0 309371 0 0 0 0 499163 0 0 0 0 0 2001867 0 0 0 6259352 0 0 12252716 0 +FFQ 46 0 0 220981 0 0 0 116347 0 0 0 0 0 0 0 0 191467 0 0 0 0 0 0 316096 0 0 0 0 498894 0 0 0 0 0 2007430 0 0 0 6270683 0 0 12210477 0 +FFQ 47 0 0 258782 0 0 0 106166 0 0 0 0 0 0 0 0 185518 0 0 0 0 0 0 319187 0 0 0 0 496114 0 0 0 0 0 2015168 0 0 0 6276041 0 0 12156632 0 +FFQ 48 0 0 310568 0 0 0 93125 0 0 0 0 0 0 0 0 177253 0 0 0 0 0 0 323208 0 0 0 0 501414 0 0 0 0 0 2033190 0 0 0 6270044 0 0 12009645 0 +FFQ 49 0 0 374982 0 0 0 66673 0 0 0 0 0 0 0 0 165208 0 0 0 0 0 0 314721 0 0 0 0 492972 0 0 0 0 0 2005393 0 0 0 6174269 0 0 11627542 0 +FFQ 50 0 0 468205 0 0 0 30279 0 0 0 0 0 0 0 0 157265 0 0 0 0 0 0 309324 0 0 0 0 497388 0 0 0 0 0 2038361 0 0 0 6218900 0 0 11502038 0 +FFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# Last Fragment Qualitites. Use `grep ^LFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 0.75 865 +GCF 1.76 1418 +GCF 2.76 1432 +GCF 3.77 2552 +GCF 4.27 2584 +GCF 5.03 2582 +GCF 5.78 4188 +GCF 6.78 4242 +GCF 7.79 6900 +GCF 8.79 6990 +GCF 9.80 12077 +GCF 10.30 12202 +GCF 11.06 12248 +GCF 11.81 20918 +GCF 12.31 21159 +GCF 13.07 21223 +GCF 13.82 35416 +GCF 14.32 35417 +GCF 14.82 35899 +GCF 15.33 35912 +GCF 16.08 58403 +GCF 16.83 59262 +GCF 17.34 59292 +GCF 17.84 92651 +GCF 18.34 92652 +GCF 18.84 93563 +GCF 19.35 93799 +GCF 20.10 141217 +GCF 20.85 142627 +GCF 21.36 143006 +GCF 21.86 205422 +GCF 22.36 205429 +GCF 22.86 207354 +GCF 23.37 207906 +GCF 23.87 290147 +GCF 24.37 290170 +GCF 24.87 292864 +GCF 25.38 293730 +GCF 25.88 405518 +GCF 26.38 405534 +GCF 26.88 408551 +GCF 27.39 408580 +GCF 27.89 570253 +GCF 28.39 570499 +GCF 28.89 570545 +GCF 29.40 575537 +GCF 29.90 829159 +GCF 30.40 829379 +GCF 30.90 829405 +GCF 31.41 836277 +GCF 31.91 1143374 +GCF 32.66 1143659 +GCF 33.42 1146746 +GCF 33.92 1501224 +GCF 34.42 1501256 +GCF 34.92 1501488 +GCF 35.43 1507360 +GCF 35.93 1778503 +GCF 36.43 1778542 +GCF 36.93 1778582 +GCF 37.44 1783301 +GCF 37.94 1767410 +GCF 38.44 1767928 +GCF 38.94 1768071 +GCF 39.45 1769688 +GCF 39.95 1656761 +GCF 40.45 1657229 +GCF 40.95 1657212 +GCF 41.46 1658172 +GCF 41.96 1509858 +GCF 42.46 1509735 +GCF 42.96 1509702 +GCF 43.47 1509894 +GCF 43.97 1444340 +GCF 44.47 1444607 +GCF 44.97 1444566 +GCF 45.48 1444635 +GCF 45.98 1405845 +GCF 46.48 1405793 +GCF 46.98 1405225 +GCF 47.49 1405190 +GCF 47.99 1360256 +GCF 48.49 1360229 +GCF 49.25 1359649 +GCF 50.25 1272600 +GCF 51.01 1271785 +GCF 51.51 1271790 +GCF 52.01 1115634 +GCF 52.51 1115609 +GCF 53.02 1114429 +GCF 53.52 1114416 +GCF 54.02 921342 +GCF 54.52 921028 +GCF 55.03 921029 +GCF 55.53 919941 +GCF 56.03 716231 +GCF 56.78 715994 +GCF 57.54 715097 +GCF 58.04 532571 +GCF 58.54 527473 +GCF 59.05 527469 +GCF 59.55 526587 +GCF 60.05 376831 +GCF 60.55 372736 +GCF 61.06 372536 +GCF 61.56 371968 +GCF 62.06 252936 +GCF 62.56 249647 +GCF 63.07 249528 +GCF 63.57 249527 +GCF 64.07 163481 +GCF 64.57 161228 +GCF 65.08 161158 +GCF 65.58 161154 +GCF 66.08 101911 +GCF 66.83 100650 +GCF 67.59 100609 +GCF 68.09 60847 +GCF 68.59 59897 +GCF 69.10 59890 +GCF 69.60 59865 +GCF 70.10 36290 +GCF 70.60 35728 +GCF 71.11 35725 +GCF 71.61 35692 +GCF 72.36 23067 +GCF 73.12 22797 +GCF 73.62 22799 +GCF 74.12 15342 +GCF 74.62 15317 +GCF 75.13 15185 +GCF 75.63 15186 +GCF 76.13 10477 +GCF 76.63 10474 +GCF 77.14 10363 +GCF 77.64 10359 +GCF 78.14 7327 +GCF 78.64 7313 +GCF 79.40 7302 +GCF 80.15 5084 +GCF 80.65 5086 +GCF 81.16 5049 +GCF 81.66 5047 +GCF 82.16 3472 +GCF 82.66 3470 +GCF 83.42 3464 +GCF 84.17 2302 +GCF 84.67 2303 +GCF 85.43 2287 +GCF 86.18 1488 +GCF 86.68 1487 +GCF 87.19 1486 +GCF 87.69 1480 +GCF 88.44 841 +GCF 89.20 842 +GCF 89.70 837 +GCF 90.70 472 +GCF 91.71 471 +GCF 92.71 248 +GCF 93.72 244 +GCF 94.97 126 +GCF 96.98 54 +GCF 98.99 21 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] +GCC 1 27.19 22.69 22.08 28.04 0.21 0.00 +GCC 2 27.70 22.16 21.57 28.57 0.00 0.00 +GCC 3 29.07 20.57 19.82 30.54 0.00 0.00 +GCC 4 28.81 20.73 20.29 30.17 0.00 0.00 +GCC 5 29.23 20.17 19.74 30.86 0.00 0.00 +GCC 6 29.00 20.47 19.91 30.62 0.00 0.00 +GCC 7 28.88 20.46 19.88 30.78 0.00 0.00 +GCC 8 28.85 20.74 20.02 30.39 0.00 0.00 +GCC 9 28.51 21.15 20.49 29.85 0.00 0.00 +GCC 10 28.05 21.54 20.95 29.46 0.00 0.00 +GCC 11 28.15 21.56 20.88 29.41 0.00 0.00 +GCC 12 28.32 21.33 20.59 29.77 0.00 0.00 +GCC 13 28.46 21.18 20.45 29.91 0.00 0.00 +GCC 14 28.36 21.04 20.35 30.25 0.00 0.00 +GCC 15 28.47 20.86 20.15 30.51 0.00 0.00 +GCC 16 28.29 21.14 20.36 30.21 0.00 0.00 +GCC 17 28.23 21.10 20.54 30.12 0.00 0.00 +GCC 18 28.35 20.96 20.66 30.02 0.00 0.00 +GCC 19 28.06 21.42 21.18 29.34 0.00 0.00 +GCC 20 28.15 21.29 21.01 29.55 0.00 0.00 +GCC 21 28.09 21.28 21.33 29.31 0.00 0.00 +GCC 22 28.07 21.26 21.17 29.51 0.00 0.00 +GCC 23 28.22 21.06 20.72 30.01 0.00 0.00 +GCC 24 28.13 21.20 20.87 29.80 0.00 0.00 +GCC 25 28.32 20.89 20.58 30.21 0.00 0.00 +GCC 26 28.13 21.20 20.74 29.92 0.00 0.00 +GCC 27 27.96 21.34 20.88 29.81 0.00 0.00 +GCC 28 28.06 21.17 20.89 29.88 0.00 0.00 +GCC 29 27.79 21.60 21.33 29.29 0.00 0.00 +GCC 30 27.84 21.56 21.24 29.35 0.00 0.00 +GCC 31 27.84 21.59 21.14 29.43 0.00 0.00 +GCC 32 27.82 21.68 21.19 29.31 0.00 0.00 +GCC 33 28.14 21.20 20.82 29.84 0.00 0.00 +GCC 34 28.00 21.30 20.78 29.92 0.00 0.00 +GCC 35 28.14 21.19 20.64 30.03 0.00 0.00 +GCC 36 28.22 21.16 20.67 29.95 0.00 0.00 +GCC 37 28.12 21.36 20.65 29.87 0.00 0.00 +GCC 38 28.15 21.52 20.76 29.58 0.00 0.00 +GCC 39 27.94 21.78 21.08 29.19 0.00 0.00 +GCC 40 27.79 21.80 21.18 29.23 0.00 0.00 +GCC 41 27.65 21.89 21.45 29.01 0.00 0.00 +GCC 42 27.94 21.65 21.15 29.26 0.01 0.00 +GCC 43 27.90 21.51 20.95 29.65 0.00 0.00 +GCC 44 27.87 21.68 21.03 29.42 0.00 0.00 +GCC 45 28.27 21.39 20.69 29.66 0.00 0.00 +GCC 46 28.12 21.20 20.68 30.00 0.01 0.00 +GCC 47 28.06 21.43 21.00 29.51 0.00 0.00 +GCC 48 28.08 21.47 20.96 29.48 0.00 0.00 +GCC 49 27.53 21.94 21.68 28.85 0.02 0.00 +GCC 50 28.35 21.19 20.97 29.49 0.00 0.00 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 30 83 +RL 31 94 +RL 32 117 +RL 33 130 +RL 34 144 +RL 35 156 +RL 36 178 +RL 37 205 +RL 38 263 +RL 39 348 +RL 40 525 +RL 41 789 +RL 42 714 +RL 43 456 +RL 44 584 +RL 45 1226 +RL 46 18767 +RL 47 95161 +RL 48 496687 +RL 50 21221760 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 64125 118566 +ID 2 11857 15129 +ID 3 1458 1538 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 1 0 0 0 1 +IC 2 0 203 0 212 +IC 3 0 552 0 878 +IC 4 0 892 0 1911 +IC 5 0 1594 0 2256 +IC 6 0 1567 0 2393 +IC 7 0 1533 0 2675 +IC 8 0 1585 0 2765 +IC 9 0 1556 0 2857 +IC 10 0 1643 0 3115 +IC 11 0 1682 0 2944 +IC 12 0 1707 0 3030 +IC 13 0 1811 0 3124 +IC 14 0 1723 0 3116 +IC 15 0 1838 0 3290 +IC 16 0 1687 0 3202 +IC 17 0 1841 0 3250 +IC 18 0 1850 0 3390 +IC 19 0 1873 0 3484 +IC 20 0 1785 0 3497 +IC 21 0 1763 0 3457 +IC 22 0 1782 0 3406 +IC 23 0 1841 0 3383 +IC 24 0 1828 0 3277 +IC 25 0 1809 0 3322 +IC 26 0 1830 0 3369 +IC 27 0 1890 0 3294 +IC 28 0 1825 0 3385 +IC 29 0 1864 0 3340 +IC 30 0 1899 0 3649 +IC 31 0 1958 0 3771 +IC 32 0 2052 0 3555 +IC 33 0 2086 0 3636 +IC 34 0 1962 0 3649 +IC 35 0 1945 0 3550 +IC 36 0 1972 0 3423 +IC 37 0 1836 0 3536 +IC 38 0 1845 0 3515 +IC 39 0 1883 0 3451 +IC 40 0 1806 0 3300 +IC 41 0 1850 0 3304 +IC 42 0 1710 0 3148 +IC 43 0 1825 0 2849 +IC 44 0 1639 0 2612 +IC 45 0 1708 0 1439 +IC 46 0 1072 0 765 +IC 47 0 659 0 340 +IC 48 0 288 0 118 +IC 49 0 91 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 609977704 +COV [2-2] 2 115063033 +COV [3-3] 3 16119927 +COV [4-4] 4 2001769 +COV [5-5] 5 294243 +COV [6-6] 6 82570 +COV [7-7] 7 41437 +COV [8-8] 8 27141 +COV [9-9] 9 19572 +COV [10-10] 10 15755 +COV [11-11] 11 12467 +COV [12-12] 12 10784 +COV [13-13] 13 8648 +COV [14-14] 14 7758 +COV [15-15] 15 6163 +COV [16-16] 16 5267 +COV [17-17] 17 4349 +COV [18-18] 18 3615 +COV [19-19] 19 3296 +COV [20-20] 20 2835 +COV [21-21] 21 2708 +COV [22-22] 22 2026 +COV [23-23] 23 1585 +COV [24-24] 24 1605 +COV [25-25] 25 1606 +COV [26-26] 26 1387 +COV [27-27] 27 1529 +COV [28-28] 28 1270 +COV [29-29] 29 1185 +COV [30-30] 30 1228 +COV [31-31] 31 1101 +COV [32-32] 32 1125 +COV [33-33] 33 1032 +COV [34-34] 34 935 +COV [35-35] 35 880 +COV [36-36] 36 985 +COV [37-37] 37 1009 +COV [38-38] 38 915 +COV [39-39] 39 838 +COV [40-40] 40 828 +COV [41-41] 41 837 +COV [42-42] 42 894 +COV [43-43] 43 903 +COV [44-44] 44 902 +COV [45-45] 45 780 +COV [46-46] 46 796 +COV [47-47] 47 854 +COV [48-48] 48 804 +COV [49-49] 49 755 +COV [50-50] 50 728 +COV [51-51] 51 753 +COV [52-52] 52 834 +COV [53-53] 53 797 +COV [54-54] 54 806 +COV [55-55] 55 748 +COV [56-56] 56 815 +COV [57-57] 57 814 +COV [58-58] 58 775 +COV [59-59] 59 779 +COV [60-60] 60 744 +COV [61-61] 61 787 +COV [62-62] 62 809 +COV [63-63] 63 788 +COV [64-64] 64 748 +COV [65-65] 65 712 +COV [66-66] 66 614 +COV [67-67] 67 631 +COV [68-68] 68 717 +COV [69-69] 69 660 +COV [70-70] 70 591 +COV [71-71] 71 559 +COV [72-72] 72 666 +COV [73-73] 73 535 +COV [74-74] 74 565 +COV [75-75] 75 526 +COV [76-76] 76 514 +COV [77-77] 77 504 +COV [78-78] 78 493 +COV [79-79] 79 452 +COV [80-80] 80 422 +COV [81-81] 81 511 +COV [82-82] 82 494 +COV [83-83] 83 445 +COV [84-84] 84 495 +COV [85-85] 85 