[2023-06-16 14:35:22,134] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-06-16 14:35:22,136] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-06-16 14:35:22,136] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-06-16 14:35:22,136] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-06-16 14:35:22,136] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-06-16 14:35:22,136] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-06-16 14:35:22,136] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-06-16 14:35:22,136] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-16 14:35:27,153] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-06-16 14:35:27,153] multiqc [INFO ] This is MultiQC v1.8 [2023-06-16 14:35:27,155] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-06-16 14:35:27,155] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/trimmed [2023-06-16 14:35:27,155] multiqc [INFO ] Template : default [2023-06-16 14:35:27,156] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-06-16 14:35:27,156] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/trimmed [2023-06-16 14:35:27,156] 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 14:35:27,157] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp4r71s36n [2023-06-16 14:35:27,329] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167_R1_001.fastp-trim.20230616_fastqc.html [2023-06-16 14:35:27,335] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167_R2_001.fastp-trim.20230616.fastq.gz [2023-06-16 14:35:27,335] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-06-16 14:35:27,336] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167.fastp-trim.20230616.report.html [2023-06-16 14:35:27,336] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167_R2_001.fastp-trim.20230616_fastqc.html [2023-06-16 14:35:27,336] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: L-T-167_R1_001.fastp-trim.20230616.fastq.gz [2023-06-16 14:35:27,609] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-16 14:35:27,610] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-06-16 14:35:27,610] multiqc [DEBUG ] No samples found: custom_content [2023-06-16 14:35:27,615] multiqc [DEBUG ] No samples found: conpair [2023-06-16 14:35:27,619] multiqc [DEBUG ] No samples found: peddy [2023-06-16 14:35:27,624] multiqc [DEBUG ] No samples found: methylQA [2023-06-16 14:35:27,629] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-06-16 14:35:27,634] multiqc [DEBUG ] No samples found: qualimap [2023-06-16 14:35:27,638] multiqc [DEBUG ] No samples found: preseq [2023-06-16 14:35:27,643] multiqc [DEBUG ] No samples found: quast [2023-06-16 14:35:27,647] multiqc [DEBUG ] No samples found: qorts [2023-06-16 14:35:27,652] multiqc [DEBUG ] No samples found: rna_seqc [2023-06-16 14:35:27,656] multiqc [DEBUG ] No samples found: rsem [2023-06-16 14:35:27,663] multiqc [DEBUG ] No samples found: rseqc [2023-06-16 14:35:27,667] multiqc [DEBUG ] No samples found: busco [2023-06-16 14:35:27,671] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-06-16 14:35:27,676] multiqc [DEBUG ] No samples found: disambiguate [2023-06-16 14:35:27,680] multiqc [DEBUG ] No samples found: supernova [2023-06-16 14:35:27,687] multiqc [DEBUG ] No samples found: deeptools [2023-06-16 14:35:27,691] multiqc [DEBUG ] No samples found: sargasso [2023-06-16 14:35:27,696] multiqc [DEBUG ] No samples found: verifybamid [2023-06-16 14:35:27,700] multiqc [DEBUG ] No samples found: mirtrace [2023-06-16 14:35:27,705] multiqc [DEBUG ] No samples found: happy [2023-06-16 14:35:27,710] multiqc [DEBUG ] No samples found: homer [2023-06-16 14:35:27,714] multiqc [DEBUG ] No samples found: macs2 [2023-06-16 14:35:27,718] multiqc [DEBUG ] No samples found: theta2 [2023-06-16 14:35:27,722] multiqc [DEBUG ] No samples found: snpeff [2023-06-16 14:35:27,728] multiqc [DEBUG ] No samples found: gatk [2023-06-16 14:35:27,732] multiqc [DEBUG ] No samples found: htseq [2023-06-16 14:35:27,737] multiqc [DEBUG ] No samples found: bcftools [2023-06-16 14:35:27,741] multiqc [DEBUG ] No samples found: featureCounts [2023-06-16 14:35:27,745] multiqc [DEBUG ] No samples found: fgbio [2023-06-16 14:35:27,749] multiqc [DEBUG ] No samples found: dedup [2023-06-16 14:35:27,754] multiqc [DEBUG ] No samples found: damageprofiler [2023-06-16 14:35:27,763] multiqc [DEBUG ] No samples found: biobambam2 [2023-06-16 14:35:27,768] multiqc [DEBUG ] No samples found: mtnucratio [2023-06-16 14:35:27,771] multiqc [DEBUG ] No