[2023-05-19 12:56:46,636] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-19 12:56:46,646] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-19 12:56:46,647] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-19 12:56:46,649] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-19 12:56:46,649] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-19 12:56:46,650] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-19 12:56:46,650] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-19 12:56:46,651] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 12:56:51,675] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-19 12:56:51,676] multiqc [INFO ] This is MultiQC v1.8 [2023-05-19 12:56:51,676] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 12:56:51,676] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed [2023-05-19 12:56:51,676] multiqc [INFO ] Template : default [2023-05-19 12:56:51,677] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-19 12:56:51,677] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed [2023-05-19 12:56:51,678] 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 [2023-05-19 12:56:51,678] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpycpi37kr [2023-05-19 12:56:52,186] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 12:56:52,187] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,193] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 12:56:52,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 12:56:52,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-178-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 12:56:52,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-05-19 12:56:52,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-173-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-150-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,198] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 12:56:52,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 12:56:52,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-145-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:52,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-ACR-140-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 12:56:55,237] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 12:56:55,238] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 12:56:55,273] multiqc [DEBUG ] No samples found: custom_content [2023-05-19 12:56:55,301] multiqc [DEBUG ] No samples found: conpair [2023-05-19 12:56:55,333] multiqc [DEBUG ] No samples found: peddy [2023-05-19 12:56:55,369] multiqc [DEBUG ] No samples found: methylQA [2023-05-19 12:56:55,379] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-19 12:56:55,430] multiqc [DEBUG ] No samples found: qualimap [2023-05-19 12:56:55,439] multiqc [DEBUG ] No samples found: preseq [2023-05-19 12:56:55,475] multiqc [DEBUG ] No samples found: quast [2023-05-19 12:56:55,489] multiqc [DEBUG ] No samples found: qorts [2023-05-19 12:56:55,498] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-19 12:56:55,513] multiqc [DEBUG ] No samples found: rsem [2023-05-19 12:56:55,552] multiqc [DEBUG ] No samples found: rseqc [2023-05-19 12:56:55,560] multiqc [DEBUG ] No samples found: busco [2023-05-19 12:56:55,589] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-19 12:56:55,612] multiqc [DEBUG ] No samples found: disambiguate [2023-05-19 12:56:55,637] multiqc [DEBUG ] No samples found: supernova [2023-05-19 12:56:55,771] multiqc [DEBUG ] No samples found: deeptools [2023-05-19 12:56:55,780] multiqc [DEBUG ] No samples found: sargasso [2023-05-19 12:56:55,834] multiqc [DEBUG ] No samples found: verifybamid [2023-05-19 12:56:55,860] multiqc [DEBUG ] No samples found: mirtrace [2023-05-19 12:56:55,890] multiqc [DEBUG ] No samples found: happy [2023-05-19 12:56:55,902] multiqc [DEBUG ] No samples found: homer [2023-05-19 12:56:55,912] multiqc [DEBUG ] No samples found: macs2 [2023-05-19 12:56:55,921] multiqc [DEBUG ] No samples found: theta2 [2023-05-19 12:56:55,929] multiqc [DEBUG ] No samples found: snpeff [2023-05-19 12:56:55,997] multiqc [DEBUG ] No samples found: gatk [2023-05-19 12:56:56,008] multiqc [DEBUG ] No samples found: htseq [2023-05-19 12:56:56,037] multiqc [DEBUG ] No samples found: bcftools [2023-05-19 12:56:56,065] multiqc [DEBUG ] No samples found: featureCounts [2023-05-19 12:56:56,076] multiqc [DEBUG ] No samples found: fgbio [2023-05-19 12:56:56,103] multiqc [DEBUG ] No samples found: dedup [2023-05-19 12:56:56,114] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-19 12:56:56,210] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-19 12:56:56,219] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-19 12:56:56,227] multiqc [DEBUG ] No samples