[2021-01-20 19:52:10,469] multiqc [DEBUG ] No MultiQC config found: /opt/software/MultiQC/1.7-foss-2018b-Python-2.7.15/lib/python2.7/site-packages/multiqc_config.yaml [2021-01-20 19:52:10,469] multiqc [DEBUG ] No MultiQC config found: /home/danielle_becker/.multiqc_config.yaml [2021-01-20 19:52:10,471] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-01-20 19:52:10,471] multiqc [DEBUG ] Command used: /opt/software/MultiQC/1.7-foss-2018b-Python-2.7.15/bin/multiqc /data/putnamlab/dbecks/Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc [2021-01-20 19:52:11,391] multiqc [WARNING] MultiQC Version v1.9 now available! [2021-01-20 19:52:11,391] multiqc [INFO ] This is MultiQC v1.7 [2021-01-20 19:52:11,391] multiqc [DEBUG ] Command : /opt/software/MultiQC/1.7-foss-2018b-Python-2.7.15/bin/multiqc /data/putnamlab/dbecks/Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc [2021-01-20 19:52:11,391] multiqc [DEBUG ] Working dir : /data/putnamlab/dbecks/Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc [2021-01-20 19:52:11,391] multiqc [INFO ] Template : default [2021-01-20 19:52:11,391] multiqc [INFO ] Searching '/data/putnamlab/dbecks/Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc' [2021-01-20 19:52:11,392] 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, dedup, damageprofiler, picard, prokka, samblaster, samtools, 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, clusterflow, bcl2fastq, interop, flash [2021-01-20 19:52:11,392] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpokaaiO [2021-01-20 19:52:12,725] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C17_R1_001_fastqc.html [2021-01-20 19:52:12,728] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C18_R1_001_fastqc.html [2021-01-20 19:52:12,757] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C19_R2_001_fastqc.html [2021-01-20 19:52:12,776] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C21_R1_001_fastqc.html [2021-01-20 19:52:12,783] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C21_R2_001_fastqc.html [2021-01-20 19:52:12,787] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C22_R1_001_fastqc.html [2021-01-20 19:52:12,805] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C28_R2_001_fastqc.html [2021-01-20 19:52:12,808] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C30_R2_001_fastqc.html [2021-01-20 19:52:12,825] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E10_R1_001_fastqc.html [2021-01-20 19:52:12,828] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E10_R2_001_fastqc.html [2021-01-20 19:52:12,831] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E12_R2_001_fastqc.html [2021-01-20 19:52:12,834] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E13_R1_001_fastqc.html [2021-01-20 19:52:12,842] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E14_R2_001_fastqc.html [2021-01-20 19:52:12,845] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E16_R1_001_fastqc.html [2021-01-20 19:52:12,858] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E4_R2_001_fastqc.html [2021-01-20 19:52:12,866] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E5_R2_001_fastqc.html [2021-01-20 19:52:12,874] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E7_R1_001_fastqc.html [2021-01-20 19:52:12,877] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E8_R2_001_fastqc.html [2021-01-20 19:52:12,880] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E9_R2_001_fastqc.html [2021-01-20 19:52:13,389] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C18_R2_001_fastqc.html [2021-01-20 19:52:13,391] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C20_R2_001_fastqc.html [2021-01-20 19:52:13,393] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C23_R2_001_fastqc.html [2021-01-20 19:52:13,405] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C26_R2_001_fastqc.html [2021-01-20 19:52:13,418] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C29_R1_001_fastqc.html [2021-01-20 19:52:13,421] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C29_R2_001_fastqc.html [2021-01-20 19:52:13,429] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C31_R2_001_fastqc.html [2021-01-20 19:52:13,442] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C32_R1_001_fastqc.html [2021-01-20 19:52:13,445] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E11_R1_001_fastqc.html [2021-01-20 19:52:13,452] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E11_R2_001_fastqc.html [2021-01-20 19:52:13,475] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E15_R2_001_fastqc.html [2021-01-20 19:52:13,497] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E2_R2_001_fastqc.html [2021-01-20 19:52:13,505] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E3_R2_001_fastqc.html [2021-01-20 19:52:13,513] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E6_R2_001_fastqc.html [2021-01-20 19:52:13,525] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E8_R1_001_fastqc.html [2021-01-20 19:52:13,546] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C20_R1_001_fastqc.html [2021-01-20 19:52:13,549] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C23_R1_001_fastqc.html [2021-01-20 19:52:13,557] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C24_R2_001_fastqc.html [2021-01-20 19:52:13,560] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C25_R2_001_fastqc.html [2021-01-20 19:52:13,568] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C26_R1_001_fastqc.html [2021-01-20 19:52:13,571] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C27_R2_001_fastqc.html [2021-01-20 19:52:13,573] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C28_R1_001_fastqc.html [2021-01-20 19:52:13,586] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C30_R1_001_fastqc.html [2021-01-20 19:52:13,595] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C32_R2_001_fastqc.html [2021-01-20 19:52:13,598] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E12_R1_001_fastqc.html [2021-01-20 19:52:13,601] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E14_R1_001_fastqc.html [2021-01-20 19:52:13,609] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E2_R1_001_fastqc.html [2021-01-20 19:52:13,617] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E3_R1_001_fastqc.html [2021-01-20 19:52:13,625] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E6_R1_001_fastqc.html [2021-01-20 19:52:13,649] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C17_R2_001_fastqc.html [2021-01-20 19:52:13,652] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C19_R1_001_fastqc.html [2021-01-20 19:52:13,676] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C22_R2_001_fastqc.html [2021-01-20 19:52:13,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C24_R1_001_fastqc.html [2021-01-20 19:52:13,689] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C25_R1_001_fastqc.html [2021-01-20 19:52:13,704] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C27_R1_001_fastqc.html [2021-01-20 19:52:13,718] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: C31_R1_001_fastqc.html [2021-01-20 19:52:13,731] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E13_R2_001_fastqc.html [2021-01-20 19:52:13,745] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E15_R1_001_fastqc.html [2021-01-20 19:52:13,749] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E16_R2_001_fastqc.html [2021-01-20 19:52:13,752] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E1_R1_001_fastqc.html [2021-01-20 19:52:13,754] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E1_R2_001_fastqc.html [2021-01-20 19:52:13,762] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E4_R1_001_fastqc.html [2021-01-20 19:52:13,770] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E5_R1_001_fastqc.html [2021-01-20 19:52:13,773] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E7_R2_001_fastqc.html [2021-01-20 19:52:13,776] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: E9_R1_001_fastqc.html [2021-01-20 19:52:14,120] multiqc [DEBUG ] No samples found: custom_content [2021-01-20 19:52:14,127] multiqc [DEBUG ] No samples found: conpair [2021-01-20 19:52:14,132] multiqc [DEBUG ] No samples found: peddy [2021-01-20 19:52:14,139] multiqc [DEBUG ] No samples found: methylQA [2021-01-20 19:52:14,145] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-01-20 19:52:14,152] multiqc [DEBUG ] No samples found: qualimap [2021-01-20 19:52:14,157] multiqc [DEBUG ] No samples found: preseq [2021-01-20 19:52:14,163] multiqc [DEBUG ] No samples found: quast [2021-01-20 19:52:14,169] multiqc [DEBUG ] No samples found: qorts [2021-01-20 19:52:14,175] multiqc [DEBUG ] No samples found: rna_seqc [2021-01-20 19:52:14,181] multiqc [DEBUG ] No samples found: rsem [2021-01-20 19:52:14,190] multiqc [DEBUG ] No samples found: rseqc [2021-01-20 19:52:14,196] multiqc [DEBUG ] No samples found: busco [2021-01-20 19:52:14,201] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-01-20 19:52:14,207] multiqc [DEBUG ] No samples found: disambiguate [2021-01-20 19:52:14,213] multiqc [DEBUG ] No samples found: supernova [2021-01-20 19:52:14,223] multiqc [DEBUG ] No samples found: deeptools [2021-01-20 19:52:14,228] multiqc [DEBUG ] No samples found: sargasso [2021-01-20 19:52:14,234] multiqc [DEBUG ] No samples found: verifybamid [2021-01-20 19:52:14,240] multiqc [DEBUG ] No samples found: mirtrace [2021-01-20 19:52:14,246] multiqc [DEBUG ] No samples found: happy [2021-01-20 19:52:14,253] multiqc [DEBUG ] No samples found: homer [2021-01-20 19:52:14,259] multiqc [DEBUG ] No samples found: macs2 [2021-01-20 19:52:14,264] multiqc [DEBUG ] No samples found: theta2 [2021-01-20 19:52:14,270] multiqc [DEBUG ] No samples found: snpeff [2021-01-20 19:52:14,277] multiqc [DEBUG ] No samples found: gatk [2021-01-20 19:52:14,283] multiqc [DEBUG ] No samples found: htseq [2021-01-20 19:52:14,289] multiqc [DEBUG ] No samples found: bcftools [2021-01-20 19:52:14,295] multiqc [DEBUG ] No samples found: featureCounts [2021-01-20 19:52:14,301] multiqc [DEBUG ] No samples found: dedup [2021-01-20 19:52:14,306] multiqc [DEBUG ] No samples found: damageprofiler [2021-01-20 19:52:14,317] multiqc [DEBUG ] No samples found: picard [2021-01-20 19:52:14,323] multiqc [DEBUG ] No samples found: prokka [2021-01-20 19:52:14,329] multiqc [DEBUG ] No samples found: samblaster [2021-01-20 19:52:14,337] multiqc [DEBUG ] No samples found: samtools [2021-01-20 19:52:14,343] multiqc [DEBUG ] No samples found: bamtools [2021-01-20 19:52:14,348] multiqc [DEBUG ] No samples found: jellyfish [2021-01-20 19:52:14,355] multiqc [DEBUG ] No samples found: vcftools [2021-01-20 19:52:14,361] multiqc [DEBUG ] No samples found: longranger [2021-01-20 19:52:14,367] multiqc [DEBUG ] No samples found: stacks [2021-01-20 19:52:14,377] multiqc [DEBUG ] No samples found: bbmap [2021-01-20 19:52:14,383] multiqc [DEBUG ] No samples found: bismark [2021-01-20 19:52:14,390] multiqc [DEBUG ] No samples found: biscuit [2021-01-20 19:52:14,396] multiqc [DEBUG ] No samples found: hicexplorer [2021-01-20 19:52:14,401] multiqc [DEBUG ] No samples found: hicup [2021-01-20 19:52:14,407] multiqc [DEBUG ] No samples found: hicpro [2021-01-20 19:52:14,413] multiqc [DEBUG ] No samples found: salmon [2021-01-20 19:52:14,419] multiqc [DEBUG ] No samples found: kallisto [2021-01-20 19:52:14,425] multiqc [DEBUG ] No samples found: slamdunk [2021-01-20 19:52:14,431] multiqc [DEBUG ] No samples found: star [2021-01-20 19:52:14,437] multiqc [DEBUG ] No samples found: hisat2 [2021-01-20 19:52:14,443] multiqc [DEBUG ] No samples found: tophat [2021-01-20 19:52:14,448] multiqc [DEBUG ] No samples found: bowtie2 [2021-01-20 19:52:14,454] multiqc [DEBUG ] No samples found: bowtie1 [2021-01-20 19:52:14,460] multiqc [DEBUG ] No samples found: kat [2021-01-20 19:52:14,465] multiqc [DEBUG ] No samples found: leehom [2021-01-20 19:52:14,471] multiqc [DEBUG ] No samples found: adapterRemoval [2021-01-20 19:52:14,477] multiqc [DEBUG ] No samples found: clipandmerge [2021-01-20 19:52:14,483] multiqc [DEBUG ] No samples found: cutadapt [2021-01-20 19:52:14,488] multiqc [DEBUG ] No samples found: flexbar [2021-01-20 19:52:14,523] multiqc [DEBUG ] No samples found: trimmomatic [2021-01-20 19:52:14,529] multiqc [DEBUG ] No samples found: skewer [2021-01-20 19:52:14,535] multiqc [DEBUG ] No samples found: sortmerna [2021-01-20 19:52:14,541] multiqc [DEBUG ] No samples found: biobloomtools [2021-01-20 19:52:14,547] multiqc [DEBUG ] No samples found: fastq_screen [2021-01-20 19:52:14,553] multiqc [DEBUG ] No samples found: afterqc [2021-01-20 19:52:14,558] multiqc [DEBUG ] No samples found: fastp [2021-01-20 19:53:08,882] multiqc.modules.fastqc.fastqc [INFO ] Found 64 reports [2021-01-20 19:53:17,816] multiqc [DEBUG ] No samples found: minionqc [2021-01-20 19:53:17,821] multiqc [DEBUG ] No samples found: clusterflow [2021-01-20 19:53:17,826] multiqc [DEBUG ] No samples found: bcl2fastq [2021-01-20 19:53:17,830] multiqc [DEBUG ] No samples found: interop [2021-01-20 19:53:17,835] multiqc [DEBUG ] No samples found: flash [2021-01-20 19:53:17,924] multiqc [INFO ] Compressing plot data [2021-01-20 19:53:20,963] multiqc [INFO ] Report : multiqc_report.html [2021-01-20 19:53:20,963] multiqc [INFO ] Data : multiqc_data [2021-01-20 19:53:21,353] multiqc [DEBUG ] Moving data file from '/tmp/tmpokaaiO/multiqc_data/multiqc_sources.txt' to '/data/putnamlab/dbecks/Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc/multiqc_data' [2021-01-20 19:53:24,708] multiqc [DEBUG ] Moving data file from '/tmp/tmpokaaiO/multiqc_data/multiqc_general_stats.txt' to '/data/putnamlab/dbecks/Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc/multiqc_data' [2021-01-20 19:53:24,763] multiqc [DEBUG ] Moving data file from '/tmp/tmpokaaiO/multiqc_data/multiqc_data.json' to '/data/putnamlab/dbecks/Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc/multiqc_data' [2021-01-20 19:53:24,818] multiqc [DEBUG ] Moving data file from '/tmp/tmpokaaiO/multiqc_data/multiqc_fastqc.txt' to '/data/putnamlab/dbecks/Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc/multiqc_data' [2021-01-20 19:53:25,045] multiqc [INFO ] MultiQC complete