[2023-04-26 13:24:59,433] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-04-26 13:24:59,458] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-04-26 13:24:59,458] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-04-26 13:24:59,458] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-04-26 13:24:59,459] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-04-26 13:24:59,459] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-04-26 13:24:59,459] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-04-26 13:24:59,459] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-04-26 13:25:04,908] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-04-26 13:25:04,908] multiqc [INFO ] This is MultiQC v1.8 [2023-04-26 13:25:04,911] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-04-26 13:25:04,911] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230426-pgen-fastqc-fastp-multiqc-RNAseq [2023-04-26 13:25:04,911] multiqc [INFO ] Template : default [2023-04-26 13:25:04,911] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-04-26 13:25:04,911] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230426-pgen-fastqc-fastp-multiqc-RNAseq [2023-04-26 13:25:04,912] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, minionqc, mosdepth, clusterflow, bcl2fastq, interop, flash, seqyclean [2023-04-26 13:25:04,912] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmphvuh3fgn [2023-04-26 13:25:05,710] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: heart_1_val_1.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,711] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ctenidia.fastp-trim.20230426.report.html [2023-04-26 13:25:05,711] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: gonad_2_val_2.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,711] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: heart_2_val_2.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,712] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: larvae_1_val_1.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,713] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: gonad_2_val_2_fastqc.html [2023-04-26 13:25:05,713] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: larvae_2_val_2.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,714] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: juvenile_2_val_2.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,715] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: gonad_1_val_1_fastqc.html [2023-04-26 13:25:05,715] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: heart_1_val_1_fastqc.html [2023-04-26 13:25:05,715] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: heart.fastp-trim.20230426.report.html [2023-04-26 13:25:05,716] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ctenidia_2_val_2.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,716] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ctenidia_1_val_1.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,744] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-4565163.out [2023-04-26 13:25:05,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-4565163.out [2023-04-26 13:25:05,814] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: heart_2_val_2.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,814] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: gonad.fastp-trim.20230426.report.html [2023-04-26 13:25:05,814] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-04-26 13:25:05,814] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ctenidia_2_val_2.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,815] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: heart_1_val_1.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,815] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: larvae.fastp-trim.20230426.report.html [2023-04-26 13:25:05,816] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: juvenile_2_val_2.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,816] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: juvenile.fastp-trim.20230426.report.html [2023-04-26 13:25:05,816] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: gonad_1_val_1.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,816] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ctenidia_1_val_1_fastqc.html [2023-04-26 13:25:05,816] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: larvae_2_val_2.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,816] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: gonad_1_val_1.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,817] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ctenidia_2_val_2_fastqc.html [2023-04-26 13:25:05,817] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: larvae_1_val_1_fastqc.html [2023-04-26 13:25:05,817] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: juvenile_2_val_2_fastqc.html [2023-04-26 13:25:05,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20230426-pgen-fastqc-fastp-multiqc-RNAseq.sh [2023-04-26 13:25:05,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20230426-pgen-fastqc-fastp-multiqc-RNAseq.sh [2023-04-26 13:25:05,892] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: input_fastq_checksums.md5 [2023-04-26 13:25:05,893] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: larvae_1_val_1.