[2020-04-14 08:03:57,161] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-04-14 08:03:57,201] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-04-14 08:03:57,201] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-04-14 08:03:57,201] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-04-14 08:03:57,201] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-04-14 08:04:02,369] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-04-14 08:04:02,370] multiqc [INFO ] This is MultiQC v1.8 [2020-04-14 08:04:02,373] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-04-14 08:04:02,373] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20200414_cbai_RNAseq_fastp_trimming [2020-04-14 08:04:02,373] multiqc [INFO ] Template : default [2020-04-14 08:04:02,374] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-04-14 08:04:02,374] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20200414_cbai_RNAseq_fastp_trimming [2020-04-14 08:04:02,375] 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 [2020-04-14 08:04:02,375] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpr7b0c7ws [2020-04-14 08:04:03,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L002_R1_001.fastp-trim.202004145558.fq.gz [2020-04-14 08:04:03,658] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L002_R1_001.fastp-trim.202004144633.fq.gz [2020-04-14 08:04:03,658] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L001_R2_001.fastp-trim.202004144409.fq.gz [2020-04-14 08:04:03,670] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L002_R2_001.fastp-trim.202004144633_fastqc.html [2020-04-14 08:04:03,670] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L001_R1_001.fastp-trim.202004144409_fastqc.html [2020-04-14 08:04:03,671] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L001_R1_001.fastp-trim.202004145835.fq.gz [2020-04-14 08:04:03,671] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L002_R1_001.fastp-trim.202004145558_fastqc.html [2020-04-14 08:04:03,671] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L002_R2_001.fastp-trim.202004145106_fastqc.html [2020-04-14 08:04:03,710] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20200414_cbai_RNAseq_fastp_trimming.sh [2020-04-14 08:04:03,718] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L001_R1_001.fastp-trim.202004143431.report.html [2020-04-14 08:04:03,718] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L001_R1_001.fastp-trim.202004145835.report.html [2020-04-14 08:04:03,718] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L002_R2_001.fastp-trim.202004140109.fq.gz [2020-04-14 08:04:03,718] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L002_R2_001.fastp-trim.202004145558.fq.gz [2020-04-14 08:04:03,718] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L001_R1_001.fastp-trim.202004145320_fastqc.html [2020-04-14 08:04:03,719] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L001_R2_001.fastp-trim.202004144852.fq.gz [2020-04-14 08:04:03,719] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L002_R2_001.fastp-trim.202004145558_fastqc.html [2020-04-14 08:04:03,719] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L002_R1_001.fastp-trim.202004145558.report.html [2020-04-14 08:04:03,719] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L002_R1_001.fastp-trim.202004144145.report.html [2020-04-14 08:04:03,719] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L001_R1_001.fastp-trim.202004145320.report.html [2020-04-14 08:04:03,719] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L002_R2_001.fastp-trim.202004143700_fastqc.html [2020-04-14 08:04:03,724] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L002_R1_001.fastp-trim.202004143700.report.html [2020-04-14 08:04:03,724] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L001_R1_001.fastp-trim.202004143925.report.html [2020-04-14 08:04:03,765] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: program_options.log [2020-04-14 08:04:03,768] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: program_options.log [2020-04-14 08:04:03,786] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L001_R1_001.fastp-trim.202004144852.fq.gz [2020-04-14 08:04:03,786] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L001_R2_001.fastp-trim.202004143925.fq.gz [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L001_R1_001.fastp-trim.202004144409.report.html [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L002_R1_001.fastp-trim.202004145106.report.html [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 20200413_cbai_checkums.md5 [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L001_R1_001.fastp-trim.202004143925_fastqc.html [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L002_R2_001.fastp-trim.202004144145.fq.gz [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L001_R1_001.fastp-trim.202004145835_fastqc.html [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L001_R2_001.fastp-trim.202004145320.fq.gz [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L002_R2_001.fastp-trim.202004145106.fq.gz [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L002_R2_001.fastp-trim.202004143700.fq.gz [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L002_R2_001.fastp-trim.202004144145_fastqc.html [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L001_R2_001.fastp-trim.202004144852_fastqc.html [2020-04-14 08:04:03,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L002_R1_001.fastp-trim.202004144145_fastqc.html [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L002_R1_001.fastp-trim.202004143700.fq.gz [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L001_R2_001.fastp-trim.202004143925_fastqc.html [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L001_R1_001.fastp-trim.202004145320.fq.gz [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L002_R1_001.fastp-trim.202004143700_fastqc.html [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L001_R1_001.fastp-trim.202004144852_fastqc.html [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L002_R1_001.fastp-trim.202004140109.report.html [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L002_R1_001.fastp-trim.202004140109_fastqc.html [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L002_R1_001.fastp-trim.202004144633_fastqc.html [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L002_R1_001.fastp-trim.202004140109.fq.gz [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L001_R1_001.fastp-trim.202004144852.report.html [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L001_R2_001.fastp-trim.202004145835.fq.gz [2020-04-14 08:04:03,788] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L001_R1_001.fastp-trim.202004143925.fq.gz [2020-04-14 08:04:03,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L002_R1_001.fastp-trim.202004145106.fq.gz [2020-04-14 08:04:03,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L001_R2_001.fastp-trim.202004144409_fastqc.html [2020-04-14 08:04:03,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L001_R2_001.fastp-trim.202004145835_fastqc.html [2020-04-14 08:04:03,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380824_S5_L001_R2_001.fastp-trim.202004145320_fastqc.html [2020-04-14 08:04:03,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L001_R2_001.fastp-trim.202004143431_fastqc.html [2020-04-14 08:04:03,789] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L001_R1_001.fastp-trim.202004144409.fq.gz [2020-04-14 08:04:03,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380821_S2_L002_R1_001.fastp-trim.202004144145.fq.gz [2020-04-14 08:04:03,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L001_R1_001.fastp-trim.202004143431_fastqc.html [2020-04-14 08:04:03,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380825_S6_L002_R2_001.fastp-trim.202004140109_fastqc.html [2020-04-14 