[2020-12-08 22:22:25,654] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-12-08 22:22:25,673] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-12-08 22:22:25,673] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2020-12-08 22:22:25,673] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2020-12-08 22:22:25,673] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-12-08 22:22:25,674] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2020-12-08 22:22:25,674] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-12-08 22:22:25,674] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-12-08 22:22:30,837] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2020-12-08 22:22:30,837] multiqc [INFO ] This is MultiQC v1.8 [2020-12-08 22:22:30,839] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2020-12-08 22:22:30,839] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9 [2020-12-08 22:22:30,839] multiqc [INFO ] Template : default [2020-12-08 22:22:30,840] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-12-08 22:22:30,840] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9 [2020-12-08 22:22:30,841] 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 [2020-12-08 22:22:30,841] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp_229ily_ [2020-12-08 22:22:31,313] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-562617.out [2020-12-08 22:22:31,321] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Aligned.sortedByCoord.out.NC_001276.1.bam.csi [2020-12-08 22:22:31,322] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Aligned.sortedByCoord.out.NC_001276.1.bam.csi [2020-12-08 22:22:31,324] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Aligned.sortedByCoord.out.bam.bai [2020-12-08 22:22:31,443] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:31,444] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:31,574] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Aligned.sortedByCoord.out.NC_001276.1.bam [2020-12-08 22:22:31,574] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Aligned.sortedByCoord.out.bam [2020-12-08 22:22:31,575] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastq_checksums.md5 [2020-12-08 22:22:31,660] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9.sh [2020-12-08 22:22:31,663] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9.sh [2020-12-08 22:22:31,721] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: chrName.txt [2020-12-08 22:22:31,723] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: chrName.txt [2020-12-08 22:22:32,009] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: exonInfo.tab [2020-12-08 22:22:32,009] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: exonInfo.tab [2020-12-08 22:22:32,009] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: exonInfo.tab [2020-12-08 22:22:32,009] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: exonInfo.tab [2020-12-08 22:22:32,009] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: exonInfo.tab [2020-12-08 22:22:32,009] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: exonInfo.tab [2020-12-08 22:22:32,009] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: exonInfo.tab [2020-12-08 22:22:32,009] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: exonInfo.tab [2020-12-08 22:22:38,405] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: geneInfo.tab [2020-12-08 22:22:38,406] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: geneInfo.tab [2020-12-08 22:22:38,406] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: geneInfo.tab [2020-12-08 22:22:38,406] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: geneInfo.tab [2020-12-08 22:22:38,406] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: geneInfo.tab [2020-12-08 22:22:38,406] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: geneInfo.tab [2020-12-08 22:22:38,414] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: geneInfo.tab [2020-12-08 22:22:38,996] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: sjdbList.out.tab [2020-12-08 22:22:38,997] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sjdbList.out.tab [2020-12-08 22:22:38,997] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: sjdbList.out.tab [2020-12-08 22:22:38,997] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: sjdbList.out.tab [2020-12-08 22:22:38,997] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: sjdbList.out.tab [2020-12-08 22:22:38,997] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: sjdbList.out.tab [2020-12-08 22:22:38,997] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: sjdbList.out.tab [2020-12-08 22:22:38,997] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: sjdbList.out.tab [2020-12-08 22:22:42,056] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: sjdbInfo.txt [2020-12-08 22:22:42,056] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sjdbInfo.txt [2020-12-08 22:22:42,056] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: