diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192396_1.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192396_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..14554796 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_1Log.final.out b/src/multiqc/test_data/rna-seq/data/SRR3192396_1Log.final.out new file mode 100644 index 00000000..ac263484 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_1Log.out b/src/multiqc/test_data/rna-seq/data/SRR3192396_1Log.out new file mode 100644 index 00000000..efc17cd1 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_1Log.progress.out b/src/multiqc/test_data/rna-seq/data/SRR3192396_1Log.progress.out new file mode 100644 index 00000000..6c94b5b1 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_1Log.std.out b/src/multiqc/test_data/rna-seq/data/SRR3192396_1Log.std.out new file mode 100644 index 00000000..f13f9ca3 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192396_1_fastqc.html new file mode 100644 index 00000000..223e4f2f --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192396_1_fastqc.zip new file mode 100644 index 00000000..4b340d8c Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192396_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192396_1_star_aligned.bam_counts.txt.summary b/src/multiqc/test_data/rna-seq/data/SRR3192396_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..18e1f3b1 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_1_val_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192396_1_val_1_fastqc.html new file mode 100644 index 00000000..b0e0cf7c --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_1_val_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192396_1_val_1_fastqc.zip new file mode 100644 index 00000000..4ed0e7b1 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192396_1_val_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192396_2.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192396_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..27d8f45f --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192396_2_fastqc.html new file mode 100644 index 00000000..b15870da --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192396_2_fastqc.zip new file mode 100644 index 00000000..221e4399 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192396_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192396_2_val_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192396_2_val_2_fastqc.html new file mode 100644 index 00000000..8792035e --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192396_2_val_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192396_2_val_2_fastqc.zip new file mode 100644 index 00000000..76f97dbb Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192396_2_val_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192397_1.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192397_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..c3948eab --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_1Log.final.out b/src/multiqc/test_data/rna-seq/data/SRR3192397_1Log.final.out new file mode 100644 index 00000000..075fa397 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_1Log.out b/src/multiqc/test_data/rna-seq/data/SRR3192397_1Log.out new file mode 100644 index 00000000..10724d6a --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_1Log.progress.out b/src/multiqc/test_data/rna-seq/data/SRR3192397_1Log.progress.out new file mode 100644 index 00000000..d18b706a --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_1Log.std.out b/src/multiqc/test_data/rna-seq/data/SRR3192397_1Log.std.out new file mode 100644 index 00000000..61b52863 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192397_1_fastqc.html new file mode 100644 index 00000000..c19ec10e --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192397_1_fastqc.zip new file mode 100644 index 00000000..a9f28635 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192397_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192397_1_star_aligned.bam_counts.txt.summary b/src/multiqc/test_data/rna-seq/data/SRR3192397_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..9a723e2d --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_1_val_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192397_1_val_1_fastqc.html new file mode 100644 index 00000000..922b75ff --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_1_val_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192397_1_val_1_fastqc.zip new file mode 100644 index 00000000..69ff4b47 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192397_1_val_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192397_2.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192397_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..89552b12 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192397_2_fastqc.html new file mode 100644 index 00000000..3bceee88 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192397_2_fastqc.zip new file mode 100644 index 00000000..909e8faf Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192397_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192397_2_val_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192397_2_val_2_fastqc.html new file mode 100644 index 00000000..5075faf1 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192397_2_val_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192397_2_val_2_fastqc.zip new file mode 100644 index 00000000..09127821 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192397_2_val_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192398_1.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192398_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..d0cc43dc --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_1Log.final.out b/src/multiqc/test_data/rna-seq/data/SRR3192398_1Log.final.out new file mode 100644 index 00000000..365819ae --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_1Log.out b/src/multiqc/test_data/rna-seq/data/SRR3192398_1Log.out new file mode 100644 index 00000000..429d9ec0 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_1Log.progress.out b/src/multiqc/test_data/rna-seq/data/SRR3192398_1Log.progress.out new file mode 100644 index 00000000..1955f5a4 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_1Log.std.out b/src/multiqc/test_data/rna-seq/data/SRR3192398_1Log.std.out new file mode 100644 index 00000000..51e6ef1e --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192398_1_fastqc.html new file mode 100644 index 00000000..a6f68753 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192398_1_fastqc.zip new file mode 100644 index 00000000..f851864c Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192398_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192398_1_star_aligned.bam_counts.txt.summary b/src/multiqc/test_data/rna-seq/data/SRR3192398_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..88d1367f --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_1_val_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192398_1_val_1_fastqc.html new file mode 100644 index 00000000..34b05e01 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_1_val_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192398_1_val_1_fastqc.zip new file mode 100644 index 00000000..aa0c980f Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192398_1_val_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192398_2.