[2020-10-29 09:08:42,181] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-10-29 09:08:42,200] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-10-29 09:08:42,200] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-10-29 09:08:42,200] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2020-10-29 09:08:42,201] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-10-29 09:08:42,201] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-10-29 09:08:47,490] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-10-29 09:08:47,491] multiqc [INFO ] This is MultiQC v1.8 [2020-10-29 09:08:47,493] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-10-29 09:08:47,493] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/202001029_ssal_RNAseq_fastp_trimming [2020-10-29 09:08:47,493] multiqc [INFO ] Template : default [2020-10-29 09:08:47,493] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-10-29 09:08:47,493] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/202001029_ssal_RNAseq_fastp_trimming [2020-10-29 09:08:47,494] 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 [2020-10-29 09:08:47,494] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpcp4w56_w [2020-10-29 09:08:48,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_8_P_31_1.fastp-trim.20201029.fq.gz [2020-10-29 09:08:48,223] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20201029_ssal_RNAseq_fastp_trimming.sh [2020-10-29 09:08:48,224] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201029_ssal_RNAseq_fastp_trimming.sh [2020-10-29 09:08:48,234] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_8_P_31_2.fastp-trim.20201029.fq.gz [2020-10-29 09:08:48,234] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_16_P_31_2.fastp-trim.20201029.fq.gz [2020-10-29 09:08:48,235] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: raw_fastq_checksums.md5 [2020-10-29 09:08:48,239] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-426294.out [2020-10-29 09:08:48,240] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-426294.out [2020-10-29 09:08:48,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2020-10-29 09:08:48,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_16_P_31_2.fastp-trim.20201029.fq.gz [2020-10-29 09:08:48,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_16_P_31_1.fastp-trim.20201029.report.html [2020-10-29 09:08:48,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_8_P_31_1.fastp-trim.20201029.report.html [2020-10-29 09:08:48,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_8_P_31_1.fastp-trim.20201029.fq.gz [2020-10-29 09:08:48,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_16_P_31_1.fastp-trim.20201029.fq.gz [2020-10-29 09:08:48,253] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_16_P_31_1.fastp-trim.20201029.report.html [2020-10-29 09:08:48,254] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_8_P_31_1.fastp-trim.20201029.report.html [2020-10-29 09:08:48,254] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_8_P_31_2.fastp-trim.20201029.fq.gz [2020-10-29 09:08:48,254] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_16_P_31_1.fastp-trim.20201029.fq.gz [2020-10-29 09:08:53,154] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-10-29 09:08:53,173] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-10-29 09:08:53,215] multiqc [DEBUG ] No samples found: custom_content [2020-10-29 09:08:53,255] multiqc [DEBUG ] No samples found: conpair [2020-10-29 09:08:53,424] multiqc [DEBUG ] No samples found: peddy [2020-10-29 09:08:53,512] multiqc [DEBUG ] No samples found: methylQA [2020-10-29 09:08:53,533] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-10-29 09:08:53,671] multiqc [DEBUG ] No samples found: qualimap [2020-10-29 09:08:53,728] multiqc [DEBUG ] No samples found: preseq [2020-10-29 09:08:53,759] multiqc [DEBUG ] No samples found: quast [2020-10-29 09:08:53,793] multiqc [DEBUG ] No samples found: qorts [2020-10-29 09:08:53,849] multiqc [DEBUG ] No samples found: rna_seqc [2020-10-29 09:08:53,887] multiqc [DEBUG ] No samples found: rsem [2020-10-29 09:08:54,067] multiqc [DEBUG ] No samples found: rseqc [2020-10-29 09:08:54,127] multiqc [DEBUG ] No samples found: busco [2020-10-29 09:08:54,201] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-10-29 09:08:54,232] multiqc [DEBUG ] No samples found: disambiguate [2020-10-29 09:08:54,256] multiqc [DEBUG ] No samples found: supernova [2020-10-29 09:08:54,366] multiqc [DEBUG ] No samples found: deeptools [2020-10-29 09:08:54,401] multiqc [DEBUG ] No samples found: sargasso [2020-10-29 09:08:54,445] multiqc [DEBUG ] No samples found: verifybamid [2020-10-29 09:08:54,483] multiqc [DEBUG ] No samples found: mirtrace [2020-10-29 09:08:54,514] multiqc [DEBUG ] No samples found: happy [2020-10-29 09:08:54,550] multiqc [DEBUG ] No samples found: homer [2020-10-29 09:08:54,575] multiqc [DEBUG ] No samples found: macs2 [2020-10-29 09:08:54,584] multiqc [DEBUG ] No samples found: theta2 [2020-10-29 09:08:54,607] multiqc [DEBUG ] No samples found: snpeff [2020-10-29 09:08:54,676] multiqc [DEBUG ] No samples found: gatk [2020-10-29 09:08:54,686] multiqc [DEBUG ] No samples found: htseq [2020-10-29 09:08:54,718] multiqc [DEBUG ] No samples found: bcftools [2020-10-29 09:08:54,726] multiqc [DEBUG ] No samples found: featureCounts [2020-10-29 09:08:54,736] multiqc [DEBUG ] No samples found: fgbio [2020-10-29 09:08:54,744] multiqc [DEBUG ] No samples found: dedup [2020-10-29 09:08:54,783] multiqc [DEBUG ] No samples found: damageprofiler [2020-10-29 09:08:55,126] multiqc [DEBUG ] No samples found: biobambam2 [2020-10-29 09:08:55,148] multiqc [DEBUG ] No samples found: mtnucratio [2020-10-29 09:08:55,153] multiqc [DEBUG ] No samples found: picard [2020-10-29 09:08:55,236] multiqc [DEBUG ] No samples found: prokka [2020-10-29 09:08:55,246] multiqc [DEBUG ] No samples found: samblaster [2020-10-29 09:08:55,337] multiqc [DEBUG ] No samples found: samtools [2020-10-29 09:08:55,373] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-10-29 09:08:55,444] multiqc [DEBUG ] No samples found: bamtools [2020-10-29 09:08:55,454] multiqc [DEBUG ] No samples found: jellyfish [2020-10-29 09:08:55,481] multiqc [DEBUG ] No samples found: vcftools [2020-10-29 09:08:55,503] multiqc [DEBUG ] No samples found: longranger [2020-10-29 09:08:55,527] multiqc [DEBUG ] No samples found: stacks [2020-10-29 09:08:55,583] multiqc [DEBUG ] No samples found: bbmap [2020-10-29 09:08:55,607] multiqc [DEBUG ] No samples found: bismark [2020-10-29 09:08:55,619] multiqc [DEBUG ] No samples found: biscuit [2020-10-29 09:08:55,670] multiqc [DEBUG ] No samples found: hicexplorer [2020-10-29 09:08:55,691] multiqc [DEBUG ] No samples found: hicup [2020-10-29 09:08:55,718] multiqc [DEBUG ] No samples found: hicpro [2020-10-29 09:08:55,726] multiqc [DEBUG ] No samples found: salmon [2020-10-29 09:08:55,760] multiqc [DEBUG ] No samples found: kallisto [2020-10-29 09:08:55,783] multiqc [DEBUG ] No samples found: slamdunk [2020-10-29 09:08:55,798] multiqc [DEBUG ] No samples found: star [2020-10-29 09:08:55,831] multiqc [DEBUG ] No samples found: hisat2 [2020-10-29 09:08:55,851] multiqc [DEBUG ] No samples found: tophat [2020-10-29 09:08:55,885] multiqc [DEBUG ] No samples found: bowtie2 [2020-10-29 09:08:55,904] multiqc [DEBUG ] No samples found: bowtie1 [2020-10-29 09:08:55,911] multiqc [DEBUG ] No samples found: kat [2020-10-29 09:08:55,918] multiqc [DEBUG ] No samples found: leehom [2020-10-29 09:08:55,947] multiqc [DEBUG ] No samples found: adapterRemoval [2020-10-29 09:08:55,954] multiqc [DEBUG ] No samples found: clipandmerge [2020-10-29 09:08:55,977] multiqc [DEBUG ] No samples found: cutadapt [2020-10-29 09:08:55,984] multiqc [DEBUG ] No samples found: flexbar [2020-10-29 09:08:56,008] multiqc [DEBUG ] No samples found: trimmomatic [2020-10-29 09:08:56,063] multiqc [DEBUG ] No samples found: skewer [2020-10-29 09:08:56,073] multiqc [DEBUG ] No samples found: sortmerna [2020-10-29 09:08:56,101] multiqc [DEBUG ] No samples found: biobloomtools [2020-10-29 09:08:56,119] multiqc [DEBUG ] No samples found: fastq_screen [2020-10-29 09:08:56,190] multiqc [DEBUG ] No samples found: afterqc [2020-10-29 09:08:56,356] multiqc.modules.fastp.fastp [INFO ] Found 4 reports [2020-10-29 09:08:56,426] multiqc [DEBUG ] No samples found: fastqc [2020-10-29 09:08:56,451] multiqc [DEBUG ] No samples found: minionqc [2020-10-29 09:08:56,490] multiqc [DEBUG ] No samples found: mosdepth [2020-10-29 09:08:56,524] multiqc [DEBUG ] No samples found: clusterflow [2020-10-29 09:08:56,568] multiqc [DEBUG ] No samples found: bcl2fastq [2020-10-29 09:08:56,590] multiqc [DEBUG ] No samples found: interop [2020-10-29 09:08:56,609] multiqc [DEBUG ] No samples found: flash [2020-10-29 09:08:56,633] multiqc [DEBUG ] No samples found: seqyclean [2020-10-29 09:08:56,646] multiqc [INFO ] Compressing plot data [2020-10-29 09:08:56,992] multiqc [INFO ] Report : multiqc_report.html [2020-10-29 09:08:56,994] multiqc [INFO ] Data : multiqc_data [2020-10-29 09:08:56,995] multiqc [DEBUG ] Moving data file from '/tmp/tmpcp4w56_w/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/202001029_ssal_RNAseq_fastp_trimming/multiqc_data' [2020-10-29 09:08:56,996] multiqc [DEBUG ] Moving data file from '/tmp/tmpcp4w56_w/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/202001029_ssal_RNAseq_fastp_trimming/multiqc_data' [2020-10-29 09:08:56,997] multiqc [DEBUG ] Moving data file from '/tmp/tmpcp4w56_w/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/202001029_ssal_RNAseq_fastp_trimming/multiqc_data' [2020-10-29 09:08:56,998] multiqc [DEBUG ] Moving data file from '/tmp/tmpcp4w56_w/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/202001029_ssal_RNAseq_fastp_trimming/multiqc_data' [2020-10-29 09:08:56,999] multiqc [DEBUG ] Moving data file from '/tmp/tmpcp4w56_w/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/202001029_ssal_RNAseq_fastp_trimming/multiqc_data' [2020-10-29 09:08:58,295] multiqc [INFO ] MultiQC complete