08:04:03,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380823_S4_L002_R1_001.fastp-trim.202004145106_fastqc.html [2020-04-14 08:04:03,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L002_R1_001.fastp-trim.202004144633.report.html [2020-04-14 08:04:03,793] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2490192.out [2020-04-14 08:04:03,793] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2490192.out [2020-04-14 08:04:03,815] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L001_R2_001.fastp-trim.202004143431.fq.gz [2020-04-14 08:04:03,815] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380820_S1_L001_R1_001.fastp-trim.202004143431.fq.gz [2020-04-14 08:04:03,815] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 380822_S3_L002_R2_001.fastp-trim.202004144633.fq.gz [2020-04-14 08:04:08,908] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-04-14 08:04:08,934] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-04-14 08:04:08,999] multiqc [DEBUG ] No samples found: custom_content [2020-04-14 08:04:09,079] multiqc [DEBUG ] No samples found: conpair [2020-04-14 08:04:09,188] multiqc [DEBUG ] No samples found: peddy [2020-04-14 08:04:09,274] multiqc [DEBUG ] No samples found: methylQA [2020-04-14 08:04:09,318] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-04-14 08:04:09,478] multiqc [DEBUG ] No samples found: qualimap [2020-04-14 08:04:09,518] multiqc [DEBUG ] No samples found: preseq [2020-04-14 08:04:09,560] multiqc [DEBUG ] No samples found: quast [2020-04-14 08:04:09,594] multiqc [DEBUG ] No samples found: qorts [2020-04-14 08:04:09,694] multiqc [DEBUG ] No samples found: rna_seqc [2020-04-14 08:04:09,780] multiqc [DEBUG ] No samples found: rsem [2020-04-14 08:04:09,953] multiqc [DEBUG ] No samples found: rseqc [2020-04-14 08:04:10,004] multiqc [DEBUG ] No samples found: busco [2020-04-14 08:04:10,159] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-04-14 08:04:10,206] multiqc [DEBUG ] No samples found: disambiguate [2020-04-14 08:04:10,236] multiqc [DEBUG ] No samples found: supernova [2020-04-14 08:04:10,422] multiqc [DEBUG ] No samples found: deeptools [2020-04-14 08:04:10,469] multiqc [DEBUG ] No samples found: sargasso [2020-04-14 08:04:10,576] multiqc [DEBUG ] No samples found: verifybamid [2020-04-14 08:04:10,603] multiqc [DEBUG ] No samples found: mirtrace [2020-04-14 08:04:10,642] multiqc [DEBUG ] No samples found: happy [2020-04-14 08:04:10,699] multiqc [DEBUG ] No samples found: homer [2020-04-14 08:04:10,727] multiqc [DEBUG ] No samples found: macs2 [2020-04-14 08:04:10,762] multiqc [DEBUG ] No samples found: theta2 [2020-04-14 08:04:10,806] multiqc [DEBUG ] No samples found: snpeff [2020-04-14 08:04:10,900] multiqc [DEBUG ] No samples found: gatk [2020-04-14 08:04:10,926] multiqc [DEBUG ] No samples found: htseq [2020-04-14 08:04:11,007] multiqc [DEBUG ] No samples found: bcftools [2020-04-14 08:04:11,020] multiqc [DEBUG ] No samples found: featureCounts [2020-04-14 08:04:11,046] multiqc [DEBUG ] No samples found: fgbio [2020-04-14 08:04:11,058] multiqc [DEBUG ] No samples found: dedup [2020-04-14 08:04:11,090] multiqc [DEBUG ] No samples found: damageprofiler [2020-04-14 08:04:11,337] multiqc [DEBUG ] No samples found: biobambam2 [2020-04-14 08:04:11,361] multiqc [DEBUG ] No samples found: mtnucratio [2020-04-14 08:04:11,369] multiqc [DEBUG ] No samples found: picard [2020-04-14 08:04:11,413] multiqc [DEBUG ] No samples found: prokka [2020-04-14 08:04:11,426] multiqc [DEBUG ] No samples found: samblaster [2020-04-14 08:04:11,574] multiqc [DEBUG ] No samples found: samtools [2020-04-14 08:04:11,629] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-04-14 08:04:11,729] multiqc [DEBUG ] No samples found: bamtools [2020-04-14 08:04:11,745] multiqc [DEBUG ] No samples found: jellyfish [2020-04-14 08:04:11,776] multiqc [DEBUG ] No samples found: vcftools [2020-04-14 08:04:11,805] multiqc [DEBUG ] No samples found: