[2023-06-16 14:23:51,895] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-06-16 14:23:51,897] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-06-16 14:23:51,897] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-06-16 14:23:51,897] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-06-16 14:23:51,897] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-06-16 14:23:51,897] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-06-16 14:23:51,897] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-16 14:23:51,897] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-16 14:23:56,912] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-06-16 14:23:56,912] multiqc [INFO ] This is MultiQC v1.8 [2023-06-16 14:23:56,914] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-16 14:23:56,914] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/raw_fastqc [2023-06-16 14:23:56,914] multiqc [INFO ] Template : default [2023-06-16 14:23:56,915] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-06-16 14:23:56,915] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/raw_fastqc [2023-06-16 14:23:56,915] 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 [2023-06-16 14:23:56,916] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpspex0n_t [2023-06-16 14:23:57,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167_R1_001_fastqc.html [2023-06-16 14:23:57,080] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167_R1_001.fastq.gz [2023-06-16 14:23:57,086] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167_R2_001_fastqc.html [2023-06-16 14:23:57,087] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167_R2_001.fastq.gz [2023-06-16 14:23:57,347] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-16 14:23:57,347] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-16 14:23:57,348] multiqc [DEBUG ] No samples found: custom_content [2023-06-16 14:23:57,352] multiqc [DEBUG ] No samples found: conpair [2023-06-16 14:23:57,357] multiqc [DEBUG ] No samples found: peddy [2023-06-16 14:23:57,361] multiqc [DEBUG ] No samples found: methylQA [2023-06-16 14:23:57,366] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-16 14:23:57,371] multiqc [DEBUG ] No samples found: qualimap [2023-06-16 14:23:57,375] multiqc [DEBUG ] No samples found: preseq [2023-06-16 14:23:57,379] multiqc [DEBUG ] No samples found: quast [2023-06-16 14:23:57,383] multiqc [DEBUG ] No samples found: qorts [2023-06-16 14:23:57,388] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-16 14:23:57,392] multiqc [DEBUG ] No samples found: rsem [2023-06-16 14:23:57,398] multiqc [DEBUG ] No samples found: rseqc [2023-06-16 14:23:57,402] multiqc [DEBUG ] No samples found: busco [2023-06-16 14:23:57,407] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-16 14:23:57,411] multiqc [DEBUG ] No samples found: disambiguate [2023-06-16 14:23:57,415] multiqc [DEBUG ] No samples found: supernova [2023-06-16 14:23:57,422] multiqc [DEBUG ] No samples found: deeptools [2023-06-16 14:23:57,426] multiqc [DEBUG ] No samples found: sargasso [2023-06-16 14:23:57,430] multiqc [DEBUG ] No samples found: verifybamid [2023-06-16 14:23:57,435] multiqc [DEBUG ] No samples found: mirtrace [2023-06-16 14:23:57,439] multiqc [DEBUG ] No samples found: happy [2023-06-16 14:23:57,444] multiqc [DEBUG ] No samples found: homer [2023-06-16 14:23:57,448] multiqc [DEBUG ] No samples found: macs2 [2023-06-16 14:23:57,452] multiqc [DEBUG ] No samples found: theta2 [2023-06-16 14:23:57,456] multiqc [DEBUG ] No samples found: snpeff [2023-06-16 14:23:57,461] multiqc [DEBUG ] No samples found: gatk [2023-06-16 14:23:57,465] multiqc [DEBUG ] No samples found: htseq [2023-06-16 14:23:57,469] multiqc [DEBUG ] No samples found: bcftools [2023-06-16 14:23:57,473] multiqc [DEBUG ] No samples found: featureCounts [2023-06-16 14:23:57,478] multiqc [DEBUG ] No samples found: fgbio [2023-06-16 14:23:57,482] multiqc [DEBUG ] No samples found: dedup [2023-06-16 14:23:57,486] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-16 14:23:57,494] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-16 14:23:57,499] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-16 