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192398_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..4873619b --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192398_2_fastqc.html new file mode 100644 index 00000000..e780d0ab --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192398_2_fastqc.zip new file mode 100644 index 00000000..97251999 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192398_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192398_2_val_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192398_2_val_2_fastqc.html new file mode 100644 index 00000000..f082fdd3 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192398_2_val_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192398_2_val_2_fastqc.zip new file mode 100644 index 00000000..bb3a5670 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192398_2_val_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192399_1.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192399_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..91fb0da6 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_1Log.final.out b/src/multiqc/test_data/rna-seq/data/SRR3192399_1Log.final.out new file mode 100644 index 00000000..8e53f654 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_1Log.out b/src/multiqc/test_data/rna-seq/data/SRR3192399_1Log.out new file mode 100644 index 00000000..96bb1828 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_1Log.progress.out b/src/multiqc/test_data/rna-seq/data/SRR3192399_1Log.progress.out new file mode 100644 index 00000000..551e8e99 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_1Log.std.out b/src/multiqc/test_data/rna-seq/data/SRR3192399_1Log.std.out new file mode 100644 index 00000000..845d28c0 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192399_1_fastqc.html new file mode 100644 index 00000000..e8c35f01 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192399_1_fastqc.zip new file mode 100644 index 00000000..dfd3c839 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192399_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192399_1_star_aligned.bam_counts.txt.summary b/src/multiqc/test_data/rna-seq/data/SRR3192399_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..55a98aeb --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_1_val_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192399_1_val_1_fastqc.html new file mode 100644 index 00000000..13fb436e --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_1_val_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192399_1_val_1_fastqc.zip new file mode 100644 index 00000000..7edab1c2 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192399_1_val_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192399_2.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192399_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..ebe557a1 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192399_2_fastqc.html new file mode 100644 index 00000000..f56a8a90 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192399_2_fastqc.zip new file mode 100644 index 00000000..110291db Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192399_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192399_2_val_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192399_2_val_2_fastqc.html new file mode 100644 index 00000000..072e499b --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192399_2_val_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192399_2_val_2_fastqc.zip new file mode 100644 index 00000000..3a2f4b18 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192399_2_val_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192400_1.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192400_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..e2b28981 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_1Log.final.out b/src/multiqc/test_data/rna-seq/data/SRR3192400_1Log.final.out new file mode 100644 index 00000000..4b155675 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_1Log.out b/src/multiqc/test_data/rna-seq/data/SRR3192400_1Log.out new file mode 100644 index 00000000..e43bfa39 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_1Log.progress.out b/src/multiqc/test_data/rna-seq/data/SRR3192400_1Log.progress.out new file mode 100644 index 00000000..599b5df1 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_1Log.std.out b/src/multiqc/test_data/rna-seq/data/SRR3192400_1Log.std.out new file mode 100644 index 00000000..174cc88f --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192400_1_fastqc.html new file mode 100644 index 00000000..384732d4 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192400_1_fastqc.zip new file mode 100644 index 00000000..6fca77d5 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192400_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192400_1_star_aligned.bam_counts.txt.summary b/src/multiqc/test_data/rna-seq/data/SRR3192400_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..27ad816e --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_1_val_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192400_1_val_1_fastqc.html new file mode 100644 index 00000000..f8b9989e --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_1_val_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192400_1_val_1_fastqc.zip new file mode 100644 index 00000000..c07d052b Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192400_1_val_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192400_2.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192400_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..ff0d52d6 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192400_2_fastqc.html new file mode 100644 index 00000000..6ab1334f --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192400_2_fastqc.zip new file mode 100644 index 00000000..d2499dd8 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192400_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192400_2_val_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192400_2_val_2_fastqc.html new file mode 100644 index 00000000..6da6ee22 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192400_2_val_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192400_2_val_2_fastqc.zip new file mode 100644 index 00000000..ea4d3f37 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192400_2_val_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192401_1.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192401_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..782739a5 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_1Log.final.out b/src/multiqc/test_data/rna-seq/data/SRR3192401_1Log.final.out new file mode 100644 index 00000000..d2747399 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_1Log.out b/src/multiqc/test_data/rna-seq/data/SRR3192401_1Log.out new file mode 100644 index 00000000..ac9a0ff9 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_1Log.progress.out b/src/multiqc/test_data/rna-seq/data/SRR3192401_1Log.progress.out new file mode 100644 index 00000000..5875ff7a --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_1Log.std.out b/src/multiqc/test_data/rna-seq/data/SRR3192401_1Log.std.out new file mode 100644 index 00000000..52550f53 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192401_1_fastqc.html new file mode 100644 index 00000000..5ba27266 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192401_1_fastqc.zip new file mode 100644 index 00000000..3e1d6bb5 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192401_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192401_1_star_aligned.bam_counts.txt.summary b/src/multiqc/test_data/rna-seq/data/SRR3192401_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..19c6e2fa --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_1_val_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192401_1_val_1_fastqc.html new file mode 100644 index 00000000..dd3e8889 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_1_val_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192401_1_val_1_fastqc.zip new file mode 100644 index 00000000..fc39cca6 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192401_1_val_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192401_2.