samples found: picard [2023-06-16 14:35:27,776] multiqc [DEBUG ] No samples found: prokka [2023-06-16 14:35:27,780] multiqc [DEBUG ] No samples found: samblaster [2023-06-16 14:35:27,785] multiqc [DEBUG ] No samples found: samtools [2023-06-16 14:35:27,790] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-06-16 14:35:27,795] multiqc [DEBUG ] No samples found: bamtools [2023-06-16 14:35:27,799] multiqc [DEBUG ] No samples found: jellyfish [2023-06-16 14:35:27,804] multiqc [DEBUG ] No samples found: vcftools [2023-06-16 14:35:27,808] multiqc [DEBUG ] No samples found: longranger [2023-06-16 14:35:27,812] multiqc [DEBUG ] No samples found: stacks [2023-06-16 14:35:27,818] multiqc [DEBUG ] No samples found: bbmap [2023-06-16 14:35:27,822] multiqc [DEBUG ] No samples found: bismark [2023-06-16 14:35:27,826] multiqc [DEBUG ] No samples found: biscuit [2023-06-16 14:35:27,830] multiqc [DEBUG ] No samples found: hicexplorer [2023-06-16 14:35:27,833] multiqc [DEBUG ] No samples found: hicup [2023-06-16 14:35:27,837] multiqc [DEBUG ] No samples found: hicpro [2023-06-16 14:35:27,840] multiqc [DEBUG ] No samples found: salmon [2023-06-16 14:35:27,844] multiqc [DEBUG ] No samples found: kallisto [2023-06-16 14:35:27,848] multiqc [DEBUG ] No samples found: slamdunk [2023-06-16 14:35:27,852] multiqc [DEBUG ] No samples found: star [2023-06-16 14:35:27,855] multiqc [DEBUG ] No samples found: hisat2 [2023-06-16 14:35:27,859] multiqc [DEBUG ] No samples found: tophat [2023-06-16 14:35:27,862] multiqc [DEBUG ] No samples found: bowtie2 [2023-06-16 14:35:27,866] multiqc [DEBUG ] No samples found: bowtie1 [2023-06-16 14:35:27,869] multiqc [DEBUG ] No samples found: kat [2023-06-16 14:35:27,873] multiqc [DEBUG ] No samples found: leehom [2023-06-16 14:35:27,876] multiqc [DEBUG ] No samples found: adapterRemoval [2023-06-16 14:35:27,880] multiqc [DEBUG ] No samples found: clipandmerge [2023-06-16 14:35:27,883] multiqc [DEBUG ] No samples found: cutadapt [2023-06-16 14:35:27,887] multiqc [DEBUG ] No samples found: flexbar [2023-06-16 14:35:27,890] multiqc [DEBUG ] No samples found: trimmomatic [2023-06-16 14:35:27,894] multiqc [DEBUG ] No samples found: skewer [2023-06-16 14:35:27,897] multiqc [DEBUG ] No samples found: sortmerna [2023-06-16 14:35:27,901] multiqc [DEBUG ] No samples found: biobloomtools [2023-06-16 14:35:27,904] multiqc [DEBUG ] No samples found: fastq_screen [2023-06-16 14:35:27,908] multiqc [DEBUG ] No samples found: afterqc [2023-06-16 14:35:27,915] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: L-T-167.fastp-trim.20230616.report.json [2023-06-16 14:35:27,916] multiqc.modules.fastp.fastp [INFO ] Found 1 reports [2023-06-16 14:35:28,433] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports [2023-06-16 14:35:28,491] multiqc [DEBUG ] No samples found: minionqc [2023-06-16 14:35:28,494] multiqc [DEBUG ] No samples found: mosdepth [2023-06-16 14:35:28,498] multiqc [DEBUG ] No samples found: clusterflow [2023-06-16 14:35:28,502] multiqc [DEBUG ] No samples found: bcl2fastq [2023-06-16 14:35:28,505] multiqc [DEBUG ] No samples found: interop [2023-06-16 14:35:28,509] multiqc [DEBUG ] No samples found: flash [2023-06-16 14:35:28,513] multiqc [DEBUG ] No samples found: seqyclean [2023-06-16 14:35:28,519] multiqc [INFO ] Compressing plot data [2023-06-16 14:35:28,624] multiqc [INFO ] Report : multiqc_report.html [2023-06-16 14:35:28,624] multiqc [INFO ] Data : multiqc_data [2023-06-16 14:35:28,626] multiqc [DEBUG ] Moving data file from '/tmp/tmp4r71s36n/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/trimmed/multiqc_data' [2023-06-16 14:35:28,628] multiqc [DEBUG ] Moving data file from '/tmp/tmp4r71s36n/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/trimmed/multiqc_data' [2023-06-16 14:35:28,629] multiqc [DEBUG ] Moving data file from '/tmp/tmp4r71s36n/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/trimmed/multiqc_data' [2023-06-16 14:35:28,630] multiqc [DEBUG ] Moving data file from '/tmp/tmp4r71s36n/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/trimmed/multiqc_data' [2023-06-16 14:35:28,632] multiqc [DEBUG ] Moving data file from '/tmp/tmp4r71s36n/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/trimmed/multiqc_data' [2023-06-16 14:35:28,634] multiqc [DEBUG ] Moving data file from '/tmp/tmp4r71s36n/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230616-lsta-fastqc-fastp-multiqc-RNAseq/trimmed/multiqc_data' [2023-06-16 14:35:28,774] multiqc [INFO ] MultiQC complete