found: picard [2023-05-19 12:56:56,247] multiqc [DEBUG ] No samples found: prokka [2023-05-19 12:56:56,256] multiqc [DEBUG ] No samples found: samblaster [2023-05-19 12:56:56,298] multiqc [DEBUG ] No samples found: samtools [2023-05-19 12:56:56,314] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-19 12:56:56,324] multiqc [DEBUG ] No samples found: bamtools [2023-05-19 12:56:56,361] multiqc [DEBUG ] No samples found: jellyfish [2023-05-19 12:56:56,373] multiqc [DEBUG ] No samples found: vcftools [2023-05-19 12:56:56,400] multiqc [DEBUG ] No samples found: longranger [2023-05-19 12:56:56,410] multiqc [DEBUG ] No samples found: stacks [2023-05-19 12:56:56,471] multiqc [DEBUG ] No samples found: bbmap [2023-05-19 12:56:56,499] multiqc [DEBUG ] No samples found: bismark [2023-05-19 12:56:56,554] multiqc [DEBUG ] No samples found: biscuit [2023-05-19 12:56:56,582] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-19 12:56:56,591] multiqc [DEBUG ] No samples found: hicup [2023-05-19 12:56:56,631] multiqc [DEBUG ] No samples found: hicpro [2023-05-19 12:56:56,659] multiqc [DEBUG ] No samples found: salmon [2023-05-19 12:56:56,686] multiqc [DEBUG ] No samples found: kallisto [2023-05-19 12:56:56,725] multiqc [DEBUG ] No samples found: slamdunk [2023-05-19 12:56:56,749] multiqc [DEBUG ] No samples found: star [2023-05-19 12:56:56,757] multiqc [DEBUG ] No samples found: hisat2 [2023-05-19 12:56:56,780] multiqc [DEBUG ] No samples found: tophat [2023-05-19 12:56:56,793] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-19 12:56:56,803] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-19 12:56:56,813] multiqc [DEBUG ] No samples found: kat [2023-05-19 12:56:56,822] multiqc [DEBUG ] No samples found: leehom [2023-05-19 12:56:56,832] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-19 12:56:56,842] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-19 12:56:56,877] multiqc [DEBUG ] No samples found: cutadapt [2023-05-19 12:56:56,887] multiqc [DEBUG ] No samples found: flexbar [2023-05-19 12:56:56,927] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-19 12:56:56,951] multiqc [DEBUG ] No samples found: skewer [2023-05-19 12:56:56,968] multiqc [DEBUG ] No samples found: sortmerna [2023-05-19 12:56:56,978] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-19 12:56:57,007] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-19 12:56:57,058] multiqc [DEBUG ] No samples found: afterqc [2023-05-19 12:56:57,097] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-ACR-140-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 12:56:57,105] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-ACR-150-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 12:56:57,113] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-ACR-173-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 12:56:57,121] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-ACR-178-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 12:56:57,147] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-ACR-145-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 12:56:57,149] multiqc.modules.fastp.fastp [INFO ] Found 5 reports [2023-05-19 12:56:59,421] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-19 12:56:59,633] multiqc [DEBUG ] No samples found: minionqc [2023-05-19 12:56:59,649] multiqc [DEBUG ] No samples found: mosdepth [2023-05-19 12:56:59,681] multiqc [DEBUG ] No samples found: clusterflow [2023-05-19 12:56:59,694] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-19 12:56:59,716] multiqc [DEBUG ] No samples found: interop [2023-05-19 12:56:59,731] multiqc [DEBUG ] No samples found: flash [2023-05-19 12:56:59,758] multiqc [DEBUG ] No samples found: seqyclean [2023-05-19 12:56:59,781] multiqc [INFO ] Compressing plot data [2023-05-19 12:57:00,244] multiqc [INFO ] Report : multiqc_report.html [2023-05-19 12:57:00,244] multiqc [INFO ] Data : multiqc_data [2023-05-19 12:57:00,245] multiqc [DEBUG ] Moving data file from '/tmp/tmpycpi37kr/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-19 12:57:00,247] multiqc [DEBUG ] Moving data file from '/tmp/tmpycpi37kr/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-19 12:57:00,248] multiqc [DEBUG ] Moving data file from '/tmp/tmpycpi37kr/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-19 12:57:00,250] multiqc [DEBUG ] Moving data file from '/tmp/tmpycpi37kr/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-19 12:57:00,251] multiqc [DEBUG ] Moving data file from '/tmp/tmpycpi37kr/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-19 12:57:00,253] multiqc [DEBUG ] Moving data file from '/tmp/tmpycpi37kr/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-19 12:57:00,761] multiqc [INFO ] MultiQC complete