sjdbInfo.txt [2020-12-08 22:22:42,056] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: sjdbInfo.txt [2020-12-08 22:22:42,057] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: sjdbInfo.txt [2020-12-08 22:22:42,057] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: sjdbInfo.txt [2020-12-08 22:22:42,057] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: sjdbInfo.txt [2020-12-08 22:22:42,057] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: sjdbInfo.txt [2020-12-08 22:22:45,085] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: transcriptInfo.tab [2020-12-08 22:22:45,086] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: transcriptInfo.tab [2020-12-08 22:22:45,086] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: transcriptInfo.tab [2020-12-08 22:22:45,086] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: transcriptInfo.tab [2020-12-08 22:22:45,086] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: transcriptInfo.tab [2020-12-08 22:22:45,086] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: transcriptInfo.tab [2020-12-08 22:22:45,098] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: transcriptInfo.tab [2020-12-08 22:22:46,022] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: sjdbList.fromGTF.out.tab [2020-12-08 22:22:46,022] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: sjdbList.fromGTF.out.tab [2020-12-08 22:22:46,023] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: sjdbList.fromGTF.out.tab [2020-12-08 22:22:46,023] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: sjdbList.fromGTF.out.tab [2020-12-08 22:22:46,023] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: sjdbList.fromGTF.out.tab [2020-12-08 22:22:46,023] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: sjdbList.fromGTF.out.tab [2020-12-08 22:22:46,023] multiqc [DEBUG ] File ignored by snpeff because it exceeded search pattern filesize limit: sjdbList.fromGTF.out.tab [2020-12-08 22:22:46,023] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: sjdbList.fromGTF.out.tab [2020-12-08 22:22:49,274] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: chrLength.txt [2020-12-08 22:22:49,277] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: chrLength.txt [2020-12-08 22:22:49,444] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:49,445] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:49,445] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:49,445] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:49,445] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:49,445] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:49,451] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: Log.out [2020-12-08 22:22:49,722] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: chrStart.txt [2020-12-08 22:22:49,723] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: chrStart.txt [2020-12-08 22:22:49,875] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: chrNameLength.txt [2020-12-08 22:22:49,877] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: chrNameLength.txt [2020-12-08 22:22:53,516] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-12-08 22:22:53,536] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-12-08 22:22:53,557] multiqc [DEBUG ] No samples found: custom_content [2020-12-08 22:22:53,581] multiqc [DEBUG ] No samples found: conpair [2020-12-08 22:22:53,619] multiqc [DEBUG ] No samples found: peddy [2020-12-08 22:22:53,661] multiqc [DEBUG ] No samples found: methylQA [2020-12-08 22:22:53,708] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-12-08 22:22:53,767] multiqc [DEBUG ] No samples found: qualimap [2020-12-08 22:22:53,820] multiqc [DEBUG ] No samples found: preseq [2020-12-08 22:22:53,884] multiqc [DEBUG ] No samples found: quast [2020-12-08 22:22:53,921] multiqc [DEBUG ] No samples found: qorts [2020-12-08 22:22:53,977] multiqc [DEBUG ] No samples found: rna_seqc [2020-12-08 22:22:54,030] multiqc [DEBUG ] No samples found: rsem [2020-12-08 22:22:54,103] multiqc [DEBUG ] No samples found: rseqc [2020-12-08 22:22:54,132] multiqc [DEBUG ] No samples found: busco [2020-12-08 22:22:54,152] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-12-08 22:22:54,165] multiqc [DEBUG ] No samples found: disambiguate [2020-12-08 22:22:54,213] multiqc [DEBUG ] No samples found: supernova [2020-12-08 22:22:54,403] multiqc [DEBUG ] No samples found: deeptools [2020-12-08 22:22:54,455] multiqc [DEBUG ] No samples found: sargasso [2020-12-08 22:22:54,492] multiqc [DEBUG ] No samples found: verifybamid [2020-12-08 22:22:54,514] multiqc [DEBUG ] No samples found: mirtrace [2020-12-08 22:22:54,551] multiqc [DEBUG ] No samples found: happy [2020-12-08 22:22:54,593] multiqc [DEBUG ] No samples found: homer [2020-12-08 22:22:54,613] multiqc [DEBUG ] No samples found: macs2 [2020-12-08 22:22:54,642] multiqc [DEBUG ] No samples found: theta2 [2020-12-08 22:22:54,686] multiqc [DEBUG ] No samples