412 +COV [86-86] 86 495 +COV [87-87] 87 447 +COV [88-88] 88 469 +COV [89-89] 89 451 +COV [90-90] 90 522 +COV [91-91] 91 471 +COV [92-92] 92 464 +COV [93-93] 93 476 +COV [94-94] 94 520 +COV [95-95] 95 497 +COV [96-96] 96 445 +COV [97-97] 97 494 +COV [98-98] 98 502 +COV [99-99] 99 490 +COV [100-100] 100 461 +COV [101-101] 101 527 +COV [102-102] 102 533 +COV [103-103] 103 515 +COV [104-104] 104 611 +COV [105-105] 105 471 +COV [106-106] 106 492 +COV [107-107] 107 445 +COV [108-108] 108 467 +COV [109-109] 109 455 +COV [110-110] 110 393 +COV [111-111] 111 394 +COV [112-112] 112 370 +COV [113-113] 113 344 +COV [114-114] 114 324 +COV [115-115] 115 308 +COV [116-116] 116 332 +COV [117-117] 117 272 +COV [118-118] 118 248 +COV [119-119] 119 220 +COV [120-120] 120 308 +COV [121-121] 121 281 +COV [122-122] 122 313 +COV [123-123] 123 259 +COV [124-124] 124 222 +COV [125-125] 125 189 +COV [126-126] 126 219 +COV [127-127] 127 194 +COV [128-128] 128 188 +COV [129-129] 129 181 +COV [130-130] 130 223 +COV [131-131] 131 200 +COV [132-132] 132 180 +COV [133-133] 133 167 +COV [134-134] 134 168 +COV [135-135] 135 153 +COV [136-136] 136 179 +COV [137-137] 137 183 +COV [138-138] 138 175 +COV [139-139] 139 177 +COV [140-140] 140 168 +COV [141-141] 141 180 +COV [142-142] 142 197 +COV [143-143] 143 194 +COV [144-144] 144 170 +COV [145-145] 145 172 +COV [146-146] 146 149 +COV [147-147] 147 173 +COV [148-148] 148 184 +COV [149-149] 149 172 +COV [150-150] 150 168 +COV [151-151] 151 187 +COV [152-152] 152 187 +COV [153-153] 153 174 +COV [154-154] 154 134 +COV [155-155] 155 179 +COV [156-156] 156 153 +COV [157-157] 157 160 +COV [158-158] 158 160 +COV [159-159] 159 171 +COV [160-160] 160 163 +COV [161-161] 161 168 +COV [162-162] 162 183 +COV [163-163] 163 175 +COV [164-164] 164 183 +COV [165-165] 165 194 +COV [166-166] 166 180 +COV [167-167] 167 174 +COV [168-168] 168 155 +COV [169-169] 169 173 +COV [170-170] 170 169 +COV [171-171] 171 199 +COV [172-172] 172 190 +COV [173-173] 173 231 +COV [174-174] 174 221 +COV [175-175] 175 235 +COV [176-176] 176 216 +COV [177-177] 177 215 +COV [178-178] 178 210 +COV [179-179] 179 226 +COV [180-180] 180 207 +COV [181-181] 181 232 +COV [182-182] 182 232 +COV [183-183] 183 214 +COV [184-184] 184 210 +COV [185-185] 185 231 +COV [186-186] 186 191 +COV [187-187] 187 216 +COV [188-188] 188 210 +COV [189-189] 189 218 +COV [190-190] 190 260 +COV [191-191] 191 240 +COV [192-192] 192 239 +COV [193-193] 193 252 +COV [194-194] 194 268 +COV [195-195] 195 237 +COV [196-196] 196 256 +COV [197-197] 197 254 +COV [198-198] 198 266 +COV [199-199] 199 297 +COV [200-200] 200 255 +COV [201-201] 201 285 +COV [202-202] 202 259 +COV [203-203] 203 249 +COV [204-204] 204 238 +COV [205-205] 205 247 +COV [206-206] 206 261 +COV [207-207] 207 244 +COV [208-208] 208 241 +COV [209-209] 209 237 +COV [210-210] 210 271 +COV [211-211] 211 245 +COV [212-212] 212 234 +COV [213-213] 213 252 +COV [214-214] 214 241 +COV [215-215] 215 215 +COV [216-216] 216 227 +COV [217-217] 217 212 +COV [218-218] 218 230 +COV [219-219] 219 184 +COV [220-220] 220 213 +COV [221-221] 221 225 +COV [222-222] 222 188 +COV [223-223] 223 214 +COV [224-224] 224 198 +COV [225-225] 225 195 +COV [226-226] 226 192 +COV [227-227] 227 191 +COV [228-228] 228 184 +COV [229-229] 229 182 +COV [230-230] 230 177 +COV [231-231] 231 169 +COV [232-232] 232 174 +COV [233-233] 233 152 +COV [234-234] 234 154 +COV [235-235] 235 132 +COV [236-236] 236 130 +COV [237-237] 237 146 +COV [238-238] 238 130 +COV [239-239] 239 103 +COV [240-240] 240 161 +COV [241-241] 241 120 +COV [242-242] 242 117 +COV [243-243] 243 132 +COV [244-244] 244 134 +COV [245-245] 245 140 +COV [246-246] 246 123 +COV [247-247] 247 126 +COV [248-248] 248 126 +COV [249-249] 249 99 +COV [250-250] 250 87 +COV [251-251] 251 103 +COV [252-252] 252 109 +COV [253-253] 253 101 +COV [254-254] 254 91 +COV [255-255] 255 72 +COV [256-256] 256 64 +COV [257-257] 257 88 +COV [258-258] 258 86 +COV [259-259] 259 87 +COV [260-260] 260 79 +COV [261-261] 261 67 +COV [262-262] 262 76 +COV [263-263] 263 89 +COV [264-264] 264 64 +COV [265-265] 265 52 +COV [266-266] 266 64 +COV [267-267] 267 69 +COV [268-268] 268 64 +COV [269-269] 269 60 +COV [270-270] 270 55 +COV [271-271] 271 44 +COV [272-272] 272 58 +COV [273-273] 273 63 +COV [274-274] 274 63 +COV [275-275] 275 75 +COV [276-276] 276 81 +COV [277-277] 277 81 +COV [278-278] 278 74 +COV [279-279] 279 44 +COV [280-280] 280 78 +COV [281-281] 281 78 +COV [282-282] 282 81 +COV [283-283] 283 75 +COV [284-284] 284 100 +COV [285-285] 285 50 +COV [286-286] 286 57 +COV [287-287] 287 52 +COV [288-288] 288 54 +COV [289-289] 289 65 +COV [290-290] 290 67 +COV [291-291] 291 58 +COV [292-292] 292 56 +COV [293-293] 293 48 +COV [294-294] 294 61 +COV [295-295] 295 51 +COV [296-296] 296 55 +COV [297-297] 297 60 +COV [298-298] 298 50 +COV [299-299] 299 47 +COV [300-300] 300 62 +COV [301-301] 301 56 +COV [302-302] 302 62 +COV [303-303] 303 49 +COV [304-304] 304 66 +COV [305-305] 305 64 +COV [306-306] 306 61 +COV [307-307] 307 53 +COV [308-308] 308 51 +COV [309-309] 309 68 +COV [310-310] 310 53 +COV [311-311] 311 60 +COV [312-312] 312 73 +COV [313-313] 313 61 +COV [314-314] 314 70 +COV [315-315] 315 47 +COV [316-316] 316 44 +COV [317-317] 317 51 +COV [318-318] 318 52 +COV [319-319] 319 56 +COV [320-320] 320 60 +COV [321-321] 321 56 +COV [322-322] 322 55 +COV [323-323] 323 51 +COV [324-324] 324 60 +COV [325-325] 325 60 +COV [326-326] 326 65 +COV [327-327] 327 75 +COV [328-328] 328 52 +COV [329-329] 329 63 +COV [330-330] 330 59 +COV [331-331] 331 50 +COV [332-332] 332 51 +COV [333-333] 333 57 +COV [334-334] 334 44 +COV [335-335] 335 32 +COV [336-336] 336 62 +COV [337-337] 337 47 +COV [338-338] 338 69 +COV [339-339] 339 64 +COV [340-340] 340 51 +COV [341-341] 341 56 +COV [342-342] 342 51 +COV [343-343] 343 49 +COV [344-344] 344 72 +COV [345-345] 345 61 +COV [346-346] 346 51 +COV [347-347] 347 76 +COV [348-348] 348 75 +COV [349-349] 349 55 +COV [350-350] 350 48 +COV [351-351] 351 52 +COV [352-352] 352 68 +COV [353-353] 353 47 +COV [354-354] 354 59 +COV [355-355] 355 52 +COV [356-356] 356 51 +COV [357-357] 357 59 +COV [358-358] 358 57 +COV [359-359] 359 69 +COV [360-360] 360 59 +COV [361-361] 361 80 +COV [362-362] 362 42 +COV [363-363] 363 46 +COV [364-364] 364 65 +COV [365-365] 365 60 +COV [366-366] 366 45 +COV [367-367] 367 48 +COV [368-368] 368 39 +COV [369-369] 369 48 +COV [370-370] 370 44 +COV [371-371] 371 49 +COV [372-372] 372 61 +COV [373-373] 373 48 +COV [374-374] 374 45 +COV [375-375] 375 55 +COV [376-376] 376 54 +COV [377-377] 377 67 +COV [378-378] 378 53 +COV [379-379] 379 65 +COV [380-380] 380 49 +COV [381-381] 381 61 +COV [382-382] 382 48 +COV [383-383] 383 49 +COV [384-384] 384 49 +COV [385-385] 385 45 +COV [386-386] 386 40 +COV [387-387] 387 38 +COV [388-388] 388 41 +COV [389-389] 389 46 +COV [390-390] 390 42 +COV [391-391] 391 53 +COV [392-392] 392 38 +COV [393-393] 393 36 +COV [394-394] 394 37 +COV [395-395] 395 40 +COV [396-396] 396 43 +COV [397-397] 397 24 +COV [398-398] 398 54 +COV [399-399] 399 36 +COV [400-400] 400 40 +COV [401-401] 401 28 +COV [402-402] 402 52 +COV [403-403] 403 70 +COV [404-404] 404 52 +COV [405-405] 405 49 +COV [406-406] 406 42 +COV [407-407] 407 37 +COV [408-408] 408 41 +COV [409-409] 409 61 +COV [410-410] 410 44 +COV [411-411] 411 36 +COV [412-412] 412 58 +COV [413-413] 413 37 +COV [414-414] 414 53 +COV [415-415] 415 33 +COV [416-416] 416 44 +COV [417-417] 417 35 +COV [418-418] 418 40 +COV [419-419] 419 43 +COV [420-420] 420 48 +COV [421-421] 421 58 +COV [422-422] 422 53 +COV [423-423] 423 44 +COV [424-424] 424 55 +COV [425-425] 425 62 +COV [426-426] 426 49 +COV [427-427] 427 43 +COV [428-428] 428 31 +COV [429-429] 429 47 +COV [430-430] 430 54 +COV [431-431] 431 43 +COV [432-432] 432 57 +COV [433-433] 433 33 +COV [434-434] 434 50 +COV [435-435] 435 49 +COV [436-436] 436 32 +COV [437-437] 437 49 +COV [438-438] 438 40 +COV [439-439] 439 44 +COV [440-440] 440 42 +COV [441-441] 441 43 +COV [442-442] 442 42 +COV [443-443] 443 50 +COV [444-444] 444 36 +COV [445-445] 445 29 +COV [446-446] 446 46 +COV [447-447] 447 34 +COV [448-448] 448 40 +COV [449-449] 449 40 +COV [450-450] 450 46 +COV [451-451] 451 28 +COV [452-452] 452 37 +COV [453-453] 453 42 +COV [454-454] 454 42 +COV [455-455] 455 44 +COV [456-456] 456 38 +COV [457-457] 457 42 +COV [458-458] 458 42 +COV [459-459] 459 38 +COV [460-460] 460 45 +COV [461-461] 461 34 +COV [462-462] 462 38 +COV [463-463] 463 36 +COV [464-464] 464 44 +COV [465-465] 465 43 +COV [466-466] 466 44 +COV [467-467] 467 31 +COV [468-468] 468 58 +COV [469-469] 469 44 +COV [470-470] 470 57 +COV [471-471] 471 39 +COV [472-472] 472 37 +COV [473-473] 473 42 +COV [474-474] 474 38 +COV [475-475] 475 41 +COV [476-476] 476 40 +COV [477-477] 477 41 +COV [478-478] 478 44 +COV [479-479] 479 40 +COV [480-480] 480 48 +COV [481-481] 481 34 +COV [482-482] 482 40 +COV [483-483] 483 41 +COV [484-484] 484 45 +COV [485-485] 485 44 +COV [486-486] 486 48 +COV [487-487] 487 32 +COV [488-488] 488 44 +COV [489-489] 489 38 +COV [490-490] 490 22 +COV [491-491] 491 32 +COV [492-492] 