14:23:57,502] multiqc [DEBUG ] No samples found: picard [2023-06-16 14:23:57,506] multiqc [DEBUG ] No samples found: prokka [2023-06-16 14:23:57,510] multiqc [DEBUG ] No samples found: samblaster [2023-06-16 14:23:57,516] multiqc [DEBUG ] No samples found: samtools [2023-06-16 14:23:57,520] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-16 14:23:57,524] multiqc [DEBUG ] No samples found: bamtools [2023-06-16 14:23:57,528] multiqc [DEBUG ] No samples found: jellyfish [2023-06-16 14:23:57,533] multiqc [DEBUG ] No samples found: vcftools [2023-06-16 14:23:57,538] multiqc [DEBUG ] No samples found: longranger [2023-06-16 14:23:57,542] multiqc [DEBUG ] No samples found: stacks [2023-06-16 14:23:57,549] multiqc [DEBUG ] No samples found: bbmap [2023-06-16 14:23:57,553] multiqc [DEBUG ] No samples found: bismark [2023-06-16 14:23:57,557] multiqc [DEBUG ] No samples found: biscuit [2023-06-16 14:23:57,561] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-16 14:23:57,564] multiqc [DEBUG ] No samples found: hicup [2023-06-16 14:23:57,568] multiqc [DEBUG ] No samples found: hicpro [2023-06-16 14:23:57,572] multiqc [DEBUG ] No samples found: salmon [2023-06-16 14:23:57,575] multiqc [DEBUG ] No samples found: kallisto [2023-06-16 14:23:57,579] multiqc [DEBUG ] No samples found: slamdunk [2023-06-16 14:23:57,582] multiqc [DEBUG ] No samples found: star [2023-06-16 14:23:57,586] multiqc [DEBUG ] No samples found: hisat2 [2023-06-16 14:23:57,589] multiqc [DEBUG ] No samples found: tophat [2023-06-16 14:23:57,593] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-16 14:23:57,596] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-16 14:23:57,599] multiqc [DEBUG ] No samples found: kat [2023-06-16 14:23:57,603] multiqc [DEBUG ] No samples found: leehom [2023-06-16 14:23:57,606] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-16 14:23:57,609] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-16 14:23:57,613] multiqc [DEBUG ] No samples found: cutadapt [2023-06-16 14:23:57,616] multiqc [DEBUG ] No samples found: flexbar [2023-06-16 14:23:57,620] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-16 14:23:57,623] multiqc [DEBUG ] No samples found: skewer [2023-06-16 14:23:57,627] multiqc [DEBUG ] No samples found: sortmerna [2023-06-16 14:23:57,630] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-16 14:23:57,633] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-16 14:23:57,637] multiqc [DEBUG ] No samples found: afterqc [2023-06-16 14:23:57,640] multiqc [DEBUG ] No samples found: fastp [2023-06-16 14:23:57,904] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2023-06-16 14:23:57,981] multiqc [DEBUG ] No samples found: minionqc [2023-06-16 14:23:57,984] multiqc [DEBUG ] No samples found: mosdepth [2023-06-16 14:23:57,988] multiqc [DEBUG ] No samples found: clusterflow [2023-06-16 14:23:57,992] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-16 14:23:57,995] multiqc [DEBUG ] No samples found: interop [2023-06-16 14:23:57,999] multiqc [DEBUG ] No samples found: flash [2023-06-16 14:23:58,002] multiqc [DEBUG ] No samples found: seqyclean [2023-06-16 14:23:58,006] multiqc [INFO ] Compressing plot data [2023-06-16 14:23:58,046] multiqc [INFO ] Report : multiqc_report.html [2023-06-16 14:23:58,046] multiqc [INFO ] Data : multiqc_data [2023-06-16 14:23:58,047] multiqc [DEBUG ] Moving data file from '/tmp/tmpspex0n_t/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/raw_fastqc/multiqc_data' [2023-06-16 14:23:58,049] multiqc [DEBUG ] Moving data file from '/tmp/tmpspex0n_t/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/raw_fastqc/multiqc_data' [2023-06-16 14:23:58,050] multiqc [DEBUG ] Moving data file from '/tmp/tmpspex0n_t/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/raw_fastqc/multiqc_data' [2023-06-16 14:23:58,052] multiqc [DEBUG ] Moving data file from '/tmp/tmpspex0n_t/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/raw_fastqc/multiqc_data' [2023-06-16 14:23:58,053] multiqc [DEBUG ] Moving data file from '/tmp/tmpspex0n_t/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/raw_fastqc/multiqc_data' [2023-06-16 14:23:58,196] multiqc [INFO ] MultiQC complete