[2021-01-17 01:34:30,056] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-01-17 01:34:30,057] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/yaaminiv/.multiqc_config.yaml [2021-01-17 01:34:30,057] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-01-17 01:34:30,057] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/. [2021-01-17 01:34:35,403] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-01-17 01:34:35,403] multiqc [INFO ] This is MultiQC v1.8 [2021-01-17 01:34:35,405] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/. [2021-01-17 01:34:35,405] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2 [2021-01-17 01:34:35,405] multiqc [INFO ] Template : default [2021-01-17 01:34:35,405] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-01-17 01:34:35,405] multiqc [INFO ] Searching : /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2 [2021-01-17 01:34:35,406] 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 [2021-01-17 01:34:35,406] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp5oqhap9x [2021-01-17 01:34:36,012] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_23_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,019] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_6_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,019] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_24_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,033] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_5_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,051] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_17_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,065] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_19_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,065] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_2_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,071] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_7_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,078] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_24_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,079] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_20_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,084] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_15_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,091] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_8_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,131] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-788394.out [2021-01-17 01:34:36,133] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-788394.out [2021-01-17 01:34:36,350] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_20_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,351] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_4_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,355] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_5_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,362] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_7_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,367] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_9_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,378] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_21_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,385] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_7_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,385] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_8_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,385] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_1_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,390] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_20_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,397] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_18_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,397] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_7_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,402] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_20_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,408] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_9_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,408] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_23_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,408] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_10_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,409] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_18_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,413] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_13_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,420] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_17_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,420] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_12_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,425] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_6_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,432] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_21_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,432] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_16_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,433] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_1_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,438] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_6_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,444] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_18_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,449] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_4_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,461] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_19_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,468] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_11_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,468] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_24_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,474] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_4_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,480] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_22_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,480] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_1_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,481] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_9_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,481] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_9_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,481] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_12_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,481] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_13_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,486] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_9_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,497] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