[2021-03-12 23:58:34,730] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-03-12 23:58:34,731] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/sr320/.multiqc_config.yaml [2021-03-12 23:58:34,731] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-03-12 23:58:34,731] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-03-12 23:58:40,048] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-03-12 23:58:40,048] multiqc [INFO ] This is MultiQC v1.8 [2021-03-12 23:58:40,049] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-03-12 23:58:40,049] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/sr320/030521-ronrosM [2021-03-12 23:58:40,049] multiqc [INFO ] Template : default [2021-03-12 23:58:40,050] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-03-12 23:58:40,050] multiqc [INFO ] Searching : /gscratch/scrubbed/sr320/030521-ronrosM [2021-03-12 23:58:40,051] 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 [2021-03-12 23:58:40,052] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp6mgeq7r5 [2021-03-12 23:58:40,563] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:40,700] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-1614683.out [2021-03-12 23:58:40,704] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-1614683.out [2021-03-12 23:58:40,705] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: slurm-1614683.out [2021-03-12 23:58:40,705] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: slurm-1614683.out [2021-03-12 23:58:40,705] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: slurm-1614683.out [2021-03-12 23:58:40,705] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: slurm-1614683.out [2021-03-12 23:58:40,746] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: slurm-1614683.out [2021-03-12 23:58:41,974] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:41,982] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,002] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,024] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_1_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,025] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,025] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:42,071] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,073] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,074] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: bismark_summary_report.html [2021-03-12 23:58:42,077] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,093] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_5_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:42,093] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,093] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,093] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_8_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,094] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,094] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:42,104] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,104] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_9_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:42,107] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,130] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: job.sh [2021-03-12 23:58:42,137] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,138] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:42,154] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,155] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_6_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:42,158] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_3_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:42,158] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.deduplicated.bam [2021-03-12 23:58:42,158] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_4_R1.fastp-trim.20201202_bismark_bt2_PE_report.html [2021-03-12 23:58:42,159] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_7_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_2_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:42,160] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3534_10_R1.fastp-trim.20201202_bismark_bt2_pe.bam [2021-03-12 23:58:46,571] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-03-12 23:58:46,595] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-03-12 23:58:46,631] multiqc [DEBUG ] No samples found: custom_content [2021-03-12 23:58:46,652] multiqc [DEBUG ] No samples found: conpair [2021-03-12 23:58:46,772] multiqc [DEBUG ] No samples found: peddy [2021-03-12 23:58:46,813] multiqc [DEBUG ] No samples found: methylQA [2021-03-12 23:58:46,824] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-03-12 23:58:46,937] multiqc [DEBUG ] No samples found: qualimap [2021-03-12 23:58:46,959] multiqc [DEBUG ] No samples found: preseq [2021-03-12 23:58:47,000] multiqc [DEBUG ] No samples found: quast [2021-03-12 23:58:47,015] multiqc [DEBUG ] No samples found: qorts [2021-03-12 23:58:47,037] multiqc [DEBUG ] No samples found: rna_seqc [2021-03-12 23:58:47,064] multiqc [DEBUG ] No samples found: rsem [2021-03-12 23:58:47,101] multiqc [DEBUG ] No samples found: rseqc [2021-03-12 23:58:47,132] multiqc [DEBUG ] No samples found: busco [2021-03-12 23:58:47,164] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-03-12 23:58:47,182] multiqc [DEBUG ] No samples found: disambiguate [2021-03-12 23:58:47,205] multiqc [DEBUG ] No samples found: supernova [2021-03-12 23:58:47,266] multiqc [DEBUG ] No samples found: deeptools [2021-03-12 23:58:47,291] multiqc [DEBUG ] No samples found: sargasso [2021-03-12 23:58:47,317] multiqc [DEBUG ] No samples found: verifybamid [2021-03-12 23:58:47,356] multiqc [DEBUG ] No samples found: mirtrace [2021-03-12 23:58:47,399] multiqc [DEBUG ] No samples