[2020-04-23 15:32:46,302] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-04-23 15:32:46,302] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/strigg/.multiqc_config.yaml [2020-04-23 15:32:46,302] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-04-23 15:32:46,303] multiqc [DEBUG ] Command used: /gscratch/srlab/strigg/bin/anaconda3/bin/multiqc -o TG_SE_local_aligned/ /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_local_aligned/ /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_FASTQS /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_FASTQS/FastQC [2020-04-23 15:32:51,586] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-04-23 15:32:51,586] multiqc [INFO ] This is MultiQC v1.8 [2020-04-23 15:32:51,588] multiqc [DEBUG ] Command : /gscratch/srlab/strigg/bin/anaconda3/bin/multiqc -o TG_SE_local_aligned/ /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_local_aligned/ /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_FASTQS /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_FASTQS/FastQC [2020-04-23 15:32:51,588] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/strigg/analyses/20200423 [2020-04-23 15:32:51,588] multiqc [INFO ] Template : default [2020-04-23 15:32:51,588] multiqc [DEBUG ] Running Python 3.7.6 | packaged by conda-forge | (default, Mar 5 2020, 15:27:18) [GCC 7.3.0] [2020-04-23 15:32:51,588] multiqc [INFO ] Searching : /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_local_aligned [2020-04-23 15:32:51,588] multiqc [INFO ] Searching : /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_FASTQS [2020-04-23 15:32:51,588] multiqc [INFO ] Searching : /gscratch/scrubbed/strigg/analyses/20200422/TG_SE_FASTQS/FastQC [2020-04-23 15:32:51,589] 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 [2020-04-23 15:32:51,589] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpabykp9z6 [2020-04-23 15:32:51,832] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CTRL_8C_26psu_1_S17_L001_R2_001_trimmed_bismark_bt2.bam [2020-04-23 15:32:51,833] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_4_S16_L002_R1_001_trimmed_bismark_bt2.bam [2020-04-23 15:32:51,834] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_4_S16_L002_R2_001_trimmed_bismark_bt2.bam [2020-04-23 15:32:51,836] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_3_S15_L001_R1_001_trimmed_bismark_bt2.bam [2020-04-23 15:32:51,838] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CTRL_8C_26psu_1_S17_L001_R1_001_trimmed_bismark_bt2.bam [2020-04-23 15:32:51,838] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8C_26psu_3_S11_L001_R1_001_trimmed_bismark_bt2.bam [2020-04-23 15:32:51,838] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8C_26psu_3_S11_L001_R2_001_trimmed_bismark_bt2.bam [2020-04-23 15:32:51,839] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_3_S15_L001_R2_001_trimmed_bismark_bt2.bam [2020-04-23 15:32:51,886] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 8C_26psu_3_S11_L001_R2_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:51,889] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 8C_26psu_3_S11_L001_R2_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:51,912] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CTRL_8C_26psu_1_S17_L001_R1_001_trimmed.fq.gz [2020-04-23 15:32:51,912] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CTRL_8C_26psu_1_S17_L001_R2_001_trimmed.fq.gz [2020-04-23 15:32:51,913] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8C_26psu_3_S11_L001_R2_001_trimmed.fq.gz [2020-04-23 15:32:51,914] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_3_S15_L001_R2_001_trimmed.fq.gz [2020-04-23 15:32:51,918] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 16C_26psu_4_S16_L002_R1_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:51,920] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 16C_26psu_4_S16_L002_R1_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:51,932] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8C_26psu_3_S11_L001_R1_001_trimmed.fq.gz [2020-04-23 15:32:51,958] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 8C_26psu_3_S11_L001_R1_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:51,959] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 8C_26psu_3_S11_L001_R1_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:51,975] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 16C_26psu_3_S15_L001_R2_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:51,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 16C_26psu_3_S15_L001_R2_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,035] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 16C_26psu_4_S16_L002_R2_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,037] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 16C_26psu_4_S16_L002_R2_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,055] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_4_S16_L002_R2_001_trimmed.fq.gz [2020-04-23 15:32:52,094] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: CTRL_8C_26psu_1_S17_L001_R2_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,096] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: CTRL_8C_26psu_1_S17_L001_R2_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,117] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_3_S15_L001_R1_001_trimmed.fq.gz [2020-04-23 15:32:52,124] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 16C_26psu_3_S15_L001_R1_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,126] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 16C_26psu_3_S15_L001_R1_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,147] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: CTRL_8C_26psu_1_S17_L001_R1_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,149] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: CTRL_8C_26psu_1_S17_L001_R1_001.fastq.gz_trimming_report.txt [2020-04-23 15:32:52,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_4_S16_L002_R1_001_trimmed.fq.gz [2020-04-23 15:32:52,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_3_S15_L001_R1_001_trimmed_fastqc.html [2020-04-23 15:32:52,165] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_3_S15_L001_R2_001_trimmed_fastqc.html [2020-04-23 15:32:52,167] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8C_26psu_3_S11_L001_R2_001_trimmed_fastqc.html [2020-04-23 15:32:52,168] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CTRL_8C_26psu_1_S17_L001_R1_001_trimmed_fastqc.html [2020-04-23 15:32:52,170] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_4_S16_L002_R1_001_trimmed_fastqc.html [2020-04-23 15:32:52,171] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8C_26psu_3_S11_L001_R1_001_trimmed_fastqc.html [2020-04-23 15:32:52,171] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CTRL_8C_26psu_1_S17_L001_R2_001_trimmed_fastqc.html [2020-04-23 15:32:52,171] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_4_S16_L002_R2_001_trimmed_fastqc.html [2020-04-23 15:32:52,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_3_S15_L001_R1_001_trimmed_fastqc.html [2020-04-23 15:32:52,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_3_S15_L001_R2_001_trimmed_fastqc.html [2020-04-23 15:32:52,172] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8C_26psu_3_S11_L001_R2_001_trimmed_fastqc.html [2020-04-23 15:32:52,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CTRL_8C_26psu_1_S17_L001_R1_001_trimmed_fastqc.html [2020-04-23 15:32:52,173] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_4_S16_L002_R1_001_trimmed_fastqc.html [2020-04-23 15:32:52,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 8C_26psu_3_S11_L001_R1_001_trimmed_fastqc.html [2020-04-23 15:32:52,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: CTRL_8C_26psu_1_S17_L001_R2_001_trimmed_fastqc.html [2020-04-23 15:32:52,174] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16C_26psu_4_S16_L002_R2_001_trimmed_fastqc.html [2020-04-23 