_8_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,504] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_11_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,509] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_15_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,520] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_8_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,531] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_24_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,553] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_3_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,560] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_4_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,560] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_13_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,560] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_3_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,565] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_14_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,576] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_23_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,582] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_19_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,583] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_4_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,583] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_8_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,583] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_16_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,583] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_6_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,583] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_3_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,583] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_16_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,584] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_3_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,589] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_13_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,595] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_14_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,600] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_3_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,611] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_16_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,618] multiqc [DEBUG ] Ignoring file as matched an 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zr3644_24_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,632] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_18_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,639] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_21_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,645] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_15_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,645] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_19_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,646] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_12_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,651] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_21_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,662] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_11_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,673] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_23_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,679] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_5_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,680] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_17_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,680] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_22_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,684] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_5_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,691] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_8_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,691] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_17_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,691] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_13_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,691] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_14_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,692] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_2_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,692] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_5_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,693] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_15_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,708] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_18_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,708] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_12_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,717] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_21_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,732] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_1_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,742] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_15_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,748] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_17_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,755] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_3_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,755] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_14_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,760] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_1_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,772] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_12_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,784] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_10_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_17_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,790] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_21_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,795] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_10_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,806] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_19_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,818] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_2_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,840] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_13_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,840] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_20_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,845] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_7_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,852] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_20_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,857] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_14_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,868] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_24_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,875] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_22_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,875] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_7_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,875] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_6_R1_val_1_val_1.fq.gz [2021-01-17 01:34:36,875] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_19_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,880] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_11_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,887] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_6_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,887] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_5_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,892] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_2_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,898] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_2_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,903] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_16_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,914] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_22_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,920] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_15_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,925] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_22_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,932] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_22_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,932] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_23_R1_val_1_val_1_fastqc.html [2021-01-17 01:34:36,932] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_16_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,932] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_4_R2_val_2_val_2_fastqc.html [2021-01-17 01:34:36,937] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_1_R1_val_1.fq.gz_trimming_report.txt [2021-01-17 01:34:36,948] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_12_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:36,972] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: zr3644_10_R2_val_2_val_2.fq.gz [2021-01-17 01:34:36,976] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: zr3644_18_R2_val_2.fq.gz_trimming_report.txt [2021-01-17 01:34:41,663] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-01-17 01:34:41,676] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-01-17 01:34:41,717] multiqc [DEBUG ] No samples found: custom_content [2021-01-17 01:34:41,867] multiqc [DEBUG ] No samples found: conpair [2021-01-17 01:34:42,037] multiqc [DEBUG ] No samples found: peddy [2021-01-17 01:34:42,168] multiqc [DEBUG ] No samples found: methylQA [2021-01-17 01:34:42,185] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-01-17 01:34:42,275] multiqc [DEBUG ] No samples found: qualimap [2021-01-17 01:34:42,303] multiqc [DEBUG ] No samples found: preseq [2021-01-17 01:34:42,350] multiqc [DEBUG ] No samples found: quast [2021-01-17 01:34:42,379] multiqc [DEBUG ] No samples found: qorts [2021-01-17 01:34:42,447] multiqc [DEBUG ] No samples found: rna_seqc [2021-01-17 01:34:42,513] multiqc [DEBUG ] No samples found: rsem [2021-01-17 01:34:42,625] multiqc [DEBUG ] No samples found: rseqc [2021-01-17 01:34:42,681] multiqc [DEBUG ] No samples found: busco [2021-01-17 01:34:42,770] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-01-17 01:34:42,819] multiqc [DEBUG ] No samples found: disambiguate [2021-01-17 01:34:42,854] multiqc [DEBUG ] No samples found: supernova [2021-01-17 01:34:42,964] multiqc [DEBUG ] No samples found: deeptools [2021-01-17 01:34:43,051] multiqc [DEBUG ] No samples found: sargasso [2021-01-17 01:34:43,086] multiqc [DEBUG ] No samples found: verifybamid [2021-01-17 01:34:43,118] multiqc [DEBUG ] No samples found: mirtrace [2021-01-17 01:34:43,137] multiqc [DEBUG ] No samples found: happy [2021-01-17 01:34:43,178] multiqc [DEBUG ] No samples found: homer [2021-01-17 01:34:43,195] multiqc [DEBUG ] No samples found: macs2 [2021-01-17 01:34:43,204] multiqc [DEBUG ] No samples found: theta2 [2021-01-17 01:34:43,228] multiqc [DEBUG ] No samples found: snpeff [2021-01-17 01:34:43,303] multiqc [DEBUG ] No samples found: gatk [2021-01-17 01:34:43,319] multiqc [DEBUG ] No samples found: htseq [2021-01-17 01:34:43,353] multiqc [DEBUG ] No samples found: bcftools [2021-01-17 01:34:43,362] multiqc [DEBUG ] No samples found: featureCounts [2021-01-17 01:34:43,372] multiqc [DEBUG ] No samples found: fgbio [2021-01-17 01:34:43,380] multiqc [DEBUG ] No samples found: dedup [2021-01-17 01:34:43,435] multiqc [DEBUG ] No samples found: damageprofiler [2021-01-17 01:34:43,752] multiqc [DEBUG ] No samples found: biobambam2 [2021-01-17 01:34:43,801] multiqc [DEBUG ] No samples found: mtnucratio [2021-01-17 01:34:43,807] multiqc [DEBUG ] No samples found: picard [2021-01-17 01:34:43,828] multiqc [DEBUG ] No samples found: prokka [2021-01-17 01:34:43,837] multiqc [DEBUG ] No samples found: samblaster [2021-01-17 01:34:43,905] multiqc [DEBUG ] No samples found: samtools [2021-01-17 01:34:43,973] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-01-17 01:34:44,097] multiqc [DEBUG ] No samples found: bamtools [2021-01-17 01:34:44,107] multiqc [DEBUG ] No samples found: jellyfish [2021-01-17 01:34:44,136] multiqc [DEBUG ] No samples found: vcftools [2021-01-17 01:34:44,187] multiqc [DEBUG ] No samples found: longranger [2021-01-17 01:34:44,224] multiqc [DEBUG ] No samples found: stacks [2021-01-17 01:34:44,371] multiqc [DEBUG ] No samples found: bbmap [2021-01-17 01:34:44,410] multiqc [DEBUG ] No samples found: bismark [2021-01-17 01:34:44,435] multiqc [DEBUG ] No samples found: biscuit [2021-01-17 01:34:44,470] multiqc [DEBUG ] No samples found: hicexplorer [2021-01-17 01:34:44,495] multiqc [DEBUG ] No samples found: hicup [2021-01-17 01:34:44,521] multiqc [DEBUG ] No samples found: hicpro [2021-01-17 01:34:44,530] multiqc [DEBUG ] No samples found: salmon [2021-01-17 01:34:44,551] multiqc [DEBUG ] No samples found: kallisto [2021-01-17 01:34:44,579] multiqc [DEBUG ] No samples found: slamdunk [2021-01-17 01:34:44,608] multiqc [DEBUG ] No samples found: star [2021-01-17 01:34:44,650] multiqc [DEBUG ] No samples found: hisat2 [2021-01-17 01:34:44,670] multiqc [DEBUG ] No samples found: tophat [2021-01-17 01:34:44,689] multiqc [DEBUG ] No samples found: bowtie2 [2021-01-17 01:34:44,721] multiqc [DEBUG ] No samples found: bowtie1 [2021-01-17 01:34:44,732] multiqc [DEBUG ] No samples found: kat [2021-01-17 