492 45 +COV [493-493] 493 28 +COV [494-494] 494 33 +COV [495-495] 495 39 +COV [496-496] 496 46 +COV [497-497] 497 32 +COV [498-498] 498 34 +COV [499-499] 499 30 +COV [500-500] 500 30 +COV [501-501] 501 31 +COV [502-502] 502 39 +COV [503-503] 503 44 +COV [504-504] 504 30 +COV [505-505] 505 34 +COV [506-506] 506 25 +COV [507-507] 507 48 +COV [508-508] 508 35 +COV [509-509] 509 41 +COV [510-510] 510 38 +COV [511-511] 511 36 +COV [512-512] 512 45 +COV [513-513] 513 26 +COV [514-514] 514 34 +COV [515-515] 515 35 +COV [516-516] 516 36 +COV [517-517] 517 29 +COV [518-518] 518 28 +COV [519-519] 519 31 +COV [520-520] 520 34 +COV [521-521] 521 47 +COV [522-522] 522 35 +COV [523-523] 523 44 +COV [524-524] 524 58 +COV [525-525] 525 26 +COV [526-526] 526 40 +COV [527-527] 527 36 +COV [528-528] 528 37 +COV [529-529] 529 55 +COV [530-530] 530 37 +COV [531-531] 531 32 +COV [532-532] 532 33 +COV [533-533] 533 39 +COV [534-534] 534 34 +COV [535-535] 535 26 +COV [536-536] 536 42 +COV [537-537] 537 25 +COV [538-538] 538 40 +COV [539-539] 539 38 +COV [540-540] 540 35 +COV [541-541] 541 31 +COV [542-542] 542 33 +COV [543-543] 543 38 +COV [544-544] 544 36 +COV [545-545] 545 39 +COV [546-546] 546 35 +COV [547-547] 547 36 +COV [548-548] 548 41 +COV [549-549] 549 38 +COV [550-550] 550 30 +COV [551-551] 551 33 +COV [552-552] 552 40 +COV [553-553] 553 33 +COV [554-554] 554 30 +COV [555-555] 555 41 +COV [556-556] 556 31 +COV [557-557] 557 37 +COV [558-558] 558 41 +COV [559-559] 559 26 +COV [560-560] 560 30 +COV [561-561] 561 35 +COV [562-562] 562 35 +COV [563-563] 563 34 +COV [564-564] 564 35 +COV [565-565] 565 39 +COV [566-566] 566 29 +COV [567-567] 567 41 +COV [568-568] 568 29 +COV [569-569] 569 27 +COV [570-570] 570 40 +COV [571-571] 571 32 +COV [572-572] 572 30 +COV [573-573] 573 25 +COV [574-574] 574 35 +COV [575-575] 575 30 +COV [576-576] 576 28 +COV [577-577] 577 34 +COV [578-578] 578 21 +COV [579-579] 579 31 +COV [580-580] 580 34 +COV [581-581] 581 18 +COV [582-582] 582 31 +COV [583-583] 583 24 +COV [584-584] 584 30 +COV [585-585] 585 31 +COV [586-586] 586 32 +COV [587-587] 587 23 +COV [588-588] 588 33 +COV [589-589] 589 31 +COV [590-590] 590 28 +COV [591-591] 591 27 +COV [592-592] 592 28 +COV [593-593] 593 40 +COV [594-594] 594 28 +COV [595-595] 595 26 +COV [596-596] 596 22 +COV [597-597] 597 34 +COV [598-598] 598 35 +COV [599-599] 599 29 +COV [600-600] 600 23 +COV [601-601] 601 34 +COV [602-602] 602 19 +COV [603-603] 603 25 +COV [604-604] 604 23 +COV [605-605] 605 33 +COV [606-606] 606 27 +COV [607-607] 607 31 +COV [608-608] 608 23 +COV [609-609] 609 29 +COV [610-610] 610 34 +COV [611-611] 611 36 +COV [612-612] 612 32 +COV [613-613] 613 27 +COV [614-614] 614 26 +COV [615-615] 615 31 +COV [616-616] 616 27 +COV [617-617] 617 36 +COV [618-618] 618 15 +COV [619-619] 619 36 +COV [620-620] 620 20 +COV [621-621] 621 30 +COV [622-622] 622 30 +COV [623-623] 623 40 +COV [624-624] 624 29 +COV [625-625] 625 24 +COV [626-626] 626 40 +COV [627-627] 627 36 +COV [628-628] 628 24 +COV [629-629] 629 20 +COV [630-630] 630 18 +COV [631-631] 631 28 +COV [632-632] 632 28 +COV [633-633] 633 23 +COV [634-634] 634 24 +COV [635-635] 635 21 +COV [636-636] 636 18 +COV [637-637] 637 22 +COV [638-638] 638 24 +COV [639-639] 639 24 +COV [640-640] 640 19 +COV [641-641] 641 26 +COV [642-642] 642 16 +COV [643-643] 643 24 +COV [644-644] 644 22 +COV [645-645] 645 19 +COV [646-646] 646 24 +COV [647-647] 647 27 +COV [648-648] 648 22 +COV [649-649] 649 15 +COV [650-650] 650 30 +COV [651-651] 651 32 +COV [652-652] 652 21 +COV [653-653] 653 25 +COV [654-654] 654 24 +COV [655-655] 655 26 +COV [656-656] 656 33 +COV [657-657] 657 20 +COV [658-658] 658 28 +COV [659-659] 659 32 +COV [660-660] 660 28 +COV [661-661] 661 29 +COV [662-662] 662 22 +COV [663-663] 663 26 +COV [664-664] 664 18 +COV [665-665] 665 28 +COV [666-666] 666 24 +COV [667-667] 667 30 +COV [668-668] 668 24 +COV [669-669] 669 24 +COV [670-670] 670 21 +COV [671-671] 671 31 +COV [672-672] 672 22 +COV [673-673] 673 24 +COV [674-674] 674 27 +COV [675-675] 675 28 +COV [676-676] 676 30 +COV [677-677] 677 34 +COV [678-678] 678 43 +COV [679-679] 679 31 +COV [680-680] 680 26 +COV [681-681] 681 26 +COV [682-682] 682 24 +COV [683-683] 683 25 +COV [684-684] 684 21 +COV [685-685] 685 16 +COV [686-686] 686 30 +COV [687-687] 687 23 +COV [688-688] 688 30 +COV [689-689] 689 19 +COV [690-690] 690 22 +COV [691-691] 691 30 +COV [692-692] 692 30 +COV [693-693] 693 23 +COV [694-694] 694 39 +COV [695-695] 695 15 +COV [696-696] 696 20 +COV [697-697] 697 29 +COV [698-698] 698 34 +COV [699-699] 699 18 +COV [700-700] 700 31 +COV [701-701] 701 23 +COV [702-702] 702 25 +COV [703-703] 703 36 +COV [704-704] 704 34 +COV [705-705] 705 35 +COV [706-706] 706 29 +COV [707-707] 707 31 +COV [708-708] 708 22 +COV [709-709] 709 22 +COV [710-710] 710 26 +COV [711-711] 711 29 +COV [712-712] 712 34 +COV [713-713] 713 33 +COV [714-714] 714 20 +COV [715-715] 715 23 +COV [716-716] 716 24 +COV [717-717] 717 25 +COV [718-718] 718 24 +COV [719-719] 719 28 +COV [720-720] 720 26 +COV [721-721] 721 24 +COV [722-722] 722 19 +COV [723-723] 723 21 +COV [724-724] 724 28 +COV [725-725] 725 23 +COV [726-726] 726 29 +COV [727-727] 727 28 +COV [728-728] 728 31 +COV [729-729] 729 15 +COV [730-730] 730 25 +COV [731-731] 731 26 +COV [732-732] 732 17 +COV [733-733] 733 20 +COV [734-734] 734 15 +COV [735-735] 735 23 +COV [736-736] 736 14 +COV [737-737] 737 20 +COV [738-738] 738 21 +COV [739-739] 739 24 +COV [740-740] 740 20 +COV [741-741] 741 24 +COV [742-742] 742 24 +COV [743-743] 743 23 +COV [744-744] 744 18 +COV [745-745] 745 18 +COV [746-746] 746 14 +COV [747-747] 747 13 +COV [748-748] 748 20 +COV [749-749] 749 37 +COV [750-750] 750 22 +COV [751-751] 751 25 +COV [752-752] 752 21 +COV [753-753] 753 16 +COV [754-754] 754 24 +COV [755-755] 755 20 +COV [756-756] 756 20 +COV [757-757] 757 29 +COV [758-758] 758 16 +COV [759-759] 759 15 +COV [760-760] 760 16 +COV [761-761] 761 21 +COV [762-762] 762 22 +COV [763-763] 763 24 +COV [764-764] 764 17 +COV [765-765] 765 15 +COV [766-766] 766 21 +COV [767-767] 767 27 +COV [768-768] 768 16 +COV [769-769] 769 29 +COV [770-770] 770 27 +COV [771-771] 771 17 +COV [772-772] 772 16 +COV [773-773] 773 23 +COV [774-774] 774 28 +COV [775-775] 775 16 +COV [776-776] 776 24 +COV [777-777] 777 16 +COV [778-778] 778 20 +COV [779-779] 779 27 +COV [780-780] 780 18 +COV [781-781] 781 27 +COV [782-782] 782 18 +COV [783-783] 783 23 +COV [784-784] 784 12 +COV [785-785] 785 33 +COV [786-786] 786 20 +COV [787-787] 787 22 +COV [788-788] 788 15 +COV [789-789] 789 18 +COV [790-790] 790 19 +COV [791-791] 791 19 +COV [792-792] 792 31 +COV [793-793] 793 17 +COV [794-794] 794 16 +COV [795-795] 795 17 +COV [796-796] 796 16 +COV [797-797] 797 18 +COV [798-798] 798 19 +COV [799-799] 799 22 +COV [800-800] 800 12 +COV [801-801] 801 19 +COV [802-802] 802 22 +COV [803-803] 803 15 +COV [804-804] 804 18 +COV [805-805] 805 20 +COV [806-806] 806 14 +COV [807-807] 807 20 +COV [808-808] 808 22 +COV [809-809] 809 16 +COV [810-810] 810 23 +COV [811-811] 811 24 +COV [812-812] 812 27 +COV [813-813] 813 15 +COV [814-814] 814 18 +COV [815-815] 815 28 +COV [816-816] 816 22 +COV [817-817] 817 32 +COV [818-818] 818 14 +COV [819-819] 819 21 +COV [820-820] 820 18 +COV [821-821] 821 21 +COV [822-822] 822 17 +COV [823-823] 823 18 +COV [824-824] 824 17 +COV [825-825] 825 21 +COV [826-826] 826 11 +COV [827-827] 827 14 +COV [828-828] 828 15 +COV [829-829] 829 18 +COV [830-830] 830 18 +COV [831-831] 831 27 +COV [832-832] 832 21 +COV [833-833] 833 24 +COV [834-834] 834 25 +COV [835-835] 835 19 +COV [836-836] 836 27 +COV [837-837] 837 19 +COV [838-838] 838 24 +COV [839-839] 839 16 +COV [840-840] 840 17 +COV [841-841] 841 12 +COV [842-842] 842 22 +COV [843-843] 843 18 +COV [844-844] 844 11 +COV [845-845] 845 29 +COV [846-846] 846 22 +COV [847-847] 847 18 +COV [848-848] 848 25 +COV [849-849] 849 19 +COV [850-850] 850 13 +COV [851-851] 851 18 +COV [852-852] 852 21 +COV [853-853] 853 19 +COV [854-854] 854 19 +COV [855-855] 855 19 +COV [856-856] 856 17 +COV [857-857] 857 21 +COV [858-858] 858 21 +COV [859-859] 859 15 +COV [860-860] 860 28 +COV [861-861] 861 14 +COV [862-862] 862 20 +COV [863-863] 863 10 +COV [864-864] 864 15 +COV [865-865] 865 20 +COV [866-866] 866 18 +COV [867-867] 867 18 +COV [868-868] 868 17 +COV [869-869] 869 13 +COV [870-870] 870 19 +COV [871-871] 871 14 +COV [872-872] 872 19 +COV [873-873] 873 14 +COV [874-874] 874 13 +COV [875-875] 875 20 +COV [876-876] 876 28 +COV [877-877] 877 21 +COV [878-878] 878 14 +COV [879-879] 879 21 +COV [880-880] 880 22 +COV [881-881] 881 16 +COV [882-882] 882 18 +COV [883-883] 883 24 +COV [884-884] 884 22 +COV [885-885] 885 22 +COV [886-886] 886 23 +COV [887-887] 887 19 +COV [888-888] 888 16 +COV [889-889] 889 11 +COV [890-890] 890 18 +COV [891-891] 891 18 +COV [892-892] 892 16 +COV [893-893] 893 20 +COV [894-894] 894 18 +COV [895-895] 895 13 +COV [896-896] 896 25 +COV [897-897] 897 15 +COV [898-898] 898 22 +COV [899-899] 899 21 +COV [900-900] 900 13 +COV [901-901] 901 16 +COV [902-902] 902 16 +COV [903-903] 903 22 +COV [904-904] 904 19 +COV [905-905] 905 24 +COV [906-906] 906 26 +COV [907-907] 907 20 +COV [908-908] 908 14 +COV [909-909] 909 15 +COV [910-910] 910 19 +COV [911-911] 911 19 +COV [912-912] 912 19 +COV [913-913] 913 17 +COV [914-914] 914 21 +COV [915-915] 915 24 +COV [916-916] 916 6 +COV [917-917] 917 21 +COV [918-918] 918 10 +COV [919-919] 919 13 +COV [920-920] 920 25 +COV [921-921] 921 12 +COV [922-922] 922 12 +COV [923-923] 923 13 +COV [924-924] 924 21 +COV [925-925] 925 13 +COV [926-926] 926 24 +COV [927-927] 927 13 +COV [928-928] 928 9 +COV [929-929] 929 17 +COV [930-930] 930 7 +COV [931-931] 931 9 +COV [932-932] 932 19 +COV [933-933] 933 16 +COV [934-934] 934 21 +COV [935-935] 935 17 +COV [936-936] 936 14 +COV [937-937] 937 13 +COV [938-938] 938 17 +COV [939-939] 939 14 +COV [940-940] 940 10 +COV [941-941] 941 20 +COV [942-942] 942 19 +COV [943-943] 943 17 +COV [944-944] 944 16 +COV [945-945] 945 13 +COV [946-946] 946 14 +COV [947-947] 947 17 +COV [948-948] 948 11 +COV [949-949] 949 12 +COV [950-950] 950 14 +COV [951-951] 951 11 +COV [952-952] 952 14 +COV [953-953] 953 11 +COV [954-954] 954 14 +COV [955-955] 955 18 +COV [956-956] 956 18 +COV [957-957] 957 17 +COV [958-958] 958 13 +COV [959-959] 959 17 +COV [960-960] 960 19 +COV [961-961] 961 14 +COV [962-962] 962 19 +COV [963-963] 963 7 +COV [964-964] 964 12 +COV [965-965] 965 13 +COV [966-966] 966 13 +COV [967-967] 967 15 +COV [968-968] 968 21 +COV [969-969] 969 16 +COV [970-970] 970 18 +COV [971-971] 971 4 +COV [972-972] 972 18 +COV [973-973] 973 14 +COV [974-974] 974 17 +COV [975-975] 975 17 +COV [976-976] 976 10 +COV [977-977] 977 11 +COV [978-978] 978 16 +COV [979-979] 979 13 +COV [980-980] 980 14 +COV [981-981] 981 27 +COV [982-982] 982 18 +COV [983-983] 983 20 +COV [984-984] 984 15 +COV [985-985] 985 18 +COV [986-986] 986 14 +COV [987-987] 987 15 +COV [988-988] 988 19 +COV [989-989] 989 22 +COV [990-990] 990 12 +COV [991-991] 991 11 +COV [992-992] 992 14 +COV [993-993] 993 20 +COV [994-994] 994 11 +COV [995-995] 995 11 +COV [996-996] 996 15 +COV [997-997] 997 17 +COV [998-998] 998 6 +COV [999-999] 999 11 +COV [1000-1000] 1000 16 +COV [1000<] 1000 29066 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 0.006 0.000 0.002 0.002 0.005 0.005 +GCD 1.0 0.007 0.007 0.007 0.007 0.007 0.007 +GCD 2.0 0.012 0.002 0.002 0.002 0.005 0.007 +GCD 3.0 0.014 0.005 0.005 0.007 0.020 0.020 +GCD 4.0 0.016 0.002 0.002 0.002 0.002 0.002 +GCD 6.0 0.020 0.002 0.002 0.002 0.002 0.002 +GCD 8.0 0.022 0.002 0.002 0.002 0.002 0.002 +GCD 10.0 0.024 0.002 0.002 0.002 0.007 0.007 +GCD 11.0 0.025 0.005 0.005 0.005 0.005 0.005 +GCD 11.6 0.025 0.047 0.047 0.047 0.047 0.047 +GCD 12.0 0.031 0.002 0.002 0.002 0.005 0.007 +GCD 13.0 0.032 0.005 0.005 0.005 0.005 0.005 +GCD 14.0 0.033 0.002 0.002 0.002 0.005 0.005 +GCD 15.0 0.035 0.010 0.010 0.010 0.017 0.017 +GCD 16.0 0.039 0.002 0.002 0.005 0.005 0.005 +GCD 17.0 0.041 0.007 0.007 0.007 0.007 0.007 +GCD 18.0 0.045 0.002 0.002 0.005 0.010 0.010 +GCD 19.0 0.048 0.002 0.002 0.002 0.005 0.012 +GCD 20.0 0.052 0.002 0.002 0.002 0.002 0.007 +GCD 21.0 0.054 0.002 0.002 0.005 0.007 0.007 +GCD 22.0 0.062 0.002 0.002 0.005 0.007 0.010 +GCD 23.0 0.068 0.002 0.005 0.005 0.007 0.017 +GCD 24.0 0.080 0.002 0.002 0.002 0.002 0.005 +GCD 25.0 0.089 0.002 0.005 0.007 0.010 0.012 +GCD 26.0 0.105 0.002 0.002 0.002 0.005 0.007 +GCD 27.0 0.112 0.007 0.007 0.007 0.419 0.691 +GCD 28.0 0.124 0.002 0.002 0.007 0.020 0.093 +GCD 29.0 0.134 0.005 0.005 0.007 0.010 0.012 +GCD 30.0 0.149 0.002 0.002 0.005 0.012 0.022 +GCD 31.0 0.171 0.005 0.005 0.010 0.120 0.255 +GCD 32.0 0.225 0.002 0.005 0.120 0.228 0.262 +GCD 33.0 0.344 0.012 0.142 0.225 0.262 0.292 +GCD 34.0 0.721 0.022 0.194 0.240 0.272 0.296 +GCD 35.0 1.791 0.167 0.223 0.255 0.282 0.304 +GCD 36.0 4.174 0.194 0.235 0.265 0.292 0.316 +GCD 37.0 8.546 0.208 0.245 0.277 0.304 0.331 +GCD 38.0 15.513 0.218 0.255 0.287 0.316 0.345 +GCD 39.0 24.259 0.228 0.267 0.299 0.328 0.358 +GCD 40.0 34.137 0.238 0.277 0.311 0.343 0.372 +GCD 41.0 44.039 0.247 0.289 0.323 0.355 0.387 +GCD 42.0 53.383 0.260 0.299 0.336 0.368 0.402 +GCD 43.0 61.865 0.274 0.314 0.348 0.382 0.417 +GCD 44.0 69.571 0.289 0.326 0.363 0.394 0.431 +GCD 45.0 76.519 0.304 0.341 0.375 0.409 0.446 +GCD 46.0 82.424 0.316 0.353 0.387 0.424 0.468 +GCD 47.0 87.213 0.326 0.365 0.402 0.441 0.488 +GCD 48.0 90.973 0.338 0.375 0.409 0.451 0.505 +GCD 49.0 93.667 0.353 0.390 0.424 0.463 0.517 +GCD 50.0 95.910 0.345 0.392 0.429 0.470 0.524 +GCD 51.0 97.447 0.365 0.404 0.439 0.480 0.537 +GCD 52.0 98.546 0.365 0.402 0.441 0.483 0.537 +GCD 53.0 99.252 0.370 0.412 0.446 0.485 0.539 +GCD 54.0 99.662 0.365 0.412 0.448 0.492 0.561 +GCD 55.0 99.840 0.387 0.426 0.461 0.502 0.573 +GCD 56.0 99.930 0.020 0.402 0.446 0.485 0.554 +GCD 57.0 99.966 0.279 0.387 0.426 0.492 0.581 +GCD 58.0 99.982 0.002 0.005 0.470 0.980 1.063 +GCD 59.0 99.988 0.397 0.461 0.475 0.987 1.333 +GCD 60.0 99.989 0.002 0.002 0.002 0.211 0.211 +GCD 61.0 99.992 0.005 0.005 0.485 0.502 0.527 +GCD 62.0 99.995 0.002 0.002 0.002 0.434 0.434 +GCD 63.0 99.997 0.892 0.892 1.105 2.472 2.472 +GCD 64.0 99.998 1.034 1.034 1.034 1.098 1.098 +GCD 65.0 99.999 12.870 12.870 12.870 12.870 12.870 +GCD 66.0 100.000 0.002 0.002 0.002 0.002 0.002 diff --git a/src/multiqc/test_data2/b.txt b/src/multiqc/test_data2/b.txt new file mode 100644 index 00000000..5df6122a --- /dev/null +++ b/src/multiqc/test_data2/b.txt @@ -0,0 +1,1505 @@ +# This file was produced by samtools stats (1.3+htslib-1.3) and can be plotted using plot-bamstats +# This file contains statistics for all reads. +# The command line was: stats mapped/b.bam +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK ee6a9cbf ecd7f501 51869fe3 +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 18576178 +SN filtered sequences: 0 +SN sequences: 18576178 +SN is sorted: 1 +SN 1st fragments: 18576178 +SN last fragments: 0 +SN reads mapped: 18166869 +SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped +SN reads unmapped: 409309 +SN reads properly paired: 0 # proper-pair bit set +SN reads paired: 0 # paired-end technology bit set +SN reads duplicated: 1674761 # PCR or optical duplicate bit set +SN reads MQ0: 3360997 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 0 +SN total length: 927580112 # ignores clipping +SN bases mapped: 907135249 # ignores clipping +SN bases mapped (cigar): 907135242 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 83676902 +SN mismatches: 4228623 # from NM fields +SN error rate: 4.661513e-03 # mismatches / bases mapped (cigar) +SN average length: 49 +SN maximum length: 50 +SN average quality: 37.1 +SN insert size average: 0.0 +SN insert size standard deviation: 0.0 +SN inward oriented pairs: 0 +SN outward oriented pairs: 0 +SN pairs with other orientation: 0 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 43365 0 0 0 0 0 0 0 0 0 0 0 0 316667 0 0 0 0 0 0 145075 0 0 0 0 1091864 0 0 0 0 0 16979207 0 0 0 0 0 0 0 0 +FFQ 2 0 0 2631 0 0 0 0 0 0 0 0 0 0 0 0 226851 0 0 0 0 0 0 117493 0 0 0 0 1044416 0 0 0 0 0 17184787 0 0 0 0 0 0 0 0 +FFQ 3 0 0 2642 0 0 0 0 0 0 0 0 0 0 0 0 150819 0 0 0 0 0 0 121280 0 0 0 0 1043537 0 0 0 0 0 17257900 0 0 0 0 0 0 0 0 +FFQ 4 0 0 2652 0 0 0 0 0 0 0 0 0 0 0 0 118535 0 0 0 0 0 0 32499 0 0 0 0 385005 0 0 0 0 0 1401276 0 0 0 16636211 0 0 0 0 +FFQ 5 0 0 2664 0 0 0 0 0 0 0 0 0 0 0 0 149178 0 0 0 0 0 0 33908 0 0 0 0 445421 0 0 0 0 0 1485286 0 0 0 16459721 0 0 0 0 +FFQ 6 0 0 2681 0 0 0 3389 0 0 0 0 0 0 0 0 146379 0 0 0 0 0 0 40576 0 0 0 0 438297 0 0 0 0 0 1478793 0 0 0 16466063 0 0 0 0 +FFQ 7 0 0 2719 0 0 0 4001 0 0 0 0 0 0 0 0 156176 0 0 0 0 0 0 40734 0 0 0 0 447501 0 0 0 0 0 1488746 0 0 0 16436301 0 0 0 0 +FFQ 8 0 0 2759 0 0 0 3952 0 0 0 0 0 0 0 0 156255 0 0 0 0 0 0 40576 0 0 0 0 446114 0 0 0 0 0 1486214 0 0 0 16440308 0 0 0 0 +FFQ 9 0 0 2822 0 0 0 4334 0 0 0 0 0 0 0 0 159441 0 0 0 0 0 0 40893 0 0 0 0 448307 0 0 0 0 0 1489379 0 0 0 16431002 0 0 0 0 +FFQ 10 0 0 2897 0 0 0 3878 0 0 0 0 0 0 0 0 153155 0 0 0 0 0 0 41101 0 0 0 0 447304 0 0 0 0 0 1484804 0 0 0 16443039 0 0 0 0 +FFQ 11 0 0 2982 0 0 0 4003 0 0 0 0 0 0 0 0 151436 0 0 0 0 0 0 42075 0 0 0 0 447020 0 0 0 0 0 1486604 0 0 0 16442058 0 0 0 0 +FFQ 12 0 0 3101 0 0 0 4242 0 0 0 0 0 0 0 0 155412 0 0 0 0 0 0 42911 0 0 0 0 449860 0 0 0 0 0 1491835 0 0 0 16428817 0 0 0 0 +FFQ 13 0 0 3240 0 0 0 4244 0 0 0 0 0 0 0 0 154472 0 0 0 0 0 0 44402 0 0 0 0 451953 0 0 0 0 0 1495686 0 0 0 16422181 0 0 0 0 +FFQ 14 0 0 3399 0 0 0 4705 0 0 0 0 0 0 0 0 158387 0 0 0 0 0 0 44832 0 0 0 0 452013 0 0 0 0 0 1422645 0 0 0 5009192 0 0 11481005 0 +FFQ 15 0 0 3574 0 0 0 4943 0 0 0 0 0 0 0 0 162629 0 0 0 0 0 0 45939 0 0 0 0 455281 0 0 0 0 0 1429083 0 0 0 5018020 0 0 11456709 0 +FFQ 16 0 0 3789 0 0 0 5204 0 0 0 0 0 0 0 0 164703 0 0 0 0 0 0 47268 0 0 0 0 459688 0 0 0 0 0 1438944 0 0 0 5025956 0 0 11430626 0 +FFQ 17 0 0 4054 0 0 0 5500 0 0 0 0 0 0 0 0 161723 0 0 0 0 0 0 49772 0 0 0 0 462909 0 0 0 0 0 1448410 0 0 0 5050556 0 0 11393254 0 +FFQ 18 0 0 4376 0 0 0 6040 0 0 0 0 0 0 0 0 163399 0 0 0 0 0 0 51435 0 0 0 0 456360 0 0 0 0 0 1447415 0 0 0 5057035 0 0 11390118 0 +FFQ 19 0 0 4895 0 0 0 6152 0 0 0 0 0 0 0 0 164137 0 0 0 0 0 0 