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,893] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ctenidia_1_val_1.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,893] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: juvenile_1_val_1.fastp-trim.20230426_fastqc.html [2023-04-26 13:25:05,894] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: gonad_2_val_2.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,895] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: heart_2_val_2_fastqc.html [2023-04-26 13:25:05,895] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: juvenile_1_val_1.fastp-trim.20230426.fq.gz [2023-04-26 13:25:05,896] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: larvae_2_val_2_fastqc.html [2023-04-26 13:25:05,896] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: juvenile_1_val_1_fastqc.html [2023-04-26 13:25:10,467] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-04-26 13:25:10,486] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-04-26 13:25:10,516] multiqc [DEBUG ] No samples found: custom_content [2023-04-26 13:25:10,542] multiqc [DEBUG ] No samples found: conpair [2023-04-26 13:25:10,628] multiqc [DEBUG ] No samples found: peddy [2023-04-26 13:25:10,741] multiqc [DEBUG ] No samples found: methylQA [2023-04-26 13:25:10,754] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-04-26 13:25:10,846] multiqc [DEBUG ] No samples found: qualimap [2023-04-26 13:25:10,878] multiqc [DEBUG ] No samples found: preseq [2023-04-26 13:25:10,911] multiqc [DEBUG ] No samples found: quast [2023-04-26 13:25:10,932] multiqc [DEBUG ] No samples found: qorts [2023-04-26 13:25:11,010] multiqc [DEBUG ] No samples found: rna_seqc [2023-04-26 13:25:11,068] multiqc [DEBUG ] No samples found: rsem [2023-04-26 13:25:11,141] multiqc [DEBUG ] No samples found: rseqc [2023-04-26 13:25:11,168] multiqc [DEBUG ] No samples found: busco [2023-04-26 13:25:11,215] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-04-26 13:25:11,247] multiqc [DEBUG ] No samples found: disambiguate [2023-04-26 13:25:11,268] multiqc [DEBUG ] No samples found: supernova [2023-04-26 13:25:11,363] multiqc [DEBUG ] No samples found: deeptools [2023-04-26 13:25:11,421] multiqc [DEBUG ] No samples found: sargasso [2023-04-26 13:25:11,476] multiqc [DEBUG ] No samples found: verifybamid [2023-04-26 13:25:11,514] multiqc [DEBUG ] No samples found: mirtrace [2023-04-26 13:25:11,550] multiqc [DEBUG ] No samples found: happy [2023-04-26 13:25:11,609] multiqc [DEBUG ] No samples found: homer [2023-04-26 13:25:11,638] multiqc [DEBUG ] No samples found: macs2 [2023-04-26 13:25:11,649] multiqc [DEBUG ] No samples found: theta2 [2023-04-26 13:25:11,662] multiqc [DEBUG ] No samples found: snpeff [2023-04-26 13:25:11,715] multiqc [DEBUG ] No samples found: gatk [2023-04-26 13:25:11,727] multiqc [DEBUG ] No samples found: htseq [2023-04-26 13:25:11,769] multiqc [DEBUG ] No samples found: bcftools [2023-04-26 13:25:11,780] multiqc [DEBUG ] No samples found: featureCounts [2023-04-26 13:25:11,794] multiqc [DEBUG ] No samples found: fgbio [2023-04-26 13:25:11,805] multiqc [DEBUG ] No samples found: dedup [2023-04-26 13:25:11,830] multiqc [DEBUG ] No samples found: damageprofiler [2023-04-26 13:25:12,030] multiqc [DEBUG ] No samples found: biobambam2 [2023-04-26 13:25:12,061] multiqc [DEBUG ] No samples found: mtnucratio [2023-04-26 13:25:12,068] multiqc [DEBUG ] No samples found: picard [2023-04-26 13:25:12,090] multiqc [DEBUG ] No samples found: prokka [2023-04-26 13:25:12,101] multiqc [DEBUG ] No samples found: samblaster [2023-04-26 13:25:12,211] multiqc [DEBUG ] No samples found: samtools [2023-04-26 13:25:12,223] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-04-26 13:25:12,272] multiqc [DEBUG ] No samples found: bamtools [2023-04-26 13:25:12,284] multiqc [DEBUG ] No samples found: jellyfish [2023-04-26 13:25:12,328] multiqc [DEBUG ] No samples found: vcftools [2023-04-26 13:25:12,365] multiqc [DEBUG ] No samples found: longranger [2023-04-26 13:25:12,410] multiqc [DEBUG ] No samples found: stacks [2023-04-26 13:25:12,501] multiqc [DEBUG ] No samples found: bbmap [2023-04-26 13:25:12,545] multiqc [DEBUG ] No samples found: bismark [2023-04-26 13:25:12,565] multiqc [DEBUG ] No samples found: biscuit [2023-04-26 13:25:12,599] multiqc [DEBUG ] No samples found: hicexplorer [2023-04-26 13:25:12,634] multiqc [DEBUG ] No samples found: hicup [2023-04-26 13:25:12,677] multiqc [DEBUG ] No samples found: hicpro [2023-04-26 13:25:12,688] multiqc [DEBUG ] No samples found: salmon [2023-04-26 13:25:12,711] multiqc [DEBUG ] No samples found: kallisto [2023-04-26 13:25:12,728] multiqc [DEBUG ] No samples found: slamdunk [2023-04-26 13:25:12,755] multiqc [DEBUG ] No samples found: star [2023-04-26 