[2021-02-02 00:15:57,186] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-02-02 00:15:57,186] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/yaaminiv/.multiqc_config.yaml [2021-02-02 00:15:57,187] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-02-02 00:15:57,187] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-02-02 00:16:02,536] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-02-02 00:16:02,536] multiqc [INFO ] This is MultiQC v1.8 [2021-02-02 00:16:02,537] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-02-02 00:16:02,537] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/yaaminiv/Manchester/analyses/fastqc [2021-02-02 00:16:02,537] multiqc [INFO ] Template : default [2021-02-02 00:16:02,537] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-02-02 00:16:02,538] multiqc [INFO ] Searching : /gscratch/scrubbed/yaaminiv/Manchester/analyses/fastqc [2021-02-02 00:16:02,538] 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 [2021-02-02 00:16:02,539] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp2o57ye5c [2021-02-02 00:16:03,150] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_5_R2_fastqc.html [2021-02-02 00:16:03,151] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_8_R1_fastqc.html [2021-02-02 00:16:03,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_1_R2_fastqc.html [2021-02-02 00:16:03,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_3_R1_fastqc.html [2021-02-02 00:16:03,163] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_4_R1_fastqc.html [2021-02-02 00:16:03,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_6_R2_fastqc.html [2021-02-02 00:16:03,164] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_2_R2_fastqc.html [2021-02-02 00:16:03,205] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_1_R1_fastqc.html [2021-02-02 00:16:03,206] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_6_R1_fastqc.html [2021-02-02 00:16:03,206] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_7_R1_fastqc.html [2021-02-02 00:16:03,206] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_2_R1_fastqc.html [2021-02-02 00:16:03,206] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_7_R2_fastqc.html [2021-02-02 00:16:03,219] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_5_R1_fastqc.html [2021-02-02 00:16:03,219] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_8_R2_fastqc.html [2021-02-02 00:16:03,224] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-1072119.out [2021-02-02 00:16:03,225] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-1072119.out [2021-02-02 00:16:03,247] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastq_checksums.md5 [2021-02-02 00:16:03,248] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_3_R2_fastqc.html [2021-02-02 00:16:03,248] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3616_4_R2_fastqc.html [2021-02-02 00:16:08,084] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-02-02 00:16:08,101] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-02-02 00:16:08,142] multiqc [DEBUG ] No samples found: custom_content [2021-02-02 00:16:08,250] multiqc [DEBUG ] No samples found: conpair [2021-02-02 00:16:08,396] multiqc [DEBUG ] No samples found: peddy [2021-02-02 00:16:08,542] multiqc [DEBUG ] No samples found: methylQA [2021-02-02 00:16:08,565] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-02-02 00:16:08,670] multiqc [DEBUG ] No samples found: qualimap [2021-02-02 00:16:08,699] multiqc [DEBUG ] No samples found: preseq [2021-02-02 00:16:08,751] multiqc [DEBUG ] No samples found: quast [2021-02-02 00:16:08,789] multiqc [DEBUG ] No samples found: qorts [2021-02-02 00:16:08,841] multiqc [DEBUG ] No samples found: rna_seqc [2021-02-02 00:16:08,912] multiqc [DEBUG ] No samples found: rsem [2021-02-02 00:16:09,042] multiqc [DEBUG ] No samples found: rseqc [2021-02-02 00:16:09,068] multiqc [DEBUG ] No samples found: busco [2021-02-02 00:16:09,178] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-02-02 00:16:09,209] multiqc [DEBUG ] No samples found: disambiguate [2021-02-02 00:16:09,243] multiqc [DEBUG ] No samples found: supernova [2021-02-02 00:16:09,363] multiqc [DEBUG ] No samples found: deeptools [2021-02-02 00:16:09,408] multiqc [DEBUG ] No samples found: sargasso [2021-02-02 00:16:09,477] multiqc [DEBUG ] No samples found: verifybamid [2021-02-02 00:16:09,543] multiqc [DEBUG ] No samples found: mirtrace [2021-02-02 00:16:09,564] multiqc [DEBUG ] No samples found: happy [2021-02-02 00:16:09,610] multiqc [DEBUG ] No samples found: homer [2021-02-02 00:16:09,653] multiqc [DEBUG ] No samples found: macs2 [2021-02-02 00:16:09,663] multiqc [DEBUG ] No samples found: theta2 [2021-02-02 00:16:09,698] multiqc [DEBUG ] No samples found: snpeff [2021-02-02 00:16:09,801] multiqc [DEBUG ] No samples found: gatk [2021-02-02 00:16:09,825] multiqc [DEBUG ] No samples found: htseq [2021-02-02 00:16:09,849] multiqc [DEBUG ] No samples found: bcftools [2021-02-02 00:16:09,858] multiqc [DEBUG ] No samples found: featureCounts [2021-02-02 00:16:09,867] multiqc [DEBUG ] No samples found: fgbio [2021-02-02 00:16:09,874] multiqc [DEBUG ] No samples found: dedup [2021-02-02 00:16:09,883] multiqc [DEBUG ] No samples found: damageprofiler [2021-02-02 00:16:10,100] multiqc [DEBUG ] No samples found: biobambam2 [2021-02-02 00:16:10,122] multiqc [DEBUG ] No samples found: mtnucratio [2021-02-02 00:16:10,126] multiqc [DEBUG ] No samples found: picard [2021-02-02 00:16:10,202] multiqc [DEBUG ] No samples found: prokka [2021-02-02 00:16:10,212] multiqc [DEBUG ] No samples found: samblaster [2021-02-02 00:16:10,441] multiqc [DEBUG ] No samples found: samtools [2021-02-02 00:16:10,510] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-02-02 00:16:10,601] multiqc [DEBUG ] No samples found: bamtools [2021-02-02 00:16:10,610] multiqc [DEBUG ] No samples found: jellyfish [2021-02-02 00:16:10,627] multiqc [DEBUG ] No samples found: vcftools [2021-02-02 00:16:10,673] multiqc [DEBUG ] No samples found: longranger [2021-02-02 00:16:10,698] multiqc [DEBUG ] No samples found: stacks [2021-02-02 00:16:10,817] multiqc [DEBUG ] No samples found: bbmap [2021-02-02 00:16:10,868] multiqc [DEBUG ] No samples found: bismark [2021-02-02 00:16:10,891] multiqc [DEBUG ] No samples found: biscuit [2021-02-02 00:16:10,944] multiqc [DEBUG ] No samples found: hicexplorer [2021-02-02 00:16:11,010] multiqc [DEBUG ] No samples found: hicup [2021-02-02 00:16:11,061] multiqc [DEBUG ] No samples found: hicpro [2021-02-02 00:16:11,071] multiqc [DEBUG ] No samples found: salmon [2021-02-02 00:16:11,090] multiqc [DEBUG ] No samples found: kallisto [2021-02-02 00:16:11,112] multiqc [DEBUG ] No samples found: slamdunk [2021-02-02 00:16:11,156] multiqc [DEBUG ] No samples found: star [2021-02-02 00:16:11,258] multiqc [DEBUG ] No samples found: hisat2 [2021-02-02 00:16:11,279] multiqc [DEBUG ] No samples found: tophat [2021-02-02 00:16:11,298] multiqc [DEBUG ] No samples found: bowtie2 [2021-02-02 00:16:11,323] multiqc [DEBUG ] No samples found: bowtie1 [2021-02-02 00:16:11,334] multiqc [DEBUG ] No samples found: kat [2021-02-02 00:16:11,342] multiqc [DEBUG ] No samples found: leehom [2021-02-02 00:16:11,386] multiqc [DEBUG ] No samples found: adapterRemoval [2021-02-02 00:16:11,394] multiqc [DEBUG ] No samples found: clipandmerge [2021-02-02 00:16:11,438] multiqc [DEBUG ] No samples found: cutadapt [2021-02-02 00:16:11,448] multiqc [DEBUG ] No samples found: flexbar [2021-02-02 00:16:11,471] multiqc [DEBUG ] No samples found: trimmomatic [2021-02-02 00:16:11,499] multiqc [DEBUG ] No samples found: skewer [2021-02-02 00:16:11,507] multiqc [DEBUG ] No samples found: sortmerna [2021-02-02 00:16:11,528] multiqc [DEBUG ] No samples found: biobloomtools [2021-02-02 00:16:11,563] multiqc [DEBUG ] No samples found: fastq_screen [2021-02-02 00:16:11,603] multiqc [DEBUG ] No samples found: afterqc [2021-02-02 00:16:11,648] multiqc [DEBUG ] No samples found: fastp [2021-02-02 00:16:15,717] multiqc.modules.fastqc.fastqc [INFO ] Found 16 reports [2021-02-02 00:16:16,125] multiqc [DEBUG ] No samples found: minionqc [2021-02-02 00:16:16,162] multiqc [DEBUG ] No samples found: mosdepth [2021-02-02 00:16:16,188] multiqc [DEBUG ] No samples found: clusterflow [2021-02-02 00:16:16,215] multiqc [DEBUG ] No samples found: bcl2fastq [2021-02-02 00:16:16,234] multiqc [DEBUG ] No samples found: interop [2021-02-02 00:16:16,257] multiqc [DEBUG ] No samples found: flash [2021-02-02 00:16:16,276] multiqc [DEBUG ] No samples found: seqyclean [2021-02-02 00:16:16,309] multiqc [INFO ] Compressing plot data [2021-02-02 00:16:16,553] multiqc [INFO ] Report : multiqc_report.html [2021-02-02 00:16:16,553] multiqc [INFO ] Data : multiqc_data [2021-02-02 00:16:16,554] multiqc [DEBUG ] Moving data file from '/tmp/tmp2o57ye5c/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/fastqc/multiqc_data' [2021-02-02 00:16:16,555] multiqc [DEBUG ] Moving data file from '/tmp/tmp2o57ye5c/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/fastqc/multiqc_data' [2021-02-02 00:16:16,556] multiqc [DEBUG ] Moving data file from '/tmp/tmp2o57ye5c/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/fastqc/multiqc_data' [2021-02-02 00:16:16,557] multiqc [DEBUG ] Moving data file from '/tmp/tmp2o57ye5c/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/fastqc/multiqc_data' [2021-02-02 00:16:16,558] multiqc [DEBUG ] Moving data file from '/tmp/tmp2o57ye5c/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/fastqc/multiqc_data' [2021-02-02 00:16:17,539] multiqc [INFO ] MultiQC complete