54177 0 0 0 0 459431 0 0 0 0 0 1452212 0 0 0 4724623 0 0 11710551 0 +FFQ 20 0 0 5278 0 0 0 6748 0 0 0 0 0 0 0 0 161669 0 0 0 0 0 0 57142 0 0 0 0 456404 0 0 0 0 0 1454134 0 0 0 4771944 0 0 11662859 0 +FFQ 21 0 0 6041 0 0 0 7654 0 0 0 0 0 0 0 0 160998 0 0 0 0 0 0 61704 0 0 0 0 453274 0 0 0 0 0 1456206 0 0 0 4832585 0 0 11597716 0 +FFQ 22 0 0 7025 0 0 0 8936 0 0 0 0 0 0 0 0 164004 0 0 0 0 0 0 69132 0 0 0 0 455154 0 0 0 0 0 1463092 0 0 0 4900894 0 0 11507941 0 +FFQ 23 0 0 8438 0 0 0 10369 0 0 0 0 0 0 0 0 166619 0 0 0 0 0 0 76781 0 0 0 0 451917 0 0 0 0 0 1473087 0 0 0 4980302 0 0 11408665 0 +FFQ 24 0 0 10137 0 0 0 12451 0 0 0 0 0 0 0 0 167661 0 0 0 0 0 0 86418 0 0 0 0 446268 0 0 0 0 0 1481414 0 0 0 4969528 0 0 11402301 0 +FFQ 25 0 0 12428 0 0 0 14892 0 0 0 0 0 0 0 0 173631 0 0 0 0 0 0 99776 0 0 0 0 442524 0 0 0 0 0 1493761 0 0 0 5016661 0 0 11322505 0 +FFQ 26 0 0 15335 0 0 0 25515 0 0 0 0 0 0 0 0 204814 0 0 0 0 0 0 111835 0 0 0 0 427338 0 0 0 0 0 1483190 0 0 0 5032460 0 0 11275691 0 +FFQ 27 0 0 18183 0 0 0 31691 0 0 0 0 0 0 0 0 211885 0 0 0 0 0 0 125826 0 0 0 0 425529 0 0 0 0 0 1495988 0 0 0 5036475 0 0 11230601 0 +FFQ 28 0 0 21234 0 0 0 38567 0 0 0 0 0 0 0 0 212153 0 0 0 0 0 0 138492 0 0 0 0 416049 0 0 0 0 0 1506817 0 0 0 5050848 0 0 11192018 0 +FFQ 29 0 0 24469 0 0 0 45921 0 0 0 0 0 0 0 0 208586 0 0 0 0 0 0 150099 0 0 0 0 406972 0 0 0 0 0 1510396 0 0 0 5061017 0 0 11168718 0 +FFQ 30 0 0 27790 0 0 0 54131 0 0 0 0 0 0 0 0 202787 0 0 0 0 0 0 159734 0 0 0 0 401982 0 0 0 0 0 1517830 0 0 0 5076275 0 0 11135649 0 +FFQ 31 0 0 31389 0 0 0 64745 0 0 0 0 0 0 0 0 197260 0 0 0 0 0 0 167040 0 0 0 0 398914 0 0 0 0 0 1522211 0 0 0 5081933 0 0 11112662 0 +FFQ 32 0 0 35265 0 0 0 73249 0 0 0 0 0 0 0 0 190526 0 0 0 0 0 0 171610 0 0 0 0 397631 0 0 0 0 0 1530272 0 0 0 5089484 0 0 11088092 0 +FFQ 33 0 0 39568 0 0 0 82173 0 0 0 0 0 0 0 0 181514 0 0 0 0 0 0 175016 0 0 0 0 397113 0 0 0 0 0 1534492 0 0 0 5098856 0 0 11067375 0 +FFQ 34 0 0 44025 0 0 0 92751 0 0 0 0 0 0 0 0 177863 0 0 0 0 0 0 177915 0 0 0 0 398138 0 0 0 0 0 1535653 0 0 0 5098622 0 0 11051118 0 +FFQ 35 0 0 49081 0 0 0 96325 0 0 0 0 0 0 0 0 171633 0 0 0 0 0 0 181304 0 0 0 0 399581 0 0 0 0 0 1542546 0 0 0 5100609 0 0 11034967 0 +FFQ 36 0 0 54552 0 0 0 101878 0 0 0 0 0 0 0 0 166948 0 0 0 0 0 0 185932 0 0 0 0 399740 0 0 0 0 0 1551353 0 0 0 5114688 0 0 11000912 0 +FFQ 37 0 0 60308 0 0 0 104644 0 0 0 0 0 0 0 0 164138 0 0 0 0 0 0 189071 0 0 0 0 399564 0 0 0 0 0 1556486 0 0 0 5126556 0 0 10975200 0 +FFQ 38 0 0 66655 0 0 0 108344 0 0 0 0 0 0 0 0 163526 0 0 0 0 0 0 194698 0 0 0 0 402462 0 0 0 0 0 1564062 0 0 0 5137844 0 0 10938345 0 +FFQ 39 0 0 74040 0 0 0 109236 0 0 0 0 0 0 0 0 163901 0 0 0 0 0 0 199818 0 0 0 0 402198 0 0 0 0 0 1573785 0 0 0 5152707 0 0 10900208 0 +FFQ 40 0 0 82117 0 0 0 113084 0 0 0 0 0 0 0 0 165347 0 0 0 0 0 0 205720 0 0 0 0 402517 0 0 0 0 0 1577961 0 0 0 5155840 0 0 10873211 0 +FFQ 41 0 0 91108 0 0 0 107424 0 0 0 0 0 0 0 0 165874 0 0 0 0 0 0 212167 0 0 0 0 403439 0 0 0 0 0 1590477 0 0 0 5168941 0 0 10836084 0 +FFQ 42 0 0 102306 0 0 0 106524 0 0 0 0 0 0 0 0 163227 0 0 0 0 0 0 217731 0 0 0 0 403568 0 0 0 0 0 1594692 0 0 0 5188518 0 0 10798521 0 +FFQ 43 0 0 113461 0 0 0 105566 0 0 0 0 0 0 0 0 163762 0 0 0 0 0 0 226845 0 0 0 0 402623 0 0 0 0 0 1602299 0 0 0 5194713 0 0 10765448 0 +FFQ 44 0 0 127992 0 0 0 103292 0 0 0 0 0 0 0 0 161844 0 0 0 0 0 0 234717 0 0 0 0 401632 0 0 0 0 0 1618498 0 0 0 5206467 0 0 10720171 0 +FFQ 45 0 0 146743 0 0 0 99382 0 0 0 0 0 0 0 0 157848 0 0 0 0 0 0 242460 0 0 0 0 401753 0 0 0 0 0 1630019 0 0 0 5184900 0 0 10711332 0 +FFQ 46 0 0 171139 0 0 0 94094 0 0 0 0 0 0 0 0 154818 0 0 0 0 0 0 248889 0 0 0 0 401705 0 0 0 0 0 1637377 0 0 0 5203803 0 0 10661983 0 +FFQ 47 0 0 200079 0 0 0 86401 0 0 0 0 0 0 0 0 149983 0 0 0 0 0 0 252443 0 0 0 0 400899 0 0 0 0 0 1643053 0 0 0 5213972 0 0 10610153 0 +FFQ 48 0 0 240223 0 0 0 76248 0 0 0 0 0 0 0 0 143739 0 0 0 0 0 0 255275 0 0 0 0 401446 0 0 0 0 0 1652184 0 0 0 5217727 0 0 10481218 0 +FFQ 49 0 0 290803 0 0 0 54802 0 0 0 0 0 0 0 0 131779 0 0 0 0 0 0 247788 0 0 0 0 392435 0 0 0 0 0 1629666 0 0 0 5126595 0 0 10156850 0 +FFQ 50 0 0 363909 0 0 0 25352 0 0 0 0 0 0 0 0 126109 0 0 0 0 0 0 245269 0 0 0 0 391546 0 0 0 0 0 1648220 0 0 0 5162006 0 0 10068307 0 +FFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# Last Fragment Qualitites. Use `grep ^LFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 0.75 1080 +GCF 1.76 1554 +GCF 2.26 1567 +GCF 3.02 1566 +GCF 3.77 2850 +GCF 4.77 2881 +GCF 5.78 4731 +GCF 6.28 4791 +GCF 7.04 4792 +GCF 7.79 8136 +GCF 8.29 8231 +GCF 9.05 8233 +GCF 9.80 14137 +GCF 10.30 14252 +GCF 10.80 14293 +GCF 11.31 14294 +GCF 11.81 24969 +GCF 12.31 25354 +GCF 13.07 25452 +GCF 13.82 43286 +GCF 14.32 43288 +GCF 14.82 43868 +GCF 15.33 43887 +GCF 15.83 72345 +GCF 16.33 72346 +GCF 16.83 73323 +GCF 17.34 73346 +GCF 17.84 115892 +GCF 18.34 115893 +GCF 18.84 117007 +GCF 19.35 117404 +GCF 19.85 176022 +GCF 20.35 176024 +GCF 20.85 177820 +GCF 21.36 178297 +GCF 21.86 256493 +GCF 22.36 256500 +GCF 22.86 258736 +GCF 23.37 259378 +GCF 23.87 358005 +GCF 24.37 358006 +GCF 24.87 361025 +GCF 25.38 362008 +GCF 25.88 484259 +GCF 26.38 484258 +GCF 26.88 487623 +GCF 27.39 487628 +GCF 27.89 641238 +GCF 28.39 641467 +GCF 28.89 641483 +GCF 29.40 645895 +GCF 29.90 848565 +GCF 30.40 848762 +GCF 30.90 848764 +GCF 31.41 854323 +GCF 31.91 1093044 +GCF 32.66 1093138 +GCF 33.42 1096936 +GCF 33.92 1331028 +GCF 34.42 1331031 +GCF 34.92 1331203 +GCF 35.43 1335750 +GCF 35.93 1505123 +GCF 36.43 1505127 +GCF 36.93 1505175 +GCF 37.44 1508624 +GCF 37.94 1493366 +GCF 38.44 1493657 +GCF 38.94 1493818 +GCF 39.45 1494636 +GCF 39.95 1420236 +GCF 40.45 1420377 +GCF 40.95 1420370 +GCF 41.46 1419738 +GCF 41.96 1313182 +GCF 42.46 1313001 +GCF 42.96 1312999 +GCF 43.47 1313043 +GCF 43.97 1231538 +GCF 44.47 1231204 +GCF 44.97 1231192 +GCF 45.48 1231260 +GCF 45.98 1148968 +GCF 46.48 1148953 +GCF 46.98 1148367 +GCF 47.49 1148340 +GCF 47.99 1059806 +GCF 48.49 1059813 +GCF 49.25 1058887 +GCF 50.25 954205 +GCF 51.01 953262 +GCF 51.51 953251 +GCF 52.01 808649 +GCF 52.51 808641 +GCF 53.02 807799 +GCF 53.52 807784 +GCF 54.02 649395 +GCF 54.52 649184 +GCF 55.03 649178 +GCF 55.53 648304 +GCF 56.03 490867 +GCF 56.53 490638 +GCF 57.04 490632 +GCF 57.54 489794 +GCF 58.04 359200 +GCF 58.54 355526 +GCF 59.05 355524 +GCF 59.55 355031 +GCF 60.05 247759 +GCF 60.55 244574 +GCF 61.06 244459 +GCF 61.56 243954 +GCF 62.06 164265 +GCF 62.56 162114 +GCF 63.07 162022 +GCF 63.57 162018 +GCF 64.07 103863 +GCF 64.57 102491 +GCF 65.08 102446 +GCF 65.58 102445 +GCF 66.08 64175 +GCF 66.83 63383 +GCF 67.59 63356 +GCF 68.09 37977 +GCF 68.59 37240 +GCF 69.10 37235 +GCF 69.60 37220 +GCF 70.10 22861 +GCF 70.60 22555 +GCF 71.11 22552 +GCF 71.61 22533 +GCF 72.11 14370 +GCF 72.61 14369 +GCF 73.37 14229 +GCF 74.12 9740 +GCF 74.62 9736 +GCF 75.13 9636 +GCF 75.63 9635 +GCF 76.13 6719 +GCF 76.63 6701 +GCF 77.14 6630 +GCF 77.64 6632 +GCF 78.14 4609 +GCF 78.64 4605 +GCF 79.40 4595 +GCF 80.15 3154 +GCF 80.65 3156 +GCF 81.41 3128 +GCF 82.16 2097 +GCF 82.66 2096 +GCF 83.42 2082 +GCF 84.17 1523 +GCF 84.67 1522 +GCF 85.43 1519 +GCF 86.68 822 +GCF 87.69 821 +GCF 88.44 544 +GCF 89.20 543 +GCF 89.70 535 +GCF 90.70 303 +GCF 91.71 304 +GCF 92.71 169 +GCF 93.72 167 +GCF 94.97 74 +GCF 96.98 47 +GCF 98.99 19 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] +GCC 1 29.99 19.73 19.50 30.79 0.22 0.00 +GCC 2 29.97 19.73 19.48 30.83 0.00 0.00 +GCC 3 29.53 20.19 19.82 30.46 0.00 0.00 +GCC 4 29.46 20.23 19.95 30.36 0.00 0.00 +GCC 5 29.50 20.16 19.89 30.46 0.00 0.00 +GCC 6 29.32 20.45 20.06 30.17 0.00 0.00 +GCC 7 29.42 20.32 19.92 30.34 0.00 0.00 +GCC 8 29.44 20.26 19.90 30.41 0.00 0.00 +GCC 9 29.45 20.23 19.91 30.41 0.00 0.00 +GCC 10 29.35 20.34 19.98 30.33 0.00 0.00 +GCC 11 29.39 20.25 19.92 30.43 0.00 0.00 +GCC 12 29.40 20.32 19.93 30.35 0.00 0.00 +GCC 13 29.45 20.28 19.86 30.42 0.00 0.00 +GCC 14 29.41 20.26 19.85 30.48 0.00 0.00 +GCC 15 29.40 20.31 19.91 30.38 0.00 0.00 +GCC 16 29.24 20.40 20.03 30.33 0.00 0.00 +GCC 17 29.29 20.29 20.02 30.39 0.00 0.00 +GCC 18 29.20 20.38 20.15 30.27 0.00 0.00 +GCC 19 29.21 20.39 20.14 30.25 0.00 0.00 +GCC 20 29.21 20.36 20.21 30.23 0.00 0.00 +GCC 21 29.18 20.39 20.26 30.17 0.00 0.00 +GCC 22 29.16 20.41 20.19 30.24 0.00 0.00 +GCC 23 29.12 20.41 20.23 30.24 0.00 0.00 +GCC 24 29.12 20.47 20.20 30.21 0.00 0.00 +GCC 25 29.13 20.47 20.20 30.20 0.00 0.00 +GCC 26 29.11 20.47 20.26 30.16 0.00 0.00 +GCC 27 29.07 20.49 20.26 30.19 0.00 0.00 +GCC 28 28.99 20.56 20.38 30.07 0.00 0.00 +GCC 29 29.09 20.48 20.30 30.13 0.00 0.00 +GCC 30 29.06 20.49 20.37 30.08 0.00 0.00 +GCC 31 29.00 20.58 20.36 30.06 0.00 0.00 +GCC 32 29.01 20.56 20.34 30.09 0.00 0.00 +GCC 33 29.00 20.59 20.31 30.10 0.00 0.00 +GCC 34 28.97 20.65 20.30 30.09 0.00 0.00 +GCC 35 29.00 20.59 20.26 30.14 0.00 0.00 +GCC 36 28.96 20.66 20.30 30.08 0.00 0.00 +GCC 37 28.98 20.73 20.26 30.03 0.00 0.00 +GCC 38 28.96 20.75 20.30 29.99 0.00 0.00 +GCC 39 28.98 20.73 20.34 29.94 0.00 0.00 +GCC 40 28.93 20.76 20.39 29.92 0.00 0.00 +GCC 41 28.97 20.69 20.35 29.99 0.00 0.00 +GCC 42 28.96 20.68 20.36 29.99 0.01 0.00 +GCC 43 28.93 20.73 