[2023-05-22 16:40:28,207] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-22 16:40:28,215] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-22 16:40:28,216] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-22 16:40:28,216] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-22 16:40:28,216] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-22 16:40:28,216] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-22 16:40:28,217] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-22 16:40:28,217] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:40:33,284] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-22 16:40:33,284] multiqc [INFO ] This is MultiQC v1.8 [2023-05-22 16:40:33,286] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-22 16:40:33,286] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/A_pulchra/trimmed [2023-05-22 16:40:33,286] multiqc [INFO ] Template : default [2023-05-22 16:40:33,287] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-22 16:40:33,287] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/A_pulchra/trimmed [2023-05-22 16:40:33,288] 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 [2023-05-22 16:40:33,288] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpzmetw599 [2023-05-22 16:40:33,542] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,542] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,549] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,549] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,549] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,550] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,550] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,551] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,552] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:40:33,552] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:40:33,552] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,552] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,552] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,553] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,553] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-05-22 16:40:33,553] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,553] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:40:33,553] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-150-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,553] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,553] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2_R2_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,554] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-140-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,555] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-145-S1-TP2_R2_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,555] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2_R1_001.fastp-trim.20230522_fastqc.html [2023-05-22 16:40:33,555] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-178-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:40:33,556] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2_R1_001.fastp-trim.20230522.fastq.gz [2023-05-22 16:40:33,556] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: sRNA-ACR-173-S1-TP2.fastp-trim.20230522.report.html [2023-05-22 16:40:34,092] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:40:34,093] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-22 16:40:34,095] multiqc [DEBUG ] No samples found: custom_content [2023-05-22 16:40:34,101] multiqc [DEBUG ] No samples found: conpair [2023-05-22 16:40:34,107] multiqc [DEBUG ] No samples found: peddy [2023-05-22 16:40:34,113] multiqc [DEBUG ] No samples found: methylQA [2023-05-22 16:40:34,120] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-22 16:40:34,128] multiqc [DEBUG ] No samples found: qualimap [2023-05-22 16:40:34,134] multiqc [DEBUG ] No samples found: preseq [2023-05-22 16:40:34,140] multiqc [DEBUG ] No samples found: quast [2023-05-22 16:40:34,146] multiqc [DEBUG ] No samples found: qorts [2023-05-22 16:40:34,153] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-22 16:40:34,158] multiqc [DEBUG ] No samples found: rsem [2023-05-22 16:40:34,168] multiqc [DEBUG ] No samples found: rseqc [2023-05-22 16:40:34,175] multiqc [DEBUG ] No samples found: busco [2023-05-22 16:40:34,180] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-22 16:40:34,186] multiqc [DEBUG ] No samples found: disambiguate [2023-05-22 16:40:34,192] multiqc [DEBUG ] No samples found: supernova [2023-05-22 16:40:34,204] multiqc [DEBUG ] No samples found: deeptools [2023-05-22 16:40:34,209] multiqc [DEBUG ] No samples found: sargasso [2023-05-22 16:40:34,215] multiqc [DEBUG ] No samples found: verifybamid [2023-05-22 16:40:34,221] multiqc [DEBUG ] No samples found: mirtrace [2023-05-22 16:40:34,226] multiqc [DEBUG ] No samples found: happy [2023-05-22 16:40:34,235] multiqc [DEBUG ] No samples found: homer [2023-05-22 16:40:34,240] multiqc [DEBUG ] No samples found: macs2 [2023-05-22 16:40:34,245] multiqc [DEBUG ] No samples found: theta2 [2023-05-22 16:40:34,250] multiqc [DEBUG ] No samples found: snpeff [2023-05-22 16:40:34,257] multiqc [DEBUG ] No samples found: gatk [2023-05-22 16:40:34,263] multiqc [DEBUG ] No samples found: htseq [2023-05-22 