[2021-05-18 11:46:13,284] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-05-18 11:46:13,319] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2021-05-18 11:46:13,319] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2021-05-18 11:46:13,320] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2021-05-18 11:46:13,320] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2021-05-18 11:46:13,320] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2021-05-18 11:46:13,320] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-05-18 11:46:13,320] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-05-18 11:46:18,644] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-05-18 11:46:18,644] multiqc [INFO ] This is MultiQC v1.8 [2021-05-18 11:46:18,647] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-05-18 11:46:18,647] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20210518_olur_fastp_bgi [2021-05-18 11:46:18,648] multiqc [INFO ] Template : default [2021-05-18 11:46:18,648] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-05-18 11:46:18,648] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20210518_olur_fastp_bgi [2021-05-18 11:46:18,649] 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 [2021-05-18 11:46:18,649] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpyy7lfft6 [2021-05-18 11:46:19,302] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66.fastp-trim.20210518.report.html [2021-05-18 11:46:19,302] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75.fastp-trim.20210518.report.html [2021-05-18 11:46:19,302] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,304] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,305] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74.fastp-trim.20210518.report.html [2021-05-18 11:46:19,364] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20210518_olur_fastp_bgi.sh [2021-05-18 11:46:19,368] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20210518_olur_fastp_bgi.sh [2021-05-18 11:46:19,399] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96.fastp-trim.20210518.report.html [2021-05-18 11:46:19,399] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75.fastp-trim.20210518.report.html [2021-05-18 11:46:19,400] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: raw_fastq_checksums.md5 [2021-05-18 11:46:19,401] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,401] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,401] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,409] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-1921654.out [2021-05-18 11:46:19,411] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-1921654.out [2021-05-18 11:46:19,437] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,437] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,437] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74.fastp-trim.20210518.report.html [2021-05-18 11:46:19,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62.fastp-trim.20210518.report.html [2021-05-18 11:46:19,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2021-05-18 11:46:19,439] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,441] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,441] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fastp-trim.20210518.fq.gz [2021-05-18 11:46:19,441] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62.fastp-trim.20210518.report.html [2021-05-18 11:46:19,441] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37.fastp-trim.20210518.report.html [2021-05-18 11:46:23,446] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-05-18 11:46:23,454] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-05-18 11:46:23,510] multiqc [DEBUG ] No samples found: custom_content [2021-05-18 11:46:23,562] multiqc [DEBUG ] No samples found: conpair [2021-05-18 11:46:23,665] multiqc [DEBUG ] No samples found: peddy [2021-05-18 11:46:23,715] multiqc [DEBUG ] No samples found: methylQA [2021-05-18 11:46:23,735] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-05-18 11:46:23,831] multiqc [DEBUG ] No samples found: qualimap [2021-05-18 11:46:23,876] multiqc [DEBUG ] No samples found: preseq [2021-05-18 11:46:23,898] multiqc [DEBUG ] No samples found: quast [2021-05-18 11:46:23,925] multiqc [DEBUG ] No samples found: qorts [2021-05-18 11:46:23,991] multiqc [DEBUG ] No samples found: rna_seqc [2021-05-18 11:46:24,031] multiqc [DEBUG ] No samples found: rsem [2021-05-18 11:46:24,134] multiqc [DEBUG ] No samples found: rseqc [2021-05-18 11:46:24,152] multiqc [DEBUG ] No samples found: busco [2021-05-18 11:46:24,206] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-05-18 11:46:24,232] multiqc [DEBUG ] No samples found: disambiguate [2021-05-18 11:46:24,263] multiqc [DEBUG ] No samples found: supernova [2021-05-18 11:46:24,354] multiqc [DEBUG ] No samples found: deeptools [2021-05-18 11:46:24,383] multiqc [DEBUG ] No samples found: sargasso [2021-05-18 11:46:24,422] multiqc [DEBUG ] No samples found: verifybamid [2021-05-18 11:46:24,446] multiqc [DEBUG ] No samples found: mirtrace [2021-05-18 11:46:24,464] multiqc [DEBUG ] No samples found: happy [2021-05-18 