20.36 29.98 0.00 0.00 +GCC 44 29.02 20.71 20.33 29.94 0.00 0.00 +GCC 45 29.04 20.69 20.30 29.98 0.00 0.00 +GCC 46 29.00 20.71 20.38 29.91 0.01 0.00 +GCC 47 29.01 20.70 20.39 29.89 0.00 0.00 +GCC 48 28.93 20.78 20.47 29.82 0.00 0.00 +GCC 49 28.54 21.12 20.84 29.50 0.02 0.00 +GCC 50 29.58 20.06 19.83 30.53 0.00 0.00 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 30 24 +RL 31 25 +RL 32 22 +RL 33 22 +RL 34 39 +RL 35 43 +RL 36 36 +RL 37 31 +RL 38 43 +RL 39 96 +RL 40 283 +RL 41 427 +RL 42 370 +RL 43 104 +RL 44 176 +RL 45 629 +RL 46 16825 +RL 47 88923 +RL 48 437342 +RL 50 18030718 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 55991 87210 +ID 2 11097 13144 +ID 3 1413 1466 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 0 135 0 131 +IC 3 0 500 0 654 +IC 4 0 799 0 1454 +IC 5 0 1390 0 1639 +IC 6 0 1371 0 1820 +IC 7 0 1345 0 1970 +IC 8 0 1321 0 2059 +IC 9 0 1429 0 2103 +IC 10 0 1477 0 2217 +IC 11 0 1488 0 2270 +IC 12 0 1593 0 2376 +IC 13 0 1586 0 2410 +IC 14 0 1602 0 2512 +IC 15 0 1664 0 2466 +IC 16 0 1631 0 2573 +IC 17 0 1711 0 2657 +IC 18 0 1651 0 2522 +IC 19 0 1667 0 2561 +IC 20 0 1661 0 2595 +IC 21 0 1644 0 2607 +IC 22 0 1725 0 2630 +IC 23 0 1690 0 2566 +IC 24 0 1725 0 2682 +IC 25 0 1625 0 2561 +IC 26 0 1624 0 2554 +IC 27 0 1636 0 2528 +IC 28 0 1694 0 2587 +IC 29 0 1729 0 2622 +IC 30 0 1712 0 2609 +IC 31 0 1846 0 2834 +IC 32 0 1834 0 2772 +IC 33 0 1820 0 2755 +IC 34 0 1850 0 2757 +IC 35 0 1754 0 2768 +IC 36 0 1744 0 2569 +IC 37 0 1665 0 2504 +IC 38 0 1622 0 2483 +IC 39 0 1559 0 2523 +IC 40 0 1544 0 2495 +IC 41 0 1518 0 2378 +IC 42 0 1406 0 2210 +IC 43 0 1353 0 2026 +IC 44 0 1295 0 1795 +IC 45 0 1290 0 1168 +IC 46 0 779 0 587 +IC 47 0 529 0 202 +IC 48 0 192 0 59 +IC 49 0 76 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 582941672 +COV [2-2] 2 97104308 +COV [3-3] 3 11593609 +COV [4-4] 4 1244538 +COV [5-5] 5 189629 +COV [6-6] 6 63129 +COV [7-7] 7 34669 +COV [8-8] 8 22305 +COV [9-9] 9 16271 +COV [10-10] 10 12620 +COV [11-11] 11 9896 +COV [12-12] 12 8348 +COV [13-13] 13 6759 +COV [14-14] 14 5217 +COV [15-15] 15 4028 +COV [16-16] 16 3370 +COV [17-17] 17 2988 +COV [18-18] 18 2649 +COV [19-19] 19 2532 +COV [20-20] 20 2332 +COV [21-21] 21 2037 +COV [22-22] 22 2291 +COV [23-23] 23 2356 +COV [24-24] 24 2209 +COV [25-25] 25 2242 +COV [26-26] 26 2173 +COV [27-27] 27 1819 +COV [28-28] 28 1955 +COV [29-29] 29 1860 +COV [30-30] 30 1861 +COV [31-31] 31 1704 +COV [32-32] 32 1602 +COV [33-33] 33 1596 +COV [34-34] 34 1526 +COV [35-35] 35 1392 +COV [36-36] 36 1437 +COV [37-37] 37 1401 +COV [38-38] 38 1429 +COV [39-39] 39 1317 +COV [40-40] 40 1334 +COV [41-41] 41 1242 +COV [42-42] 42 1199 +COV [43-43] 43 1198 +COV [44-44] 44 1031 +COV [45-45] 45 1130 +COV [46-46] 46 1146 +COV [47-47] 47 1000 +COV [48-48] 48 1025 +COV [49-49] 49 1051 +COV [50-50] 50 1080 +COV [51-51] 51 1077 +COV [52-52] 52 1071 +COV [53-53] 53 1005 +COV [54-54] 54 965 +COV [55-55] 55 931 +COV [56-56] 56 1060 +COV [57-57] 57 1035 +COV [58-58] 58 965 +COV [59-59] 59 938 +COV [60-60] 60 1023 +COV [61-61] 61 1011 +COV [62-62] 62 995 +COV [63-63] 63 966 +COV [64-64] 64 881 +COV [65-65] 65 818 +COV [66-66] 66 810 +COV [67-67] 67 772 +COV [68-68] 68 780 +COV [69-69] 69 717 +COV [70-70] 70 566 +COV [71-71] 71 587 +COV [72-72] 72 557 +COV [73-73] 73 515 +COV [74-74] 74 530 +COV [75-75] 75 531 +COV [76-76] 76 435 +COV [77-77] 77 418 +COV [78-78] 78 443 +COV [79-79] 79 433 +COV [80-80] 80 361 +COV [81-81] 81 358 +COV [82-82] 82 351 +COV [83-83] 83 339 +COV [84-84] 84 274 +COV [85-85] 85 303 +COV [86-86] 86 243 +COV [87-87] 87 299 +COV [88-88] 88 258 +COV [89-89] 89 275 +COV [90-90] 90 235 +COV [91-91] 91 229 +COV [92-92] 92 208 +COV [93-93] 93 234 +COV [94-94] 94 205 +COV [95-95] 95 240 +COV [96-96] 96 253 +COV [97-97] 97 199 +COV [98-98] 98 200 +COV [99-99] 99 216 +COV [100-100] 100 223 +COV [101-101] 101 202 +COV [102-102] 102 187 +COV [103-103] 103 189 +COV [104-104] 104 186 +COV [105-105] 105 229 +COV [106-106] 106 182 +COV [107-107] 107 180 +COV [108-108] 108 181 +COV [109-109] 109 190 +COV [110-110] 110 149 +COV [111-111] 111 197 +COV [112-112] 112 189 +COV [113-113] 113 199 +COV [114-114] 114 208 +COV [115-115] 115 167 +COV [116-116] 116 166 +COV [117-117] 117 134 +COV [118-118] 118 165 +COV [119-119] 119 146 +COV [120-120] 120 149 +COV [121-121] 121 144 +COV [122-122] 122 169 +COV [123-123] 123 148 +COV [124-124] 124 140 +COV [125-125] 125 151 +COV [126-126] 126 141 +COV [127-127] 127 162 +COV [128-128] 128 149 +COV [129-129] 129 133 +COV [130-130] 130 143 +COV [131-131] 131 164 +COV [132-132] 132 141 +COV [133-133] 133 121 +COV [134-134] 134 136 +COV [135-135] 135 150 +COV [136-136] 136 134 +COV [137-137] 137 131 +COV [138-138] 138 139 +COV [139-139] 139 117 +COV [140-140] 140 141 +COV [141-141] 141 138 +COV [142-142] 142 116 +COV [143-143] 143 120 +COV [144-144] 144 127 +COV [145-145] 145 107 +COV [146-146] 146 130 +COV [147-147] 147 137 +COV [148-148] 148 149 +COV [149-149] 149 132 +COV [150-150] 150 125 +COV [151-151] 151 102 +COV [152-152] 152 105 +COV [153-153] 153 111 +COV [154-154] 154 115 +COV [155-155] 155 104 +COV [156-156] 156 104 +COV [157-157] 157 120 +COV [158-158] 158 104 +COV [159-159] 159 123 +COV [160-160] 160 126 +COV [161-161] 161 99 +COV [162-162] 162 125 +COV [163-163] 163 103 +COV [164-164] 164 124 +COV [165-165] 165 113 +COV [166-166] 166 103 +COV [167-167] 167 141 +COV [168-168] 168 121 +COV [169-169] 169 118 +COV [170-170] 170 130 +COV [171-171] 171 158 +COV [172-172] 172 121 +COV [173-173] 173 101 +COV [174-174] 174 110 +COV [175-175] 175 123 +COV [176-176] 176 121 +COV [177-177] 177 101 +COV [178-178] 178 106 +COV [179-179] 179 108 +COV [180-180] 180 103 +COV [181-181] 181 115 +COV [182-182] 182 99 +COV [183-183] 183 122 +COV [184-184] 184 102 +COV [185-185] 185 104 +COV [186-186] 186 123 +COV [187-187] 187 104 +COV [188-188] 188 115 +COV [189-189] 189 97 +COV [190-190] 190 121 +COV [191-191] 191 89 +COV [192-192] 192 118 +COV [193-193] 193 122 +COV [194-194] 194 104 +COV [195-195] 195 85 +COV [196-196] 196 96 +COV [197-197] 197 87 +COV [198-198] 198 92 +COV [199-199] 199 78 +COV [200-200] 200 92 +COV [201-201] 201 96 +COV [202-202] 202 75 +COV [203-203] 203 88 +COV [204-204] 204 87 +COV [205-205] 205 100 +COV [206-206] 206 91 +COV [207-207] 207 79 +COV [208-208] 208 89 +COV [209-209] 209 92 +COV [210-210] 210 91 +COV [211-211] 211 73 +COV [212-212] 212 112 +COV [213-213] 213 119 +COV [214-214] 214 98 +COV [215-215] 215 95 +COV [216-216] 216 93 +COV [217-217] 217 95 +COV [218-218] 218 95 +COV [219-219] 219 79 +COV [220-220] 220 76 +COV [221-221] 221 61 +COV [222-222] 222 90 +COV [223-223] 223 74 +COV [224-224] 224 64 +COV [225-225] 225 75 +COV [226-226] 226 77 +COV [227-227] 227 74 +COV [228-228] 228 79 +COV [229-229] 229 63 +COV [230-230] 230 57 +COV [231-231] 231 68 +COV [232-232] 232 66 +COV [233-233] 233 65 +COV [234-234] 234 75 +COV [235-235] 235 71 +COV [236-236] 236 63 +COV [237-237] 237 72 +COV [238-238] 238 95 +COV [239-239] 239 67 +COV [240-240] 240 86 +COV [241-241] 241 81 +COV [242-242] 242 77 +COV [243-243] 243 99 +COV [244-244] 244 80 +COV [245-245] 245 68 +COV [246-246] 246 66 +COV [247-247] 247 61 +COV [248-248] 248 82 +COV [249-249] 249 75 +COV [250-250] 250 59 +COV [251-251] 251 74 +COV [252-252] 252 79 +COV [253-253] 253 78 +COV [254-254] 254 61 +COV [255-255] 255 79 +COV [256-256] 256 74 +COV [257-257] 257 71 +COV [258-258] 258 82 +COV [259-259] 259 77 +COV [260-260] 260 76 +COV [261-261] 261 65 +COV [262-262] 262 65 +COV [263-263] 263 90 +COV [264-264] 264 70 +COV [265-265] 265 69 +COV [266-266] 266 82 +COV [267-267] 267 65 +COV [268-268] 268 91 +COV [269-269] 269 74 +COV [270-270] 270 83 +COV [271-271] 271 79 +COV [272-272] 272 69 +COV [273-273] 273 63 +COV [274-274] 274 73 +COV [275-275] 275 80 +COV [276-276] 276 68 +COV [277-277] 277 69 +COV [278-278] 278 64 +COV [279-279] 279 60 +COV [280-280] 280 67 +COV [281-281] 281 55 +COV [282-282] 282 54 +COV [283-283] 283 59 +COV [284-284] 284 74 +COV [285-285] 285 63 +COV [286-286] 286 69 +COV [287-287] 287 72 +COV [288-288] 288 72 +COV [289-289] 289 73 +COV [290-290] 290 61 +COV [291-291] 291 72 +COV [292-292] 292 72 +COV [293-293] 293 64 +COV [294-294] 294 68 +COV [295-295] 295 73 +COV [296-296] 296 60 +COV [297-297] 297 65 +COV [298-298] 298 59 +COV [299-299] 299 71 +COV [300-300] 300 51 +COV [301-301] 301 55 +COV [302-302] 302 69 +COV [303-303] 303 65 +COV [304-304] 304 49 +COV [305-305] 305 59 +COV [306-306] 306 56 +COV [307-307] 307 66 +COV [308-308] 308 68 +COV [309-309] 309 58 +COV [310-310] 310 67 +COV [311-311] 311 59 +COV [312-312] 312 50 +COV [313-313] 313 64 +COV [314-314] 314 57 +COV [315-315] 315 62 +COV [316-316] 316 56 +COV [317-317] 317 46 +COV [318-318] 318 50 +COV [319-319] 319 51 +COV [320-320] 320 51 +COV [321-321] 321 49 +COV [322-322] 322 52 +COV [323-323] 323 51 +COV [324-324] 324 46 +COV [325-325] 325 50 +COV [326-326] 326 50 +COV [327-327] 327 53 +COV [328-328] 328 59 +COV [329-329] 329 54 +COV [330-330] 330 55 +COV [331-331] 331 58 +COV [332-332] 332 58 +COV [333-333] 333 52 +COV [334-334] 334 52 +COV [335-335] 335 50 +COV [336-336] 336 60 +COV [337-337] 337 63 +COV [338-338] 338 53 +COV [339-339] 339 50 +COV [340-340] 340 57 +COV [341-341] 341 69 +COV [342-342] 342 53 +COV [343-343] 343 46 +COV [344-344] 344 63 +COV [345-345] 345 53 +COV [346-346] 346 50 +COV [347-347] 347 52 +COV [348-348] 348 48 +COV [349-349] 349 52 +COV [350-350] 350 44 +COV [351-351] 351 59 +COV [352-352] 352 51 +COV [353-353] 353 51 +COV [354-354] 354 48 +COV [355-355] 355 52 +COV [356-356] 356 81 +COV [357-357] 357 49 +COV [358-358] 358 58 +COV [359-359] 359 51 +COV [360-360] 360 39 +COV [361-361] 361 37 +COV [362-362] 362 39 +COV [363-363] 363 50 +COV [364-364] 364 41 +COV [365-365] 365 39 +COV [366-366] 366 46 +COV [367-367] 367 58 +COV [368-368] 368 40 +COV [369-369] 369 52 +COV [370-370] 370 41 +COV [371-371] 371 42 +COV [372-372] 372 45 +COV [373-373] 373 40 +COV [374-374] 374 43 +COV [375-375] 375 53 +COV [376-376] 376 42 +COV [377-377] 377 55 +COV [378-378] 378 47 +COV [379-379] 379 45 +COV [380-380] 380 40 +COV [381-381] 381 43 +COV [382-382] 382 39 +COV [383-383] 383 51 +COV [384-384] 384 43 +COV [385-385] 385 58 +COV [386-386] 386 43 +COV [387-387] 387 55 +COV [388-388] 388 50 +COV [389-389] 389 42 +COV [390-390] 390 40 +COV [391-391] 391 54 +COV [392-392] 392 40 +COV [393-393] 393 41 +COV [394-394] 394 41 +COV [395-395] 395 33 +COV [396-396] 396 36 +COV [397-397] 397 29 +COV [398-398] 398 47 +COV [399-399] 399 49 +COV [400-400] 400 31 +COV [401-401] 401 37 +COV [402-402] 402 34 +COV [403-403] 403 38 +COV [404-404] 404 40 +COV [405-405] 405 44 +COV [406-406] 406 47 +COV [407-407] 407 52 +COV [408-408] 408 40 +COV [409-409] 409 50 +COV [410-410] 410 38 +COV [411-411] 411 40 +COV [412-412] 412 35 +COV [413-413] 413 39 +COV [414-414] 414 36 +COV [415-415] 415 44 +COV [416-416] 416 42 +COV [417-417] 417 44 +COV [418-418] 418 53 +COV [419-419] 419 51 +COV [420-420] 420 41 +COV [421-421] 421 36 +COV [422-422] 422 46 +COV [423-423] 423 35 +COV [424-424] 424 38 +COV [425-425] 425 33 +COV [426-426] 426 55 +COV [427-427] 427 47 +COV [428-428] 428 34 +COV [429-429] 429 35 +COV [430-430] 430 43 +COV [431-431] 431 42 +COV [432-432] 432 35 +COV [433-433] 433 40 +COV [434-434] 434 34 +COV [435-435] 435 33 +COV [436-436] 436 42 +COV [437-437] 437 42 +COV [438-438] 438 34 +COV [439-439] 439 47 +COV [440-440] 440 44 +COV [441-441] 441 39 +COV [442-442] 442 28 +COV [443-443] 443 37 +COV [444-444] 444 45 +COV [445-445] 445 32 +COV [446-446] 446 34 +COV [447-447] 447 40 +COV [448-448] 448 31 +COV [449-449] 449 38 +COV [450-450] 450 34 +COV [451-451] 451 40 +COV [452-452] 452 27 +COV [453-453] 453 59 +COV [454-454] 454 45 +COV [455-455] 455 41 +COV [456-456] 456 44 +COV [457-457] 457 42 +COV [458-458] 458 52 +COV [459-459] 459 37 +COV [460-460] 460 48 +COV [461-461] 461 43 +COV [462-462] 462 40 +COV [463-463] 463 40 +COV [464-464] 464 39 +COV [465-465] 465 38 +COV [466-466] 466 38 +COV [467-467] 467 30 +COV [468-468] 468 24 +COV [469-469] 469 37 +COV [470-470] 470 33 +COV [471-471] 471 26 +COV [472-472] 472 28 +COV [473-473] 473 30 +COV [474-474] 474 35 +COV [475-475] 475 22 +COV [476-476] 476 31 +COV [477-477] 477 26 +COV [478-478] 478 31 +COV [479-479] 479 36 +COV [480-480] 480 37 +COV [481-481] 481 22 +COV [482-482] 482 31 +COV [483-483] 483 39 +COV [484-484] 484 38 +COV [485-485] 485 40 +COV [486-486] 486 31 +COV [487-487] 487 41 +COV [488-488] 488 40 +COV [489-489] 489 38 +COV [490-490] 490 28 +COV [491-491] 491 24 +COV [492-492] 492 35 +COV [493-493] 493 23 +COV [494-494] 494 39 +COV [495-495] 495 23 +COV [496-496] 496 24 +COV [497-497] 497 20 +COV [498-498] 498 31 +COV [499-499] 499 23 +COV [500-500] 500 38 +COV [501-501] 501 23 +COV [502-502] 502 27 +COV [503-503] 503 29 +COV [504-504] 504 17 +COV [505-505] 505 34 +COV [506-506] 506 36 +COV [507-507] 507 20 +COV [508-508] 508 25 +COV [509-509] 509 31 +COV [510-510] 510 26 +COV [511-511] 511 25 +COV [512-512] 512 39 +COV [513-513] 513 21 +COV [514-514] 514 25 +COV [515-515] 515 49 +COV [516-516] 516 28 +COV [517-517] 517 31 +COV [518-518] 518 33 +COV [519-519] 519 27 +COV [520-520] 520 35 +COV [521-521] 521 30 +COV [522-522] 522 34 +COV [523-523] 523 22 +COV [524-524] 524 27 +COV [525-525] 525 30 +COV [526-526] 526 30 +COV [527-527] 527 29 +COV [528-528] 528 25 +COV [529-529] 529 23 +COV [530-530] 530 27 +COV [531-531] 531 18 +COV [532-532] 532 19 +COV [533-533] 533 19 +COV [534-534] 534 31 +COV [535-535] 535 27 +COV [536-536] 536 26 +COV [537-537] 537 23 +COV [538-538] 538 24 +COV [539-539] 539 23 +COV [540-540] 540 21 +COV [541-541] 541 37 +COV [542-542] 542 31 +COV [543-543] 543 26 +COV [544-544] 544 29 +COV [545-545] 545 25 +COV [546-546] 546 26 +COV [547-547] 547 22 +COV [548-548] 548 32 +COV [549-549] 549 36 +COV [550-550] 550 24 +COV [551-551] 551 33 +COV [552-552] 552 18 +COV [553-553] 553 31 +COV [554-554] 554 21 +COV [555-555] 555 25 +COV [556-556] 556 20 +COV [557-557] 557 25 +COV [558-558] 558 33 +COV [559-559] 559 18 +COV [560-560] 560 37 +COV [561-561] 561 24 +COV [562-562] 562 23 +COV [563-563] 563 27 +COV [564-564] 564 26 +COV [565-565] 565 28 +COV [566-566] 566 23 +COV [567-567] 567 24 +COV [568-568] 568 29 +COV [569-569] 569 26 +COV [570-570] 570 19 +COV [571-571] 571 21 +COV [572-572] 572 25 +COV [573-573] 573 15 +COV [574-574] 574 21 +COV [575-575] 575 17 +COV [576-576] 576 16 +COV [577-577] 577 26 +COV [578-578] 578 22 +COV [579-579] 579 25 +COV [580-580] 580 28 +COV [581-581] 581 25 +COV [582-582] 582 33 +COV [583-583] 583 13 +COV [584-584] 584 19 +COV [585-585] 585 28 +COV [586-586] 586 28 +COV [587-587] 587 22 +COV [588-588] 588 23 +COV [589-589] 589 28 +COV [590-590] 590 20 +COV [591-591] 591 18 +COV [592-592] 592 36 +COV [593-593] 593 26 +COV [594-594] 594 28 +COV [595-595] 595 28 +COV [596-596] 596 18 +COV [597-597] 597 28 +COV [598-598] 598 21 +COV [599-599] 599 25 +COV [600-600] 600 20 +COV [601-601] 601 22 +COV [602-602] 602 21 +COV [603-603] 603 34 +COV [604-604] 604 21 +COV [605-605] 605 28 +COV [606-606] 606 19 +COV [607-607] 607 22 +COV [608-608] 608 19 +COV [609-609] 609 20 +COV [610-610] 610 19 +COV [611-611] 611 33 +COV [612-612] 612 20 +COV [613-613] 613 19 +COV [614-614] 614 20 +COV [615-615] 615 34 +COV [616-616] 616 26 +COV [617-617] 617 22 +COV [618-618] 618 16 +COV [619-619] 619 14 +COV [620-620] 620 26 +COV [621-621] 621 28 +COV [622-622] 622 29 +COV [623-623] 623 26 +COV [624-624] 624 32 +COV [625-625] 625 36 +COV [626-626] 626 24 +COV [627-627] 627 21 +COV [628-628] 628 20 +COV [629-629] 629 26 +COV [630-630] 630 32 +COV [631-631] 631 17 +COV [632-632] 632 22 +COV [633-633] 633 27 +COV [634-634] 634 17 +COV [635-635] 635 20 +COV [636-636] 636 27 +COV [637-637] 637 24 +COV [638-638] 638 21 +COV [639-639] 639 19 +COV [640-640] 640 38 +COV [641-641] 641 22 +COV [642-642] 642 18 +COV [643-643] 643 27 +COV [644-644] 644 19 +COV [645-645] 645 22 +COV [646-646] 646 24 +COV [647-647] 647 20 +COV [648-648] 648 15 +COV [649-649] 649 28 +COV [650-650] 650 25 +COV [651-651] 651 26 +COV [652-652] 652 25 +COV [653-653] 653 22 +COV [654-654] 654 22 +COV [655-655] 655 21 +COV [656-656] 656 16 +COV [657-657] 657 17 +COV [658-658] 658 19 +COV [659-659] 659 22 +COV [660-660] 660 18 +COV [661-661] 661 31 +COV [662-662] 662 14 +COV [663-663] 663 18 +COV [664-664] 664 13 +COV [665-665] 665 21 +COV [666-666] 666 25 +COV [667-667] 667 17 +COV [668-668] 668 21 +COV [669-669] 669 17 +COV [670-670] 670 20 +COV [671-671] 671 23 +COV [672-672] 672 18 +COV [673-673] 673 26 +COV [674-674] 674 23 +COV [675-675] 675 16 +COV [676-676] 676 18 +COV [677-677] 677 13 +COV [678-678] 678 20 +COV [679-679] 679 20 +COV [680-680] 680 21 +COV [681-681] 681 21 +COV [682-682] 682 22 +COV [683-683] 683 19 +COV [684-684] 684 20 +COV [685-685] 685 32 +COV [686-686] 686 26 +COV [687-687] 687 19 +COV [688-688] 688 19 +COV [689-689] 689 21 +COV [690-690] 690 24 +COV [691-691] 691 19 +COV [692-692] 692 30 +COV [693-693] 693 23 +COV [694-694] 694 16 +COV [695-695] 695 17 +COV [696-696] 696 26 +COV [697-697] 697 25 +COV [698-698] 698 20 +COV [699-699] 699 33 +COV [700-700] 700 30 +COV [701-701] 701 23 +COV [702-702] 702 33 +COV [703-703] 703 24 +COV [704-704] 704 18 +COV [705-705] 705 31 +COV [706-706] 706 22 +COV [707-707] 707 36 +COV [708-708] 708 32 +COV [709-709] 709 34 +COV [710-710] 710 27 +COV [711-711] 711 23 +COV [712-712] 712 23 +COV [713-713] 713 31 +COV [714-714] 714 43 +COV [715-715] 715 34 +COV [716-716] 716 21 +COV [717-717] 717 19 +COV [718-718] 718 29 +COV [719-719] 719 21 +COV [720-720] 720 24 +COV [721-721] 721 25 +COV [722-722] 722 26 +COV [723-723] 723 19 +COV [724-724] 724 33 +COV [725-725] 725 25 +COV [726-726] 726 19 +COV [727-727] 727 27 +COV [728-728] 728 22 +COV [729-729] 729 18 +COV [730-730] 730 20 +COV [731-731] 731 22 +COV [732-732] 732 19 +COV [733-733] 733 19 +COV [734-734] 734 22 +COV [735-735] 735 21 +COV [736-736] 736 24 +COV [737-737] 737 29 +COV [738-738] 738 17 +COV [739-739] 739 29 +COV [740-740] 740 30 +COV [741-741] 741 30 +COV [742-742] 742 26 +COV [743-743] 743 26 +COV [744-744] 744 29 +COV [745-745] 745 27 +COV [746-746] 746 23 +COV [747-747] 747 21 +COV [748-748] 