01:34:44,741] multiqc [DEBUG ] No samples found: leehom [2021-01-17 01:34:44,773] multiqc [DEBUG ] No samples found: adapterRemoval [2021-01-17 01:34:44,782] multiqc [DEBUG ] No samples found: clipandmerge [2021-01-17 01:34:44,947] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_7_R1_val_1 [2021-01-17 01:34:44,980] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_15_R2_val_2 [2021-01-17 01:34:44,986] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_17_R1_val_1 [2021-01-17 01:34:45,012] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_5_R1_val_1 [2021-01-17 01:34:45,013] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_9_R2_val_2 [2021-01-17 01:34:45,014] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_21_R2_val_2 [2021-01-17 01:34:45,015] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_20_R2_val_2 [2021-01-17 01:34:45,016] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_20_R1_val_1 [2021-01-17 01:34:45,017] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_13_R1_val_1 [2021-01-17 01:34:45,018] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_6_R1_val_1 [2021-01-17 01:34:45,019] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_6_R2_val_2 [2021-01-17 01:34:45,020] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_4_R2_val_2 [2021-01-17 01:34:45,021] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_19_R1_val_1 [2021-01-17 01:34:45,022] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_4_R1_val_1 [2021-01-17 01:34:45,023] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_9_R1_val_1 [2021-01-17 01:34:45,023] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_8_R2_val_2 [2021-01-17 01:34:45,024] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_15_R1_val_1 [2021-01-17 01:34:45,025] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_8_R1_val_1 [2021-01-17 01:34:45,026] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_24_R2_val_2 [2021-01-17 01:34:45,027] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_3_R1_val_1 [2021-01-17 01:34:45,028] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_14_R2_val_2 [2021-01-17 01:34:45,029] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_23_R2_val_2 [2021-01-17 01:34:45,030] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_13_R2_val_2 [2021-01-17 01:34:45,031] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_3_R2_val_2 [2021-01-17 01:34:45,032] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_16_R1_val_1 [2021-01-17 01:34:45,033] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_18_R1_val_1 [2021-01-17 01:34:45,034] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_21_R1_val_1 [2021-01-17 01:34:45,035] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_11_R2_val_2 [2021-01-17 01:34:45,036] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_23_R1_val_1 [2021-01-17 01:34:45,037] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_5_R2_val_2 [2021-01-17 01:34:45,038] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_17_R2_val_2 [2021-01-17 01:34:45,039] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_1_R2_val_2 [2021-01-17 01:34:45,040] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_12_R1_val_1 [2021-01-17 01:34:45,040] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_10_R1_val_1 [2021-01-17 01:34:45,041] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_10_R2_val_2 [2021-01-17 01:34:45,042] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_19_R2_val_2 [2021-01-17 01:34:45,043] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_2_R1_val_1 [2021-01-17 01:34:45,044] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_7_R2_val_2 [2021-01-17 01:34:45,045] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_14_R1_val_1 [2021-01-17 01:34:45,046] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_24_R1_val_1 [2021-01-17 01:34:45,047] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_11_R1_val_1 [2021-01-17 01:34:45,048] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_2_R2_val_2 [2021-01-17 01:34:45,048] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_16_R2_val_2 [2021-01-17 01:34:45,049] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_22_R2_val_2 [2021-01-17 01:34:45,050] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_22_R1_val_1 [2021-01-17 01:34:45,051] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_1_R1_val_1 [2021-01-17 01:34:45,052] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_12_R2_val_2 [2021-01-17 01:34:45,053] multiqc.modules.cutadapt.cutadapt [DEBUG ] Duplicate sample name found! Overwriting: zr3644_18_R2_val_2 [2021-01-17 01:34:45,054] multiqc.modules.cutadapt.cutadapt [INFO ] Found 48 reports [2021-01-17 01:34:45,069] multiqc [DEBUG ] No samples found: flexbar [2021-01-17 01:34:45,109] multiqc [DEBUG ] No samples found: trimmomatic [2021-01-17 01:34:45,221] multiqc [DEBUG ] No samples found: skewer [2021-01-17 01:34:45,231] multiqc [DEBUG ] No samples found: sortmerna [2021-01-17 01:34:45,252] multiqc [DEBUG ] No samples found: biobloomtools [2021-01-17 01:34:45,279] multiqc [DEBUG ] No samples found: fastq_screen [2021-01-17 01:34:45,319] multiqc [DEBUG ] No samples found: afterqc [2021-01-17 01:34:45,345] multiqc [DEBUG ] No samples found: fastp [2021-01-17 01:35:01,299] multiqc.modules.fastqc.fastqc [INFO ] Found 48 reports [2021-01-17 01:35:02,127] multiqc [DEBUG ] No samples found: minionqc [2021-01-17 01:35:02,148] multiqc [DEBUG ] No samples found: mosdepth [2021-01-17 01:35:02,184] multiqc [DEBUG ] No samples found: clusterflow [2021-01-17 01:35:02,218] multiqc [DEBUG ] No samples found: bcl2fastq [2021-01-17 01:35:02,251] multiqc [DEBUG ] No samples found: interop [2021-01-17 01:35:02,275] multiqc [DEBUG ] No samples found: flash [2021-01-17 01:35:02,305] multiqc [DEBUG ] No samples found: seqyclean [2021-01-17 01:35:02,422] multiqc [INFO ] Compressing plot data [2021-01-17 01:35:03,229] multiqc [INFO ] Report : multiqc_report.html [2021-01-17 01:35:03,229] multiqc [INFO ] Data : multiqc_data [2021-01-17 01:35:03,232] multiqc [DEBUG ] Moving data file from '/tmp/tmp5oqhap9x/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/multiqc_data' [2021-01-17 01:35:03,232] multiqc [DEBUG ] Moving data file from '/tmp/tmp5oqhap9x/multiqc_data/multiqc_cutadapt.txt' to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/multiqc_data' [2021-01-17 01:35:03,233] multiqc [DEBUG ] Moving data file from '/tmp/tmp5oqhap9x/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/multiqc_data' [2021-01-17 01:35:03,234] multiqc [DEBUG ] Moving data file from '/tmp/tmp5oqhap9x/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/multiqc_data' [2021-01-17 01:35:03,235] multiqc [DEBUG ] Moving data file from '/tmp/tmp5oqhap9x/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/multiqc_data' [2021-01-17 01:35:03,236] multiqc [DEBUG ] Moving data file from '/tmp/tmp5oqhap9x/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/multiqc_data' [2021-01-17 01:35:04,700] multiqc [INFO ] MultiQC complete