found: happy [2021-03-12 23:58:47,437] multiqc [DEBUG ] No samples found: homer [2021-03-12 23:58:47,448] multiqc [DEBUG ] No samples found: macs2 [2021-03-12 23:58:47,458] multiqc [DEBUG ] No samples found: theta2 [2021-03-12 23:58:47,482] multiqc [DEBUG ] No samples found: snpeff [2021-03-12 23:58:47,588] multiqc [DEBUG ] No samples found: gatk [2021-03-12 23:58:47,599] multiqc [DEBUG ] No samples found: htseq [2021-03-12 23:58:47,679] multiqc [DEBUG ] No samples found: bcftools [2021-03-12 23:58:47,690] multiqc [DEBUG ] No samples found: featureCounts [2021-03-12 23:58:47,702] multiqc [DEBUG ] No samples found: fgbio [2021-03-12 23:58:47,712] multiqc [DEBUG ] No samples found: dedup [2021-03-12 23:58:47,737] multiqc [DEBUG ] No samples found: damageprofiler [2021-03-12 23:58:47,833] multiqc [DEBUG ] No samples found: biobambam2 [2021-03-12 23:58:47,853] multiqc [DEBUG ] No samples found: mtnucratio [2021-03-12 23:58:47,859] multiqc [DEBUG ] No samples found: picard [2021-03-12 23:58:47,870] multiqc [DEBUG ] No samples found: prokka [2021-03-12 23:58:47,880] multiqc [DEBUG ] No samples found: samblaster [2021-03-12 23:58:47,926] multiqc [DEBUG ] No samples found: samtools [2021-03-12 23:58:47,954] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-03-12 23:58:47,988] multiqc [DEBUG ] No samples found: bamtools [2021-03-12 23:58:47,999] multiqc [DEBUG ] No samples found: jellyfish [2021-03-12 23:58:48,016] multiqc [DEBUG ] No samples found: vcftools [2021-03-12 23:58:48,048] multiqc [DEBUG ] No samples found: longranger [2021-03-12 23:58:48,068] multiqc [DEBUG ] No samples found: stacks [2021-03-12 23:58:48,123] multiqc [DEBUG ] No samples found: bbmap [2021-03-12 23:58:48,193] multiqc.modules.bismark.bismark [INFO ] Found 10 bismark alignment reports [2021-03-12 23:58:48,199] multiqc.modules.bismark.bismark [INFO ] Found 10 bismark dedup reports [2021-03-12 23:58:48,200] multiqc.modules.bismark.bismark [INFO ] Found 10 bismark methextract reports [2021-03-12 23:58:48,242] multiqc [DEBUG ] No samples found: biscuit [2021-03-12 23:58:48,250] multiqc [DEBUG ] No samples found: hicexplorer [2021-03-12 23:58:48,272] multiqc [DEBUG ] No samples found: hicup [2021-03-12 23:58:48,280] multiqc [DEBUG ] No samples found: hicpro [2021-03-12 23:58:48,287] multiqc [DEBUG ] No samples found: salmon [2021-03-12 23:58:48,305] multiqc [DEBUG ] No samples found: kallisto [2021-03-12 23:58:48,322] multiqc [DEBUG ] No samples found: slamdunk [2021-03-12 23:58:48,345] multiqc [DEBUG ] No samples found: star [2021-03-12 23:58:48,372] multiqc [DEBUG ] No samples found: hisat2 [2021-03-12 23:58:48,394] multiqc [DEBUG ] No samples found: tophat [2021-03-12 23:58:48,405] multiqc [DEBUG ] No samples found: bowtie2 [2021-03-12 23:58:48,434] multiqc [DEBUG ] No samples found: bowtie1 [2021-03-12 23:58:48,444] multiqc [DEBUG ] No samples found: kat [2021-03-12 23:58:48,454] multiqc [DEBUG ] No samples found: leehom [2021-03-12 23:58:48,502] multiqc [DEBUG ] No samples found: adapterRemoval [2021-03-12 23:58:48,513] multiqc [DEBUG ] No samples found: clipandmerge [2021-03-12 23:58:48,570] multiqc [DEBUG ] No samples found: cutadapt [2021-03-12 23:58:48,580] multiqc [DEBUG ] No samples found: flexbar [2021-03-12 23:58:48,603] multiqc [DEBUG ] No samples found: trimmomatic [2021-03-12 23:58:48,627] multiqc [DEBUG ] No samples found: skewer [2021-03-12 23:58:48,637] multiqc [DEBUG ] No samples found: sortmerna [2021-03-12 23:58:48,648] multiqc [DEBUG ] No samples found: biobloomtools [2021-03-12 23:58:48,659] multiqc [DEBUG ] No samples found: fastq_screen [2021-03-12 23:58:48,712] multiqc [DEBUG ] No samples found: afterqc [2021-03-12 23:58:48,726] multiqc [DEBUG ] No samples found: fastp [2021-03-12 23:58:48,750] multiqc [DEBUG ] No samples found: fastqc [2021-03-12 23:58:48,816] multiqc [DEBUG ] No samples found: minionqc [2021-03-12 23:58:48,836] multiqc [DEBUG ] No samples found: mosdepth [2021-03-12 23:58:48,865] multiqc [DEBUG ] No samples found: clusterflow [2021-03-12 23:58:48,877] multiqc [DEBUG ] No samples found: bcl2fastq [2021-03-12 23:58:48,933] multiqc [DEBUG ] No samples found: interop [2021-03-12 23:58:48,956] multiqc [DEBUG ] No samples found: flash [2021-03-12 23:58:48,975] multiqc [DEBUG ] No samples found: seqyclean [2021-03-12 23:58:49,025] multiqc [INFO ] Compressing plot data [2021-03-12 23:58:49,184] multiqc [INFO ] Report : multiqc_report.html [2021-03-12 23:58:49,184] multiqc [INFO ] Data : multiqc_data [2021-03-12 23:58:49,184] multiqc [DEBUG ] Moving data file from '/tmp/tmp6mgeq7r5/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/sr320/030521-ronrosM/multiqc_data' [2021-03-12 23:58:49,185] multiqc [DEBUG ] Moving data file from '/tmp/tmp6mgeq7r5/multiqc_data/multiqc_bismark_alignment.txt' to '/gscratch/scrubbed/sr320/030521-ronrosM/multiqc_data' [2021-03-12 23:58:49,186] multiqc [DEBUG ] Moving data file from '/tmp/tmp6mgeq7r5/multiqc_data/multiqc_bismark_dedup.txt' to '/gscratch/scrubbed/sr320/030521-ronrosM/multiqc_data' [2021-03-12 23:58:49,187] multiqc [DEBUG ] Moving data file from '/tmp/tmp6mgeq7r5/multiqc_data/multiqc_bismark_methextract.txt' to '/gscratch/scrubbed/sr320/030521-ronrosM/multiqc_data' [2021-03-12 23:58:49,188] multiqc [DEBUG ] Moving data file from '/tmp/tmp6mgeq7r5/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/sr320/030521-ronrosM/multiqc_data' [2021-03-12 23:58:49,188] multiqc [DEBUG ] Moving data file from '/tmp/tmp6mgeq7r5/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/sr320/030521-ronrosM/multiqc_data' [2021-03-12 23:58:49,189] multiqc [DEBUG ] Moving data file from '/tmp/tmp6mgeq7r5/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/sr320/030521-ronrosM/multiqc_data' [2021-03-12 23:58:50,024] multiqc [INFO ] MultiQC complete