748 26 +COV [749-749] 749 24 +COV [750-750] 750 30 +COV [751-751] 751 22 +COV [752-752] 752 31 +COV [753-753] 753 29 +COV [754-754] 754 17 +COV [755-755] 755 22 +COV [756-756] 756 30 +COV [757-757] 757 30 +COV [758-758] 758 20 +COV [759-759] 759 25 +COV [760-760] 760 24 +COV [761-761] 761 33 +COV [762-762] 762 24 +COV [763-763] 763 20 +COV [764-764] 764 12 +COV [765-765] 765 16 +COV [766-766] 766 24 +COV [767-767] 767 19 +COV [768-768] 768 19 +COV [769-769] 769 22 +COV [770-770] 770 14 +COV [771-771] 771 17 +COV [772-772] 772 16 +COV [773-773] 773 23 +COV [774-774] 774 17 +COV [775-775] 775 18 +COV [776-776] 776 21 +COV [777-777] 777 15 +COV [778-778] 778 15 +COV [779-779] 779 18 +COV [780-780] 780 24 +COV [781-781] 781 16 +COV [782-782] 782 22 +COV [783-783] 783 22 +COV [784-784] 784 10 +COV [785-785] 785 16 +COV [786-786] 786 13 +COV [787-787] 787 9 +COV [788-788] 788 20 +COV [789-789] 789 23 +COV [790-790] 790 16 +COV [791-791] 791 23 +COV [792-792] 792 22 +COV [793-793] 793 24 +COV [794-794] 794 15 +COV [795-795] 795 26 +COV [796-796] 796 23 +COV [797-797] 797 23 +COV [798-798] 798 12 +COV [799-799] 799 12 +COV [800-800] 800 20 +COV [801-801] 801 21 +COV [802-802] 802 15 +COV [803-803] 803 17 +COV [804-804] 804 17 +COV [805-805] 805 11 +COV [806-806] 806 10 +COV [807-807] 807 18 +COV [808-808] 808 16 +COV [809-809] 809 19 +COV [810-810] 810 22 +COV [811-811] 811 19 +COV [812-812] 812 10 +COV [813-813] 813 17 +COV [814-814] 814 10 +COV [815-815] 815 21 +COV [816-816] 816 28 +COV [817-817] 817 11 +COV [818-818] 818 19 +COV [819-819] 819 21 +COV [820-820] 820 12 +COV [821-821] 821 18 +COV [822-822] 822 11 +COV [823-823] 823 21 +COV [824-824] 824 13 +COV [825-825] 825 16 +COV [826-826] 826 18 +COV [827-827] 827 20 +COV [828-828] 828 23 +COV [829-829] 829 12 +COV [830-830] 830 20 +COV [831-831] 831 9 +COV [832-832] 832 19 +COV [833-833] 833 14 +COV [834-834] 834 23 +COV [835-835] 835 18 +COV [836-836] 836 20 +COV [837-837] 837 14 +COV [838-838] 838 18 +COV [839-839] 839 15 +COV [840-840] 840 18 +COV [841-841] 841 8 +COV [842-842] 842 22 +COV [843-843] 843 15 +COV [844-844] 844 23 +COV [845-845] 845 16 +COV [846-846] 846 20 +COV [847-847] 847 18 +COV [848-848] 848 13 +COV [849-849] 849 14 +COV [850-850] 850 19 +COV [851-851] 851 18 +COV [852-852] 852 19 +COV [853-853] 853 20 +COV [854-854] 854 16 +COV [855-855] 855 11 +COV [856-856] 856 18 +COV [857-857] 857 9 +COV [858-858] 858 15 +COV [859-859] 859 25 +COV [860-860] 860 17 +COV [861-861] 861 18 +COV [862-862] 862 14 +COV [863-863] 863 22 +COV [864-864] 864 9 +COV [865-865] 865 15 +COV [866-866] 866 20 +COV [867-867] 867 9 +COV [868-868] 868 20 +COV [869-869] 869 15 +COV [870-870] 870 19 +COV [871-871] 871 12 +COV [872-872] 872 23 +COV [873-873] 873 13 +COV [874-874] 874 25 +COV [875-875] 875 15 +COV [876-876] 876 15 +COV [877-877] 877 22 +COV [878-878] 878 19 +COV [879-879] 879 12 +COV [880-880] 880 22 +COV [881-881] 881 16 +COV [882-882] 882 23 +COV [883-883] 883 12 +COV [884-884] 884 15 +COV [885-885] 885 18 +COV [886-886] 886 16 +COV [887-887] 887 11 +COV [888-888] 888 19 +COV [889-889] 889 24 +COV [890-890] 890 17 +COV [891-891] 891 11 +COV [892-892] 892 24 +COV [893-893] 893 25 +COV [894-894] 894 16 +COV [895-895] 895 21 +COV [896-896] 896 17 +COV [897-897] 897 23 +COV [898-898] 898 18 +COV [899-899] 899 16 +COV [900-900] 900 14 +COV [901-901] 901 25 +COV [902-902] 902 19 +COV [903-903] 903 19 +COV [904-904] 904 18 +COV [905-905] 905 15 +COV [906-906] 906 9 +COV [907-907] 907 20 +COV [908-908] 908 11 +COV [909-909] 909 14 +COV [910-910] 910 20 +COV [911-911] 911 12 +COV [912-912] 912 15 +COV [913-913] 913 8 +COV [914-914] 914 20 +COV [915-915] 915 15 +COV [916-916] 916 19 +COV [917-917] 917 16 +COV [918-918] 918 13 +COV [919-919] 919 23 +COV [920-920] 920 7 +COV [921-921] 921 17 +COV [922-922] 922 16 +COV [923-923] 923 13 +COV [924-924] 924 15 +COV [925-925] 925 7 +COV [926-926] 926 12 +COV [927-927] 927 3 +COV [928-928] 928 16 +COV [929-929] 929 10 +COV [930-930] 930 12 +COV [931-931] 931 11 +COV [932-932] 932 15 +COV [933-933] 933 12 +COV [934-934] 934 18 +COV [935-935] 935 15 +COV [936-936] 936 16 +COV [937-937] 937 10 +COV [938-938] 938 11 +COV [939-939] 939 16 +COV [940-940] 940 20 +COV [941-941] 941 18 +COV [942-942] 942 20 +COV [943-943] 943 17 +COV [944-944] 944 14 +COV [945-945] 945 10 +COV [946-946] 946 15 +COV [947-947] 947 12 +COV [948-948] 948 7 +COV [949-949] 949 9 +COV [950-950] 950 16 +COV [951-951] 951 9 +COV [952-952] 952 25 +COV [953-953] 953 16 +COV [954-954] 954 12 +COV [955-955] 955 12 +COV [956-956] 956 24 +COV [957-957] 957 19 +COV [958-958] 958 11 +COV [959-959] 959 14 +COV [960-960] 960 18 +COV [961-961] 961 17 +COV [962-962] 962 14 +COV [963-963] 963 18 +COV [964-964] 964 15 +COV [965-965] 965 14 +COV [966-966] 966 9 +COV [967-967] 967 7 +COV [968-968] 968 12 +COV [969-969] 969 20 +COV [970-970] 970 20 +COV [971-971] 971 13 +COV [972-972] 972 14 +COV [973-973] 973 11 +COV [974-974] 974 12 +COV [975-975] 975 16 +COV [976-976] 976 13 +COV [977-977] 977 16 +COV [978-978] 978 11 +COV [979-979] 979 11 +COV [980-980] 980 22 +COV [981-981] 981 13 +COV [982-982] 982 16 +COV [983-983] 983 19 +COV [984-984] 984 17 +COV [985-985] 985 16 +COV [986-986] 986 13 +COV [987-987] 987 14 +COV [988-988] 988 24 +COV [989-989] 989 10 +COV [990-990] 990 16 +COV [991-991] 991 12 +COV [992-992] 992 16 +COV [993-993] 993 18 +COV [994-994] 994 16 +COV [995-995] 995 15 +COV [996-996] 996 14 +COV [997-997] 997 20 +COV [998-998] 998 17 +COV [999-999] 999 13 +COV [1000-1000] 1000 19 +COV [1000<] 1000 19954 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 0.004 0.000 0.000 0.002 0.002 0.002 +GCD 2.0 0.008 0.002 0.002 0.002 0.007 0.012 +GCD 3.0 0.010 0.005 0.005 0.005 0.007 0.007 +GCD 4.0 0.014 0.002 0.002 0.002 0.002 0.005 +GCD 5.0 0.015 0.005 0.005 0.005 0.005 0.005 +GCD 5.3 0.015 0.020 0.020 0.020 0.020 0.020 +GCD 6.0 0.016 0.002 0.002 0.002 0.002 0.002 +GCD 7.0 0.018 0.005 0.005 0.005 0.005 0.005 +GCD 10.0 0.020 0.002 0.002 0.002 0.010 0.010 +GCD 11.0 0.021 0.005 0.005 0.005 0.005 0.005 +GCD 12.0 0.024 0.002 0.002 0.002 0.002 0.002 +GCD 13.0 0.026 0.005 0.005 0.005 0.005 0.005 +GCD 14.0 0.032 0.002 0.002 0.002 0.005 0.005 +GCD 15.0 0.035 0.005 0.005 0.005 0.005 0.017 +GCD 16.0 0.039 0.002 0.002 0.002 0.002 0.005 +GCD 17.0 0.042 0.007 0.007 0.007 0.010 0.010 +GCD 18.0 0.045 0.002 0.002 0.002 0.007 0.007 +GCD 19.0 0.049 0.005 0.005 0.007 0.015 0.020 +GCD 20.0 0.057 0.002 0.002 0.002 0.005 0.007 +GCD 21.0 0.061 0.002 0.002 0.005 0.005 0.007 +GCD 22.0 0.067 0.002 0.002 0.002 0.005 0.007 +GCD 23.0 0.074 0.002 0.005 0.007 0.010 0.022 +GCD 24.0 0.092 0.002 0.002 0.002 0.005 0.010 +GCD 25.0 0.104 0.002 0.005 0.005 0.005 0.005 +GCD 26.0 0.120 0.002 0.002 0.002 0.005 0.010 +GCD 27.0 0.132 0.002 0.005 0.007 0.015 0.919 +GCD 28.0 0.146 0.002 0.002 0.005 0.012 0.044 +GCD 29.0 0.158 0.005 0.005 0.007 0.010 0.020 +GCD 30.0 0.180 0.002 0.002 0.012 0.027 0.301 +GCD 31.0 0.231 0.007 0.020 0.252 0.309 0.321 +GCD 32.0 0.420 0.007 0.235 0.287 0.316 0.336 +GCD 33.0 1.041 0.235 0.272 0.299 0.321 0.345 +GCD 34.0 2.836 0.245 0.277 0.301 0.326 0.345 +GCD 35.0 6.596 0.250 0.279 0.306 0.331 0.353 +GCD 36.0 12.687 0.252 0.282 0.309 0.333 0.355 +GCD 37.0 21.038 0.252 0.284 0.309 0.336 0.360 +GCD 38.0 30.804 0.257 0.287 0.314 0.338 0.363 +GCD 39.0 40.686 0.255 0.287 0.314 0.341 0.368 +GCD 40.0 50.215 0.255 0.289 0.316 0.341 0.368 +GCD 41.0 58.702 0.252 0.287 0.316 0.343 0.370 +GCD 42.0 66.415 0.252 0.284 0.314 0.341 0.370 +GCD 43.0 73.332 0.255 0.287 0.314 0.341 0.370 +GCD 44.0 79.256 0.252 0.284 0.314 0.341 0.370 +GCD 45.0 84.178 0.255 0.284 0.314 0.341 0.372 +GCD 46.0 88.180 0.250 0.282 0.311 0.341 0.375 +GCD 47.0 91.323 0.247 0.282 0.311 0.341 0.375 +GCD 48.0 93.860 0.245 0.277 0.309 0.341 0.375 +GCD 49.0 95.781 0.250 0.279 0.309 0.341 0.375 +GCD 50.0 97.275 0.240 0.277 0.309 0.336 0.375 +GCD 51.0 98.341 0.247 0.277 0.306 0.341 0.380 +GCD 52.0 99.080 0.240 0.274 0.306 0.341 0.382 +GCD 53.0 99.534 0.240 0.274 0.306 0.345 0.399 +GCD 54.0 99.780 0.221 0.265 0.299 0.336 0.390 +GCD 55.0 99.894 0.233 0.267 0.296 0.326 0.350 +GCD 56.0 99.952 0.211 0.255 0.299 0.331 0.392 +GCD 57.0 99.976 0.223 0.265 0.309 0.345 0.639 +GCD 58.0 99.985 0.002 0.265 0.490 0.615 0.649 +GCD 59.0 99.988 0.260 0.260 0.289 0.835 0.835 +GCD 60.0 99.992 0.002 0.002 0.123 0.289 0.404 +GCD 62.0 99.995 0.002 0.002 0.002 0.002 0.713 +GCD 63.0 99.996 0.652 0.652 0.652 0.711 0.711 +GCD 64.0 99.998 0.622 0.622 0.622 11.324 11.324 +GCD 65.0 99.999 0.002 0.002 0.002 0.002 0.002 +GCD 66.0 100.000 0.002 0.002 0.002 0.002 0.002 diff --git a/src/multiqc/test_data2/script.sh b/src/multiqc/test_data2/script.sh new file mode 100644 index 00000000..614b032e --- /dev/null +++ b/src/multiqc/test_data2/script.sh @@ -0,0 +1,9 @@ +# multiqc test data + +# Test data from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/busco/test + +if [ ! -d /tmp/snakemake-wrappers ]; then + git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers +fi + +cp -r /tmp/snakemake-wrappers/bio/multiqc/test/samtools_stats/* src/multiqc/test_data