diff --git a/nohup.out b/nohup.out deleted file mode 100644 index 16a6d90..0000000 --- a/nohup.out +++ /dev/null @@ -1,419 +0,0 @@ -N E X T F L O W ~ version 20.01.0 -Launching `main.nf` [sick_lumiere] - revision: 423d13acef -WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE - - - *** Using debug mode *** - - -▗▖ ▝▜ ▝ ▗ ▗▖ ▖▗▄▄▖ - ▐▌ ▐ ▗▄ ▄▄ ▗▗▖ ▗▄▄ ▄▖ ▗▗▖ ▗▟▄ ▐▚ ▌▐ - ▌▐ ▐ ▐ ▐▘▜ ▐▘▐ ▐▐▐ ▐▘▐ ▐▘▐ ▐ ▐▐▖▌▐▄▄▖ - ▙▟ ▐ ▐ ▐ ▐ ▐ ▐ ▐▐▐ ▐▀▀ ▐ ▐ ▐ ▀▘ ▐ ▌▌▐ - ▐ ▌ ▝▄ ▗▟▄ ▝▙▜ ▐ ▐ ▐▐▐ ▝▙▞ ▐ ▐ ▝▄ ▐ ▐▌▐ - ▖▐ - ▝▘ - -To run the pipeline: - -nextflow main.nf --debug -nextflow main.nf --sample_sheet=name_of_sample_sheet.tsv --species=ce - - parameters description Set/Default - ========== =========== ======================== - --debug Use --debug to indicate debug mode true - --sample_sheet See test_data/sample_sheet for example /projects/b1059/projects/Katie/alignment-nf/test_data/sample_sheet.tsv - --species Species to map: 'c_elegans', 'c_briggsae' c_elegans - or 'c_tropicalis' - --fq_prefix Path to fastq if not in sample_sheet /projects/b1059/projects/Katie/alignment-nf/test_data - --kmers Whether to count kmers false - --reference genome.fasta.gz to use in place of default /projects/b1059/data/c_elegans/genomes/PRJNA13758/WS283/c_elegans.PRJNA13758.WS283.genome.fa.gz - --output Output folder name. alignment-20220228-debug - - username kek973 - - ---------------------------------------------------------------------------------------------- - Git info: null - null [null] -WARN: Access to undefined parameter `help` -- Initialise it to a default value eg. `params.help = some_value` -[- ] process > alignment - -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[- ] process > merge_bam - -[- ] process > mark_dups - -[- ] process > coverage_id - -params blob is: true -yes to blobtools - -[- ] process > alignment - -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[- ] process > merge_bam - -[- ] process > mark_dups - -[- ] process > coverage_id - -[- ] process > idxstats_id - -[- ] process > flagstat_id - -[- ] process > stats_id - -[- ] process > multiqc_id - -[- ] process > coverage_strain - -[- ] process > idxstats_strain - -[- ] process > flagstat_strain - -[- ] process > stats_strain - -[- ] process > validatebam_strain - -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[- ] process > npr1_allele_check - -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - - -[- ] process > alignment - -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[- ] process > merge_bam - -[- ] process > mark_dups - -[- ] process > coverage_id - -[- ] process > idxstats_id - -[- ] process > flagstat_id - -[- ] process > stats_id - -[- ] process > multiqc_id - -[- ] process > coverage_strain - -[- ] process > idxstats_strain - -[- ] process > flagstat_strain - -[- ] process > stats_strain - -[- ] process > validatebam_strain - -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[- ] process > npr1_allele_check - -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[- ] process > alignment - -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[- ] process > merge_bam - -[- ] process > mark_dups - -[- ] process > coverage_id - -[- ] process > idxstats_id - -[- ] process > flagstat_id - -[- ] process > stats_id - -[- ] process > multiqc_id - -[- ] process > coverage_strain - -[- ] process > idxstats_strain - -[- ] process > flagstat_strain - -[- ] process > stats_strain - -[- ] process > validatebam_strain - -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[- ] process > npr1_allele_check - -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[- ] process > merge_bam - -[- ] process > mark_dups - -[- ] process > coverage_id - -[- ] process > idxstats_id - -[- ] process > flagstat_id - -[- ] process > stats_id - -[- ] process > multiqc_id - -[- ] process > coverage_strain - -[- ] process > idxstats_strain - -[- ] process > flagstat_strain - -[- ] process > stats_strain - -[- ] process > validatebam_strain - -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[- ] process > npr1_allele_check - -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[- ] process > merge_bam - -[- ] process > mark_dups - -[90/ee9928] process > coverage_id [100%] 7 of 7, cached: 7 -[0d/093474] process > idxstats_id [100%] 9 of 9, cached: 9 -[ad/a6f0a1] process > flagstat_id [100%] 10 of 10, cached: 10 -[f5/807728] process > stats_id [100%] 9 of 9, cached: 9 -[- ] process > multiqc_id - -[- ] process > coverage_strain - -[- ] process > idxstats_strain - -[- ] process > flagstat_strain - -[- ] process > stats_strain - -[- ] process > validatebam_strain - -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[- ] process > npr1_allele_check - -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[09/8fc635] process > merge_bam [100%] 1 of 1, cached: 1 -[- ] process > mark_dups - -[f8/5ca40f] process > coverage_id [100%] 15 of 15, cached: 15 -[16/c6b7f1] process > idxstats_id [100%] 15 of 15, cached: 15 -[e7/41830e] process > flagstat_id [100%] 15 of 15, cached: 15 -[4f/059cc3] process > stats_id [100%] 15 of 15, cached: 15 -[- ] process > multiqc_id - -[- ] process > coverage_strain - -[- ] process > idxstats_strain - -[- ] process > flagstat_strain - -[- ] process > stats_strain - -[- ] process > validatebam_strain - -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[- ] process > npr1_allele_check - -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[03/671a30] process > merge_bam [100%] 7 of 7, cached: 7 -[- ] process > mark_dups - -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 -[- ] process > multiqc_id - -[- ] process > coverage_strain - -[- ] process > idxstats_strain - -[- ] process > flagstat_strain - -[- ] process > stats_strain - -[- ] process > validatebam_strain - -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[- ] process > npr1_allele_check - -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[2a/e4d06f] process > merge_bam [100%] 16 of 16, cached: 16 -[f3/ac61de] process > mark_dups [100%] 7 of 7, cached: 7 -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 ✔ -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 ✔ -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 ✔ -[- ] process > multiqc_id - -[f3/b5f4df] process > coverage_strain [100%] 1 of 1, cached: 1 -[- ] process > idxstats_strain - -[2f/f0e454] process > flagstat_strain [100%] 1 of 1, cached: 1 -[49/45a00e] process > stats_strain [100%] 1 of 1, cached: 1 -[3f/40059b] process > validatebam_strain [100%] 1 of 1, cached: 1 -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[dd/8010e0] process > npr1_allele_check [100%] 7 of 7, cached: 7 -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[2a/e4d06f] process > merge_bam [100%] 16 of 16, cached: 16 ✔ -[8e/518159] process > mark_dups [100%] 15 of 15, cached: 15 -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 ✔ -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 ✔ -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 ✔ -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 ✔ -[- ] process > multiqc_id - -[af/d86c7b] process > coverage_strain [100%] 7 of 7, cached: 7 -[6f/016763] process > idxstats_strain [100%] 8 of 8, cached: 8 -[6d/da1c35] process > flagstat_strain [100%] 8 of 8, cached: 8 -[7e/b83e21] process > stats_strain [100%] 7 of 7, cached: 7 -[2b/1f7a43] process > validatebam_strain [100%] 8 of 8, cached: 8 -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[2b/7fe307] process > npr1_allele_check [100%] 16 of 16, cached: 16 ✔ -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[2a/e4d06f] process > merge_bam [100%] 16 of 16, cached: 16 ✔ -[55/9d5354] process > mark_dups [100%] 16 of 16, cached: 16 -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 ✔ -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 ✔ -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 ✔ -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 ✔ -[- ] process > multiqc_id - -[84/978f6c] process > coverage_strain [100%] 16 of 16, cached: 16 -[e4/9fff45] process > idxstats_strain [100%] 16 of 16, cached: 16 -[df/23e07b] process > flagstat_strain [100%] 15 of 15, cached: 15 -[12/159583] process > stats_strain [100%] 16 of 16, cached: 16 -[f6/e57d85] process > validatebam_strain [100%] 16 of 16, cached: 16 -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[2b/7fe307] process > npr1_allele_check [100%] 16 of 16, cached: 16 ✔ -[- ] process > npr1_allele_count - -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[2a/e4d06f] process > merge_bam [100%] 16 of 16, cached: 16 ✔ -[55/9d5354] process > mark_dups [100%] 16 of 16, cached: 16 ✔ -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 ✔ -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 ✔ -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 ✔ -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 ✔ -[- ] process > multiqc_id - -[84/978f6c] process > coverage_strain [100%] 16 of 16, cached: 16 ✔ -[e4/9fff45] process > idxstats_strain [100%] 16 of 16, cached: 16 ✔ -[1e/cf80cd] process > flagstat_strain [100%] 16 of 16, cached: 16 ✔ -[12/159583] process > stats_strain [100%] 16 of 16, cached: 16 ✔ -[f6/e57d85] process > validatebam_strain [100%] 16 of 16, cached: 16 ✔ -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[2b/7fe307] process > npr1_allele_check [100%] 16 of 16, cached: 16 ✔ -[de/129301] process > npr1_allele_count [100%] 1 of 1, cached: 1 ✔ -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[2a/e4d06f] process > merge_bam [100%] 16 of 16, cached: 16 ✔ -[55/9d5354] process > mark_dups [100%] 16 of 16, cached: 16 ✔ -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 ✔ -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 ✔ -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 ✔ -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 ✔ -[d3/c9174f] process > multiqc_id [100%] 1 of 1, cached: 1 ✔ -[84/978f6c] process > coverage_strain [100%] 16 of 16, cached: 16 ✔ -[e4/9fff45] process > idxstats_strain [100%] 16 of 16, cached: 16 ✔ -[1e/cf80cd] process > flagstat_strain [100%] 16 of 16, cached: 16 ✔ -[12/159583] process > stats_strain [100%] 16 of 16, cached: 16 ✔ -[f6/e57d85] process > validatebam_strain [100%] 16 of 16, cached: 16 ✔ -[- ] process > multiqc_strain - -[- ] process > coverage_report - -[2b/7fe307] process > npr1_allele_check [100%] 16 of 16, cached: 16 ✔ -[de/129301] process > npr1_allele_count [100%] 1 of 1, cached: 1 ✔ -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[2a/e4d06f] process > merge_bam [100%] 16 of 16, cached: 16 ✔ -[55/9d5354] process > mark_dups [100%] 16 of 16, cached: 16 ✔ -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 ✔ -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 ✔ -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 ✔ -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 ✔ -[d3/c9174f] process > multiqc_id [100%] 1 of 1, cached: 1 ✔ -[84/978f6c] process > coverage_strain [100%] 16 of 16, cached: 16 ✔ -[e4/9fff45] process > idxstats_strain [100%] 16 of 16, cached: 16 ✔ -[1e/cf80cd] process > flagstat_strain [100%] 16 of 16, cached: 16 ✔ -[12/159583] process > stats_strain [100%] 16 of 16, cached: 16 ✔ -[f6/e57d85] process > validatebam_strain [100%] 16 of 16, cached: 16 ✔ -[cb/480fb6] process > multiqc_strain [100%] 1 of 1, cached: 1 ✔ -[- ] process > coverage_report - -[2b/7fe307] process > npr1_allele_check [100%] 16 of 16, cached: 16 ✔ -[de/129301] process > npr1_allele_count [100%] 1 of 1, cached: 1 ✔ -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[2a/e4d06f] process > merge_bam [100%] 16 of 16, cached: 16 ✔ -[55/9d5354] process > mark_dups [100%] 16 of 16, cached: 16 ✔ -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 ✔ -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 ✔ -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 ✔ -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 ✔ -[d3/c9174f] process > multiqc_id [100%] 1 of 1, cached: 1 ✔ -[84/978f6c] process > coverage_strain [100%] 16 of 16, cached: 16 ✔ -[e4/9fff45] process > idxstats_strain [100%] 16 of 16, cached: 16 ✔ -[1e/cf80cd] process > flagstat_strain [100%] 16 of 16, cached: 16 ✔ -[12/159583] process > stats_strain [100%] 16 of 16, cached: 16 ✔ -[f6/e57d85] process > validatebam_strain [100%] 16 of 16, cached: 16 ✔ -[cb/480fb6] process > multiqc_strain [100%] 1 of 1, cached: 1 ✔ -[8b/21e375] process > coverage_report [100%] 1 of 1, cached: 1 ✔ -[2b/7fe307] process > npr1_allele_check [100%] 16 of 16, cached: 16 ✔ -[de/129301] process > npr1_allele_count [100%] 1 of 1, cached: 1 ✔ -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - - -[e1/7ebab5] process > alignment [100%] 16 of 16, cached: 16 ✔ -[- ] process > kmer_counting - -[- ] process > aggregate_kmer - -[2a/e4d06f] process > merge_bam [100%] 16 of 16, cached: 16 ✔ -[55/9d5354] process > mark_dups [100%] 16 of 16, cached: 16 ✔ -[ea/cc4eda] process > coverage_id [100%] 16 of 16, cached: 16 ✔ -[c1/89b8b5] process > idxstats_id [100%] 16 of 16, cached: 16 ✔ -[bd/ac46a5] process > flagstat_id [100%] 16 of 16, cached: 16 ✔ -[23/cae4ab] process > stats_id [100%] 16 of 16, cached: 16 ✔ -[d3/c9174f] process > multiqc_id [100%] 1 of 1, cached: 1 ✔ -[84/978f6c] process > coverage_strain [100%] 16 of 16, cached: 16 ✔ -[e4/9fff45] process > idxstats_strain [100%] 16 of 16, cached: 16 ✔ -[1e/cf80cd] process > flagstat_strain [100%] 16 of 16, cached: 16 ✔ -[12/159583] process > stats_strain [100%] 16 of 16, cached: 16 ✔ -[f6/e57d85] process > validatebam_strain [100%] 16 of 16, cached: 16 ✔ -[cb/480fb6] process > multiqc_strain [100%] 1 of 1, cached: 1 ✔ -[8b/21e375] process > coverage_report [100%] 1 of 1, cached: 1 ✔ -[2b/7fe307] process > npr1_allele_check [100%] 16 of 16, cached: 16 ✔ -[de/129301] process > npr1_allele_count [100%] 1 of 1, cached: 1 ✔ -[- ] process > blob_align - -[- ] process > blob_assemble - -[- ] process > blob_unmapped - -[- ] process > blob_blast - -[- ] process > blob_plot - -WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.