11:46:24,492] multiqc [DEBUG ] No samples found: homer [2021-05-18 11:46:24,514] multiqc [DEBUG ] No samples found: macs2 [2021-05-18 11:46:24,524] multiqc [DEBUG ] No samples found: theta2 [2021-05-18 11:46:24,550] multiqc [DEBUG ] No samples found: snpeff [2021-05-18 11:46:24,605] multiqc [DEBUG ] No samples found: gatk [2021-05-18 11:46:24,616] multiqc [DEBUG ] No samples found: htseq [2021-05-18 11:46:24,653] multiqc [DEBUG ] No samples found: bcftools [2021-05-18 11:46:24,663] multiqc [DEBUG ] No samples found: featureCounts [2021-05-18 11:46:24,676] multiqc [DEBUG ] No samples found: fgbio [2021-05-18 11:46:24,686] multiqc [DEBUG ] No samples found: dedup [2021-05-18 11:46:24,712] multiqc [DEBUG ] No samples found: damageprofiler [2021-05-18 11:46:24,858] multiqc [DEBUG ] No samples found: biobambam2 [2021-05-18 11:46:24,951] multiqc [DEBUG ] No samples found: mtnucratio [2021-05-18 11:46:24,961] multiqc [DEBUG ] No samples found: picard [2021-05-18 11:46:24,993] multiqc [DEBUG ] No samples found: prokka [2021-05-18 11:46:25,003] multiqc [DEBUG ] No samples found: samblaster [2021-05-18 11:46:25,074] multiqc [DEBUG ] No samples found: samtools [2021-05-18 11:46:25,118] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-05-18 11:46:25,182] multiqc [DEBUG ] No samples found: bamtools [2021-05-18 11:46:25,192] multiqc [DEBUG ] No samples found: jellyfish [2021-05-18 11:46:25,210] multiqc [DEBUG ] No samples found: vcftools [2021-05-18 11:46:25,235] multiqc [DEBUG ] No samples found: longranger [2021-05-18 11:46:25,268] multiqc [DEBUG ] No samples found: stacks [2021-05-18 11:46:25,343] multiqc [DEBUG ] No samples found: bbmap [2021-05-18 11:46:25,371] multiqc [DEBUG ] No samples found: bismark [2021-05-18 11:46:25,391] multiqc [DEBUG ] No samples found: biscuit [2021-05-18 11:46:25,419] multiqc [DEBUG ] No samples found: hicexplorer [2021-05-18 11:46:25,453] multiqc [DEBUG ] No samples found: hicup [2021-05-18 11:46:25,477] multiqc [DEBUG ] No samples found: hicpro [2021-05-18 11:46:25,487] multiqc [DEBUG ] No samples found: salmon [2021-05-18 11:46:25,513] multiqc [DEBUG ] No samples found: kallisto [2021-05-18 11:46:25,531] multiqc [DEBUG ] No samples found: slamdunk [2021-05-18 11:46:25,560] multiqc [DEBUG ] No samples found: star [2021-05-18 11:46:25,583] multiqc [DEBUG ] No samples found: hisat2 [2021-05-18 11:46:25,609] multiqc [DEBUG ] No samples found: tophat [2021-05-18 11:46:25,642] multiqc [DEBUG ] No samples found: bowtie2 [2021-05-18 11:46:25,660] multiqc [DEBUG ] No samples found: bowtie1 [2021-05-18 11:46:25,671] multiqc [DEBUG ] No samples found: kat [2021-05-18 11:46:25,680] multiqc [DEBUG ] No samples found: leehom [2021-05-18 11:46:25,713] multiqc [DEBUG ] No samples found: adapterRemoval [2021-05-18 11:46:25,723] multiqc [DEBUG ] No samples found: clipandmerge [2021-05-18 11:46:25,751] multiqc [DEBUG ] No samples found: cutadapt [2021-05-18 11:46:25,761] multiqc [DEBUG ] No samples found: flexbar [2021-05-18 11:46:25,782] multiqc [DEBUG ] No samples found: trimmomatic [2021-05-18 11:46:25,805] multiqc [DEBUG ] No samples found: skewer [2021-05-18 11:46:25,815] multiqc [DEBUG ] No samples found: sortmerna [2021-05-18 11:46:25,837] multiqc [DEBUG ] No samples found: biobloomtools [2021-05-18 11:46:25,859] multiqc [DEBUG ] No samples found: fastq_screen [2021-05-18 11:46:25,887] multiqc [DEBUG ] No samples found: afterqc [2021-05-18 11:46:26,151] multiqc.modules.fastp.fastp [INFO ] Found 9 reports [2021-05-18 11:46:26,224] multiqc [DEBUG ] No samples found: fastqc [2021-05-18 11:46:26,243] multiqc [DEBUG ] No samples found: minionqc [2021-05-18 11:46:26,270] multiqc [DEBUG ] No samples found: mosdepth [2021-05-18 11:46:26,299] multiqc [DEBUG ] No samples found: clusterflow [2021-05-18 11:46:26,356] multiqc [DEBUG ] No samples found: bcl2fastq [2021-05-18 11:46:26,391] multiqc [DEBUG ] No samples found: interop [2021-05-18 11:46:26,416] multiqc [DEBUG ] No samples found: flash [2021-05-18 11:46:26,440] multiqc [DEBUG ] No samples found: seqyclean [2021-05-18 11:46:26,479] multiqc [INFO ] Compressing plot data [2021-05-18 11:46:26,951] multiqc [INFO ] Report : multiqc_report.html [2021-05-18 11:46:26,952] multiqc [INFO ] Data : multiqc_data [2021-05-18 11:46:26,953] multiqc [DEBUG ] Moving data file from '/tmp/tmpyy7lfft6/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20210518_olur_fastp_bgi/multiqc_data' [2021-05-18 11:46:26,954] multiqc [DEBUG ] Moving data file from '/tmp/tmpyy7lfft6/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20210518_olur_fastp_bgi/multiqc_data' [2021-05-18 11:46:26,955] multiqc [DEBUG ] Moving data file from '/tmp/tmpyy7lfft6/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20210518_olur_fastp_bgi/multiqc_data' [2021-05-18 11:46:26,956] multiqc [DEBUG ] Moving data file from '/tmp/tmpyy7lfft6/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20210518_olur_fastp_bgi/multiqc_data' [2021-05-18 11:46:26,957] multiqc [DEBUG ] Moving data file from '/tmp/tmpyy7lfft6/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20210518_olur_fastp_bgi/multiqc_data' [2021-05-18 11:46:27,856] multiqc [INFO ] MultiQC complete