longranger [2020-04-14 08:04:11,841] multiqc [DEBUG ] No samples found: stacks [2020-04-14 08:04:11,993] multiqc [DEBUG ] No samples found: bbmap [2020-04-14 08:04:12,035] multiqc [DEBUG ] No samples found: bismark [2020-04-14 08:04:12,071] multiqc [DEBUG ] No samples found: biscuit [2020-04-14 08:04:12,097] multiqc [DEBUG ] No samples found: hicexplorer [2020-04-14 08:04:12,129] multiqc [DEBUG ] No samples found: hicup [2020-04-14 08:04:12,158] multiqc [DEBUG ] No samples found: hicpro [2020-04-14 08:04:12,170] multiqc [DEBUG ] No samples found: salmon [2020-04-14 08:04:12,203] multiqc [DEBUG ] No samples found: kallisto [2020-04-14 08:04:12,230] multiqc [DEBUG ] No samples found: slamdunk [2020-04-14 08:04:12,259] multiqc [DEBUG ] No samples found: star [2020-04-14 08:04:12,293] multiqc [DEBUG ] No samples found: hisat2 [2020-04-14 08:04:12,319] multiqc [DEBUG ] No samples found: tophat [2020-04-14 08:04:12,365] multiqc [DEBUG ] No samples found: bowtie2 [2020-04-14 08:04:12,398] multiqc [DEBUG ] No samples found: bowtie1 [2020-04-14 08:04:12,411] multiqc [DEBUG ] No samples found: kat [2020-04-14 08:04:12,420] multiqc [DEBUG ] No samples found: leehom [2020-04-14 08:04:12,476] multiqc [DEBUG ] No samples found: adapterRemoval [2020-04-14 08:04:12,489] multiqc [DEBUG ] No samples found: clipandmerge [2020-04-14 08:04:12,527] multiqc [DEBUG ] No samples found: cutadapt [2020-04-14 08:04:12,540] multiqc [DEBUG ] No samples found: flexbar [2020-04-14 08:04:12,569] multiqc [DEBUG ] No samples found: trimmomatic [2020-04-14 08:04:12,604] multiqc [DEBUG ] No samples found: skewer [2020-04-14 08:04:12,618] multiqc [DEBUG ] No samples found: sortmerna [2020-04-14 08:04:12,640] multiqc [DEBUG ] No samples found: biobloomtools [2020-04-14 08:04:12,655] multiqc [DEBUG ] No samples found: fastq_screen [2020-04-14 08:04:12,702] multiqc [DEBUG ] No samples found: afterqc [2020-04-14 08:04:13,011] multiqc.modules.fastp.fastp [INFO ] Found 12 reports [2020-04-14 08:04:15,581] multiqc.modules.fastqc.fastqc [INFO ] Found 24 reports [2020-04-14 08:04:15,823] multiqc [DEBUG ] No samples found: minionqc [2020-04-14 08:04:15,886] multiqc [DEBUG ] No samples found: mosdepth [2020-04-14 08:04:15,923] multiqc [DEBUG ] No samples found: clusterflow [2020-04-14 08:04:15,997] multiqc [DEBUG ] No samples found: bcl2fastq [2020-04-14 08:04:16,045] multiqc [DEBUG ] No samples found: interop [2020-04-14 08:04:16,070] multiqc [DEBUG ] No samples found: flash [2020-04-14 08:04:16,102] multiqc [DEBUG ] No samples found: seqyclean [2020-04-14 08:04:16,148] multiqc [INFO ] Compressing plot data [2020-04-14 08:04:16,781] multiqc [INFO ] Report : multiqc_report.html [2020-04-14 08:04:16,782] multiqc [INFO ] Data : multiqc_data [2020-04-14 08:04:16,783] multiqc [DEBUG ] Moving data file from '/tmp/tmpr7b0c7ws/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20200414_cbai_RNAseq_fastp_trimming/multiqc_data' [2020-04-14 08:04:16,784] multiqc [DEBUG ] Moving data file from '/tmp/tmpr7b0c7ws/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20200414_cbai_RNAseq_fastp_trimming/multiqc_data' [2020-04-14 08:04:16,785] multiqc [DEBUG ] Moving data file from '/tmp/tmpr7b0c7ws/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20200414_cbai_RNAseq_fastp_trimming/multiqc_data' [2020-04-14 08:04:16,786] multiqc [DEBUG ] Moving data file from '/tmp/tmpr7b0c7ws/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20200414_cbai_RNAseq_fastp_trimming/multiqc_data' [2020-04-14 08:04:16,787] multiqc [DEBUG ] Moving data file from '/tmp/tmpr7b0c7ws/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20200414_cbai_RNAseq_fastp_trimming/multiqc_data' [2020-04-14 08:04:16,788] multiqc [DEBUG ] Moving data file from '/tmp/tmpr7b0c7ws/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20200414_cbai_RNAseq_fastp_trimming/multiqc_data' [2020-04-14 08:04:18,090] multiqc [INFO ] MultiQC complete