16:40:34,269] multiqc [DEBUG ] No samples found: bcftools [2023-05-22 16:40:34,274] multiqc [DEBUG ] No samples found: featureCounts [2023-05-22 16:40:34,280] multiqc [DEBUG ] No samples found: fgbio [2023-05-22 16:40:34,285] multiqc [DEBUG ] No samples found: dedup [2023-05-22 16:40:34,291] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-22 16:40:34,311] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-22 16:40:34,316] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-22 16:40:34,320] multiqc [DEBUG ] No samples found: picard [2023-05-22 16:40:34,325] multiqc [DEBUG ] No samples found: prokka [2023-05-22 16:40:34,331] multiqc [DEBUG ] No samples found: samblaster [2023-05-22 16:40:34,339] multiqc [DEBUG ] No samples found: samtools [2023-05-22 16:40:34,344] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-22 16:40:34,350] multiqc [DEBUG ] No samples found: bamtools [2023-05-22 16:40:34,355] multiqc [DEBUG ] No samples found: jellyfish [2023-05-22 16:40:34,362] multiqc [DEBUG ] No samples found: vcftools [2023-05-22 16:40:34,367] multiqc [DEBUG ] No samples found: longranger [2023-05-22 16:40:34,373] multiqc [DEBUG ] No samples found: stacks [2023-05-22 16:40:34,386] multiqc [DEBUG ] No samples found: bbmap [2023-05-22 16:40:34,391] multiqc [DEBUG ] No samples found: bismark [2023-05-22 16:40:34,398] multiqc [DEBUG ] No samples found: biscuit [2023-05-22 16:40:34,403] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-22 16:40:34,409] multiqc [DEBUG ] No samples found: hicup [2023-05-22 16:40:34,414] multiqc [DEBUG ] No samples found: hicpro [2023-05-22 16:40:34,419] multiqc [DEBUG ] No samples found: salmon [2023-05-22 16:40:34,425] multiqc [DEBUG ] No samples found: kallisto [2023-05-22 16:40:34,430] multiqc [DEBUG ] No samples found: slamdunk [2023-05-22 16:40:34,436] multiqc [DEBUG ] No samples found: star [2023-05-22 16:40:34,442] multiqc [DEBUG ] No samples found: hisat2 [2023-05-22 16:40:34,448] multiqc [DEBUG ] No samples found: tophat [2023-05-22 16:40:34,454] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-22 16:40:34,459] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-22 16:40:34,464] multiqc [DEBUG ] No samples found: kat [2023-05-22 16:40:34,470] multiqc [DEBUG ] No samples found: leehom [2023-05-22 16:40:34,475] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-22 16:40:34,480] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-22 16:40:34,485] multiqc [DEBUG ] No samples found: cutadapt [2023-05-22 16:40:34,491] multiqc [DEBUG ] No samples found: flexbar [2023-05-22 16:40:34,495] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-22 16:40:34,500] multiqc [DEBUG ] No samples found: skewer [2023-05-22 16:40:34,504] multiqc [DEBUG ] No samples found: sortmerna [2023-05-22 16:40:34,509] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-22 16:40:34,514] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-22 16:40:34,520] multiqc [DEBUG ] No samples found: afterqc [2023-05-22 16:40:34,528] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-ACR-150-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:40:34,531] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-ACR-178-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:40:34,535] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-ACR-140-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:40:34,538] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-ACR-173-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:40:34,542] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: sRNA-ACR-145-S1-TP2.fastp-trim.20230522.report.json [2023-05-22 16:40:34,543] multiqc.modules.fastp.fastp [INFO ] Found 5 reports [2023-05-22 16:40:35,750] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-22 16:40:35,993] multiqc [DEBUG ] No samples found: minionqc [2023-05-22 16:40:35,998] multiqc [DEBUG ] No samples found: mosdepth [2023-05-22 16:40:36,003] multiqc [DEBUG ] No samples found: clusterflow [2023-05-22 16:40:36,008] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-22 16:40:36,012] multiqc [DEBUG ] No samples found: interop [2023-05-22 16:40:36,018] multiqc [DEBUG ] No samples found: flash [2023-05-22 16:40:36,023] multiqc [DEBUG ] No samples found: seqyclean [2023-05-22 16:40:36,046] multiqc [INFO ] Compressing plot data [2023-05-22 16:40:36,543] multiqc [INFO ] Report : multiqc_report.html [2023-05-22 16:40:36,543] multiqc [INFO ] Data : multiqc_data [2023-05-22 16:40:36,544] multiqc [DEBUG ] Moving data file from '/tmp/tmpzmetw599/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-22 16:40:36,546] multiqc [DEBUG ] Moving data file from '/tmp/tmpzmetw599/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-22 16:40:36,547] multiqc [DEBUG ] Moving data file from '/tmp/tmpzmetw599/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-22 16:40:36,548] multiqc [DEBUG ] Moving data file from '/tmp/tmpzmetw599/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-22 16:40:36,549] multiqc [DEBUG ] Moving data file from '/tmp/tmpzmetw599/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-22 16:40:36,551] multiqc [DEBUG ] Moving data file from '/tmp/tmpzmetw599/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-sRNAseq/A_pulchra/trimmed/multiqc_data' [2023-05-22 16:40:36,686] multiqc [INFO ] MultiQC complete