13:25:12,780] multiqc [DEBUG ] No samples found: hisat2 [2023-04-26 13:25:12,810] multiqc [DEBUG ] No samples found: tophat [2023-04-26 13:25:12,838] multiqc [DEBUG ] No samples found: bowtie2 [2023-04-26 13:25:12,859] multiqc [DEBUG ] No samples found: bowtie1 [2023-04-26 13:25:12,870] multiqc [DEBUG ] No samples found: kat [2023-04-26 13:25:12,882] multiqc [DEBUG ] No samples found: leehom [2023-04-26 13:25:12,922] multiqc [DEBUG ] No samples found: adapterRemoval [2023-04-26 13:25:12,934] multiqc [DEBUG ] No samples found: clipandmerge [2023-04-26 13:25:12,959] multiqc [DEBUG ] No samples found: cutadapt [2023-04-26 13:25:12,971] multiqc [DEBUG ] No samples found: flexbar [2023-04-26 13:25:13,003] multiqc [DEBUG ] No samples found: trimmomatic [2023-04-26 13:25:13,016] multiqc [DEBUG ] No samples found: skewer [2023-04-26 13:25:13,027] multiqc [DEBUG ] No samples found: sortmerna [2023-04-26 13:25:13,039] multiqc [DEBUG ] No samples found: biobloomtools [2023-04-26 13:25:13,075] multiqc [DEBUG ] No samples found: fastq_screen [2023-04-26 13:25:13,133] multiqc [DEBUG ] No samples found: afterqc [2023-04-26 13:25:13,167] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: ctenidia.fastp-trim.20230426.report.json [2023-04-26 13:25:13,195] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: heart.fastp-trim.20230426.report.json [2023-04-26 13:25:13,241] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: juvenile.fastp-trim.20230426.report.json [2023-04-26 13:25:13,261] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: larvae.fastp-trim.20230426.report.json [2023-04-26 13:25:13,276] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: gonad.fastp-trim.20230426.report.json [2023-04-26 13:25:13,278] multiqc.modules.fastp.fastp [INFO ] Found 5 reports [2023-04-26 13:25:13,429] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'juvenile_2_val_2_fastqc.zip' as already parsed 'juvenile_2_val_2' [2023-04-26 13:25:13,473] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'larvae_2_val_2_fastqc.zip' as already parsed 'larvae_2_val_2' [2023-04-26 13:25:13,473] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'gonad_1_val_1_fastqc.zip' as already parsed 'gonad_1_val_1' [2023-04-26 13:25:13,501] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: gonad_2_val_2 [2023-04-26 13:25:13,539] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'juvenile_1_val_1_fastqc.zip' as already parsed 'juvenile_1_val_1' [2023-04-26 13:25:13,544] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'heart_1_val_1_fastqc.zip' as already parsed 'heart_1_val_1' [2023-04-26 13:25:13,545] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'ctenidia_1_val_1_fastqc.zip' as already parsed 'ctenidia_1_val_1' [2023-04-26 13:25:13,545] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'larvae_1_val_1_fastqc.zip' as already parsed 'larvae_1_val_1' [2023-04-26 13:25:13,546] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: ctenidia_2_val_2 [2023-04-26 13:25:13,551] multiqc.modules.fastqc.fastqc [DEBUG ] Skipping 'heart_2_val_2_fastqc.zip' as already parsed 'heart_2_val_2' [2023-04-26 13:25:13,551] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-04-26 13:25:13,840] multiqc [DEBUG ] No samples found: minionqc [2023-04-26 13:25:13,857] multiqc [DEBUG ] No samples found: mosdepth [2023-04-26 13:25:13,874] multiqc [DEBUG ] No samples found: clusterflow [2023-04-26 13:25:13,882] multiqc [DEBUG ] No samples found: bcl2fastq [2023-04-26 13:25:13,901] multiqc [DEBUG ] No samples found: interop [2023-04-26 13:25:13,915] multiqc [DEBUG ] No samples found: flash [2023-04-26 13:25:13,944] multiqc [DEBUG ] No samples found: seqyclean [2023-04-26 13:25:13,972] multiqc [INFO ] Compressing plot data [2023-04-26 13:25:14,494] multiqc [INFO ] Report : multiqc_report.html [2023-04-26 13:25:14,495] multiqc [INFO ] Data : multiqc_data [2023-04-26 13:25:14,496] multiqc [DEBUG ] Moving data file from '/tmp/tmphvuh3fgn/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230426-pgen-fastqc-fastp-multiqc-RNAseq/multiqc_data' [2023-04-26 13:25:14,497] multiqc [DEBUG ] Moving data file from '/tmp/tmphvuh3fgn/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230426-pgen-fastqc-fastp-multiqc-RNAseq/multiqc_data' [2023-04-26 13:25:14,498] multiqc [DEBUG ] Moving data file from '/tmp/tmphvuh3fgn/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230426-pgen-fastqc-fastp-multiqc-RNAseq/multiqc_data' [2023-04-26 13:25:14,499] multiqc [DEBUG ] Moving data file from '/tmp/tmphvuh3fgn/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230426-pgen-fastqc-fastp-multiqc-RNAseq/multiqc_data' [2023-04-26 13:25:14,500] multiqc [DEBUG ] Moving data file from '/tmp/tmphvuh3fgn/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230426-pgen-fastqc-fastp-multiqc-RNAseq/multiqc_data' [2023-04-26 13:25:14,501] multiqc [DEBUG ] Moving data file from '/tmp/tmphvuh3fgn/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230426-pgen-fastqc-fastp-multiqc-RNAseq/multiqc_data' [2023-04-26 13:25:15,101] multiqc [INFO ] MultiQC complete