15:32:55,311] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.5 [2020-04-23 15:32:55,313] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.5 [2020-04-23 15:32:55,315] multiqc [DEBUG ] No samples found: custom_content [2020-04-23 15:32:55,321] multiqc [DEBUG ] No samples found: conpair [2020-04-23 15:32:55,329] multiqc [DEBUG ] No samples found: peddy [2020-04-23 15:32:55,350] multiqc [DEBUG ] No samples found: methylQA [2020-04-23 15:32:55,356] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-04-23 15:32:55,470] multiqc [DEBUG ] No samples found: qualimap [2020-04-23 15:32:55,479] multiqc [DEBUG ] No samples found: preseq [2020-04-23 15:32:55,487] multiqc [DEBUG ] No samples found: quast [2020-04-23 15:32:55,507] multiqc [DEBUG ] No samples found: qorts [2020-04-23 15:32:55,514] multiqc [DEBUG ] No samples found: rna_seqc [2020-04-23 15:32:55,521] multiqc [DEBUG ] No samples found: rsem [2020-04-23 15:32:55,537] multiqc [DEBUG ] No samples found: rseqc [2020-04-23 15:32:55,545] multiqc [DEBUG ] No samples found: busco [2020-04-23 15:32:55,563] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-04-23 15:32:55,570] multiqc [DEBUG ] No samples found: disambiguate [2020-04-23 15:32:55,575] multiqc [DEBUG ] No samples found: supernova [2020-04-23 15:32:55,687] multiqc [DEBUG ] No samples found: deeptools [2020-04-23 15:32:55,735] multiqc [DEBUG ] No samples found: sargasso [2020-04-23 15:32:55,744] multiqc [DEBUG ] No samples found: verifybamid [2020-04-23 15:32:55,751] multiqc [DEBUG ] No samples found: mirtrace [2020-04-23 15:32:55,779] multiqc [DEBUG ] No samples found: happy [2020-04-23 15:32:55,819] multiqc [DEBUG ] No samples found: homer [2020-04-23 15:32:55,828] multiqc [DEBUG ] No samples found: macs2 [2020-04-23 15:32:55,837] multiqc [DEBUG ] No samples found: theta2 [2020-04-23 15:32:55,862] multiqc [DEBUG ] No samples found: snpeff [2020-04-23 15:32:55,906] multiqc [DEBUG ] No samples found: gatk [2020-04-23 15:32:55,915] multiqc [DEBUG ] No samples found: htseq [2020-04-23 15:32:55,946] multiqc [DEBUG ] No samples found: bcftools [2020-04-23 15:32:55,954] multiqc [DEBUG ] No samples found: featureCounts [2020-04-23 15:32:55,962] multiqc [DEBUG ] No samples found: fgbio [2020-04-23 15:32:55,970] multiqc [DEBUG ] No samples found: dedup [2020-04-23 15:32:55,977] multiqc [DEBUG ] No samples found: damageprofiler [2020-04-23 15:32:55,998] multiqc [DEBUG ] No samples found: biobambam2 [2020-04-23 15:32:56,005] multiqc [DEBUG ] No samples found: mtnucratio [2020-04-23 15:32:56,009] multiqc [DEBUG ] No samples found: picard [2020-04-23 15:32:56,016] multiqc [DEBUG ] No samples found: prokka [2020-04-23 15:32:56,023] multiqc [DEBUG ] No samples found: samblaster [2020-04-23 15:32:56,031] multiqc [DEBUG ] No samples found: samtools [2020-04-23 15:32:56,037] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-04-23 15:32:56,043] multiqc [DEBUG ] No samples found: bamtools [2020-04-23 15:32:56,049] multiqc [DEBUG ] No samples found: jellyfish [2020-04-23 15:32:56,058] multiqc [DEBUG ] No samples found: vcftools [2020-04-23 15:32:56,064] multiqc [DEBUG ] No samples found: longranger [2020-04-23 15:32:56,071] multiqc [DEBUG ] No samples found: stacks [2020-04-23 15:32:56,118] multiqc [DEBUG ] No samples found: bbmap [2020-04-23 15:32:56,138] multiqc.modules.bismark.bismark [INFO ] Found 8 bismark alignment reports [2020-04-23 15:32:56,167] multiqc [DEBUG ] No samples found: biscuit [2020-04-23 15:32:56,176] multiqc [DEBUG ] No samples found: hicexplorer [2020-04-23 15:32:56,184] multiqc [DEBUG ] No samples found: hicup [2020-04-23 15:32:56,192] multiqc [DEBUG ] No samples found: hicpro [2020-04-23 15:32:56,200] multiqc [DEBUG ] No samples found: salmon [2020-04-23 15:32:56,206] multiqc [DEBUG ] No samples found: kallisto [2020-04-23 15:32:56,243] multiqc [DEBUG ] No samples found: slamdunk [2020-04-23 15:32:56,252] multiqc [DEBUG ] No samples found: star [2020-04-23 15:32:56,261] multiqc [DEBUG ] No samples found: hisat2 [2020-04-23 