found: snpeff [2020-12-08 22:22:54,760] multiqc [DEBUG ] No samples found: gatk [2020-12-08 22:22:54,797] multiqc [DEBUG ] No samples found: htseq [2020-12-08 22:22:54,856] multiqc [DEBUG ] No samples found: bcftools [2020-12-08 22:22:54,887] multiqc [DEBUG ] No samples found: featureCounts [2020-12-08 22:22:54,920] multiqc [DEBUG ] No samples found: fgbio [2020-12-08 22:22:54,933] multiqc [DEBUG ] No samples found: dedup [2020-12-08 22:22:54,984] multiqc [DEBUG ] No samples found: damageprofiler [2020-12-08 22:22:55,155] multiqc [DEBUG ] No samples found: biobambam2 [2020-12-08 22:22:55,187] multiqc [DEBUG ] No samples found: mtnucratio [2020-12-08 22:22:55,195] multiqc [DEBUG ] No samples found: picard [2020-12-08 22:22:55,205] multiqc [DEBUG ] No samples found: prokka [2020-12-08 22:22:55,212] multiqc [DEBUG ] No samples found: samblaster [2020-12-08 22:22:55,284] multiqc [DEBUG ] No samples found: samtools [2020-12-08 22:22:55,306] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-12-08 22:22:55,343] multiqc [DEBUG ] No samples found: bamtools [2020-12-08 22:22:55,355] multiqc [DEBUG ] No samples found: jellyfish [2020-12-08 22:22:55,394] multiqc [DEBUG ] No samples found: vcftools [2020-12-08 22:22:55,419] multiqc [DEBUG ] No samples found: longranger [2020-12-08 22:22:55,449] multiqc [DEBUG ] No samples found: stacks [2020-12-08 22:22:55,587] multiqc [DEBUG ] No samples found: bbmap [2020-12-08 22:22:55,636] multiqc [DEBUG ] No samples found: bismark [2020-12-08 22:22:55,665] multiqc [DEBUG ] No samples found: biscuit [2020-12-08 22:22:55,678] multiqc [DEBUG ] No samples found: hicexplorer [2020-12-08 22:22:55,697] multiqc [DEBUG ] No samples found: hicup [2020-12-08 22:22:55,711] multiqc [DEBUG ] No samples found: hicpro [2020-12-08 22:22:55,721] multiqc [DEBUG ] No samples found: salmon [2020-12-08 22:22:55,744] multiqc [DEBUG ] No samples found: kallisto [2020-12-08 22:22:55,786] multiqc [DEBUG ] No samples found: slamdunk [2020-12-08 22:22:55,863] multiqc.modules.star.star [INFO ] Found 1 reports [2020-12-08 22:22:55,892] multiqc [DEBUG ] No samples found: hisat2 [2020-12-08 22:22:55,918] multiqc [DEBUG ] No samples found: tophat [2020-12-08 22:22:55,971] multiqc [DEBUG ] No samples found: bowtie2 [2020-12-08 22:22:56,000] multiqc [DEBUG ] No samples found: bowtie1 [2020-12-08 22:22:56,027] multiqc [DEBUG ] No samples found: kat [2020-12-08 22:22:56,053] multiqc [DEBUG ] No samples found: leehom [2020-12-08 22:22:56,088] multiqc [DEBUG ] No samples found: adapterRemoval [2020-12-08 22:22:56,103] multiqc [DEBUG ] No samples found: clipandmerge [2020-12-08 22:22:56,180] multiqc [DEBUG ] No samples found: cutadapt [2020-12-08 22:22:56,192] multiqc [DEBUG ] No samples found: flexbar [2020-12-08 22:22:56,233] multiqc [DEBUG ] No samples found: trimmomatic [2020-12-08 22:22:56,255] multiqc [DEBUG ] No samples found: skewer [2020-12-08 22:22:56,267] multiqc [DEBUG ] No samples found: sortmerna [2020-12-08 22:22:56,277] multiqc [DEBUG ] No samples found: biobloomtools [2020-12-08 22:22:56,307] multiqc [DEBUG ] No samples found: fastq_screen [2020-12-08 22:22:56,340] multiqc [DEBUG ] No samples found: afterqc [2020-12-08 22:22:56,380] multiqc [DEBUG ] No samples found: fastp [2020-12-08 22:22:56,405] multiqc [DEBUG ] No samples found: fastqc [2020-12-08 22:22:56,439] multiqc [DEBUG ] No samples found: minionqc [2020-12-08 22:22:56,473] multiqc [DEBUG ] No samples found: mosdepth [2020-12-08 22:22:56,538] multiqc [DEBUG ] No samples found: clusterflow [2020-12-08 22:22:56,568] multiqc [DEBUG ] No samples found: bcl2fastq [2020-12-08 22:22:56,594] multiqc [DEBUG ] No samples found: interop [2020-12-08 22:22:56,621] multiqc [DEBUG ] No samples found: flash [2020-12-08 22:22:56,658] multiqc [DEBUG ] No samples found: seqyclean [2020-12-08 22:22:56,663] multiqc [INFO ] Compressing plot data [2020-12-08 22:22:56,669] multiqc [INFO ] Report : multiqc_report.html [2020-12-08 22:22:56,670] multiqc [INFO ] Data : multiqc_data [2020-12-08 22:22:56,671] multiqc [DEBUG ] Moving data file from '/tmp/tmp_229ily_/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9/multiqc_data' [2020-12-08 22:22:56,672] multiqc [DEBUG ] Moving data file from '/tmp/tmp_229ily_/multiqc_data/multiqc_star.txt' to '/gscratch/scrubbed/samwhite/outputs/20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9/multiqc_data' [2020-12-08 22:22:56,673] multiqc [DEBUG ] Moving data file from '/tmp/tmp_229ily_/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9/multiqc_data' [2020-12-08 22:22:56,674] multiqc [DEBUG ] Moving data file from '/tmp/tmp_229ily_/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9/multiqc_data' [2020-12-08 22:22:56,675] multiqc [DEBUG ] Moving data file from '/tmp/tmp_229ily_/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20201208_cgig_STAR_RNAseq-to-NCBI-GCF_000297895.1_oyster_v9/multiqc_data' [2020-12-08 22:22:57,532] multiqc [INFO ] MultiQC complete