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192401_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..becd737b --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192401_2_fastqc.html new file mode 100644 index 00000000..e1a53fd2 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192401_2_fastqc.zip new file mode 100644 index 00000000..0c12c50a Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192401_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192401_2_val_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192401_2_val_2_fastqc.html new file mode 100644 index 00000000..e35d2e16 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192401_2_val_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192401_2_val_2_fastqc.zip new file mode 100644 index 00000000..70659623 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192401_2_val_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192657_1.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192657_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..e3c44e33 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_1Log.final.out b/src/multiqc/test_data/rna-seq/data/SRR3192657_1Log.final.out new file mode 100644 index 00000000..23c0f248 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_1Log.out b/src/multiqc/test_data/rna-seq/data/SRR3192657_1Log.out new file mode 100644 index 00000000..3f6d02de --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_1Log.progress.out b/src/multiqc/test_data/rna-seq/data/SRR3192657_1Log.progress.out new file mode 100644 index 00000000..042a7675 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_1Log.std.out b/src/multiqc/test_data/rna-seq/data/SRR3192657_1Log.std.out new file mode 100644 index 00000000..28ba4aab --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192657_1_fastqc.html new file mode 100644 index 00000000..70f19bbb --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192657_1_fastqc.zip new file mode 100644 index 00000000..de18b146 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192657_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192657_1_star_aligned.bam_counts.txt.summary b/src/multiqc/test_data/rna-seq/data/SRR3192657_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..bb70c458 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_1_val_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192657_1_val_1_fastqc.html new file mode 100644 index 00000000..50b3e090 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_1_val_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192657_1_val_1_fastqc.zip new file mode 100644 index 00000000..e54b5f09 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192657_1_val_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192657_2.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192657_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..462bbdd0 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192657_2_fastqc.html new file mode 100644 index 00000000..eebc8f08 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192657_2_fastqc.zip new file mode 100644 index 00000000..76ed23a9 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192657_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192657_2_val_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192657_2_val_2_fastqc.html new file mode 100644 index 00000000..eccba4c1 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192657_2_val_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192657_2_val_2_fastqc.zip new file mode 100644 index 00000000..f7ade59e Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192657_2_val_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192658_1.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192658_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..39cd2377 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_1Log.final.out b/src/multiqc/test_data/rna-seq/data/SRR3192658_1Log.final.out new file mode 100644 index 00000000..87a01735 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_1Log.out b/src/multiqc/test_data/rna-seq/data/SRR3192658_1Log.out new file mode 100644 index 00000000..76b24b44 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_1Log.progress.out b/src/multiqc/test_data/rna-seq/data/SRR3192658_1Log.progress.out new file mode 100644 index 00000000..d74f5a4a --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_1Log.std.out b/src/multiqc/test_data/rna-seq/data/SRR3192658_1Log.std.out new file mode 100644 index 00000000..c1a05ff0 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192658_1_fastqc.html new file mode 100644 index 00000000..2188d5d6 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192658_1_fastqc.zip new file mode 100644 index 00000000..5e4c6920 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192658_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192658_1_star_aligned.bam_counts.txt.summary b/src/multiqc/test_data/rna-seq/data/SRR3192658_1_star_aligned.bam_counts.txt.summary new file mode 100644 index 00000000..d43b3bff --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_1_val_1_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192658_1_val_1_fastqc.html new file mode 100644 index 00000000..fe0990e8 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_1_val_1_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192658_1_val_1_fastqc.zip new file mode 100644 index 00000000..ae039fd6 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192658_1_val_1_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192658_2.fastq.gz_trimming_report.txt b/src/multiqc/test_data/rna-seq/data/SRR3192658_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..86b73e98 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192658_2_fastqc.html new file mode 100644 index 00000000..6b841f43 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192658_2_fastqc.zip new file mode 100644 index 00000000..78e796f1 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192658_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/SRR3192658_2_val_2_fastqc.html b/src/multiqc/test_data/rna-seq/data/SRR3192658_2_val_2_fastqc.html new file mode 100644 index 00000000..9525e0e7 --- /dev/null +++ b/src/multiqc/test_data/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/test_data/rna-seq/data/SRR3192658_2_val_2_fastqc.zip b/src/multiqc/test_data/rna-seq/data/SRR3192658_2_val_2_fastqc.zip new file mode 100644 index 00000000..ed983500 Binary files /dev/null and b/src/multiqc/test_data/rna-seq/data/SRR3192658_2_val_2_fastqc.zip differ diff --git a/src/multiqc/test_data/rna-seq/data/fastqc_theoretical_gc_hg38_txome.txt b/src/multiqc/test_data/rna-seq/data/fastqc_theoretical_gc_hg38_txome.txt new file mode 100644 index 00000000..b2fbc90e --- /dev/null +++ b/src/multiqc/test_data/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/test_data/script.sh b/src/multiqc/test_data/script.sh new file mode 100644 index 00000000..fc528fb3 --- /dev/null +++ b/src/multiqc/test_data/script.sh @@ -0,0 +1,7 @@ +# multiqc test data + +# Test data was obtained from https://multiqc.info/example-reports/ + +curl -O -J -L http://multiqc.info/examples/rna-seq/data.zip +unzip -q "data.zip" -d "src/multiqc/test_data/rna-seq" +