15:32:56,268] multiqc [DEBUG ] No samples found: tophat [2020-04-23 15:32:56,276] multiqc [DEBUG ] No samples found: bowtie2 [2020-04-23 15:32:56,284] multiqc [DEBUG ] No samples found: bowtie1 [2020-04-23 15:32:56,291] multiqc [DEBUG ] No samples found: kat [2020-04-23 15:32:56,298] multiqc [DEBUG ] No samples found: leehom [2020-04-23 15:32:56,306] multiqc [DEBUG ] No samples found: adapterRemoval [2020-04-23 15:32:56,329] multiqc [DEBUG ] No samples found: clipandmerge [2020-04-23 15:32:56,353] multiqc.modules.cutadapt.cutadapt [INFO ] Found 8 reports [2020-04-23 15:32:56,371] multiqc [DEBUG ] No samples found: flexbar [2020-04-23 15:32:56,377] multiqc [DEBUG ] No samples found: trimmomatic [2020-04-23 15:32:56,383] multiqc [DEBUG ] No samples found: skewer [2020-04-23 15:32:56,388] multiqc [DEBUG ] No samples found: sortmerna [2020-04-23 15:32:56,395] multiqc [DEBUG ] No samples found: biobloomtools [2020-04-23 15:32:56,401] multiqc [DEBUG ] No samples found: fastq_screen [2020-04-23 15:32:56,406] multiqc [DEBUG ] No samples found: afterqc [2020-04-23 15:32:56,411] multiqc [DEBUG ] No samples found: fastp [2020-04-23 15:32:57,792] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: 16C_26psu_4_S16_L002_R1_001 [2020-04-23 15:32:57,846] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: 16C_26psu_3_S15_L001_R2_001 [2020-04-23 15:32:57,894] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: 8C_26psu_3_S11_L001_R1_001 [2020-04-23 15:32:57,940] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: CTRL_8C_26psu_1_S17_L001_R2_001 [2020-04-23 15:32:57,985] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: 16C_26psu_3_S15_L001_R1_001 [2020-04-23 15:32:58,031] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: 16C_26psu_4_S16_L002_R2_001 [2020-04-23 15:32:58,077] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: CTRL_8C_26psu_1_S17_L001_R1_001 [2020-04-23 15:32:58,123] multiqc.modules.fastqc.fastqc [DEBUG ] Duplicate sample name found! Overwriting: 8C_26psu_3_S11_L001_R2_001 [2020-04-23 15:32:58,166] multiqc.modules.fastqc.fastqc [INFO ] Found 8 reports [2020-04-23 15:32:58,361] multiqc [DEBUG ] No samples found: minionqc [2020-04-23 15:32:58,367] multiqc [DEBUG ] No samples found: mosdepth [2020-04-23 15:32:58,372] multiqc [DEBUG ] No samples found: clusterflow [2020-04-23 15:32:58,397] multiqc [DEBUG ] No samples found: bcl2fastq [2020-04-23 15:32:58,422] multiqc [DEBUG ] No samples found: interop [2020-04-23 15:32:58,428] multiqc [DEBUG ] No samples found: flash [2020-04-23 15:32:58,434] multiqc [DEBUG ] No samples found: seqyclean [2020-04-23 15:32:58,456] multiqc [INFO ] Compressing plot data [2020-04-23 15:32:58,686] multiqc [INFO ] Report : TG_SE_local_aligned/multiqc_report.html [2020-04-23 15:32:58,686] multiqc [INFO ] Data : TG_SE_local_aligned/multiqc_data [2020-04-23 15:32:58,687] multiqc [DEBUG ] Moving data file from '/tmp/tmpabykp9z6/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to 'TG_SE_local_aligned/multiqc_data' [2020-04-23 15:32:58,688] multiqc [DEBUG ] Moving data file from '/tmp/tmpabykp9z6/multiqc_data/multiqc_bismark_alignment.txt' to 'TG_SE_local_aligned/multiqc_data' [2020-04-23 15:32:58,688] multiqc [DEBUG ] Moving data file from '/tmp/tmpabykp9z6/multiqc_data/multiqc_cutadapt.txt' to 'TG_SE_local_aligned/multiqc_data' [2020-04-23 15:32:58,689] multiqc [DEBUG ] Moving data file from '/tmp/tmpabykp9z6/multiqc_data/multiqc_fastqc.txt' to 'TG_SE_local_aligned/multiqc_data' [2020-04-23 15:32:58,690] multiqc [DEBUG ] Moving data file from '/tmp/tmpabykp9z6/multiqc_data/multiqc_general_stats.txt' to 'TG_SE_local_aligned/multiqc_data' [2020-04-23 15:32:58,690] multiqc [DEBUG ] Moving data file from '/tmp/tmpabykp9z6/multiqc_data/multiqc_sources.txt' to 'TG_SE_local_aligned/multiqc_data' [2020-04-23 15:32:58,691] multiqc [DEBUG ] Moving data file from '/tmp/tmpabykp9z6/multiqc_data/multiqc_data.json' to 'TG_SE_local_aligned/multiqc_data' [2020-04-23 15:32:59,453] multiqc [INFO ] MultiQC complete