[2023-05-19 14:21:33,713] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-19 14:21:33,717] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-19 14:21:33,717] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-19 14:21:33,718] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-19 14:21:33,718] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-19 14:21:33,718] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-19 14:21:33,718] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-19 14:21:33,718] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 14:21:38,814] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-19 14:21:38,814] multiqc [INFO ] This is MultiQC v1.8 [2023-05-19 14:21:38,815] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 14:21:38,815] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed [2023-05-19 14:21:38,815] multiqc [INFO ] Template : default [2023-05-19 14:21:38,815] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-19 14:21:38,815] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed [2023-05-19 14:21:38,816] 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 14:21:38,816] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmples5gz1v [2023-05-19 14:21:39,107] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,107] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 14:21:39,107] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,107] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 14:21:39,107] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,108] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,108] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,108] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,108] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,109] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,109] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 14:21:39,109] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 14:21:39,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-05-19 14:21:39,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,110] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,111] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,111] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,111] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 14:21:39,111] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-47-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,111] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-53-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-50-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 14:21:39,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-57-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:39,112] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POC-48-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 14:21:41,408] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 14:21:41,409] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 14:21:41,411] multiqc [DEBUG ] No samples found: custom_content [2023-05-19 14:21:41,420] multiqc [DEBUG ] No samples found: conpair [2023-05-19 14:21:41,443] multiqc [DEBUG ] No samples found: peddy [2023-05-19 14:21:41,451] multiqc [DEBUG ] No samples found: methylQA [2023-05-19 14:21:41,461] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-19 14:21:41,494] multiqc [DEBUG ] No samples found: qualimap [2023-05-19 14:21:41,502] multiqc [DEBUG ] No samples found: preseq [2023-05-19 14:21:41,511] multiqc [DEBUG ] No samples found: quast [2023-05-19 14:21:41,519] multiqc [DEBUG ] No samples found: qorts [2023-05-19 14:21:41,527] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-19 14:21:41,536] multiqc [DEBUG ] No samples found: rsem [2023-05-19 14:21:41,548] multiqc [DEBUG ] No samples found: rseqc [2023-05-19 14:21:41,557] multiqc [DEBUG ] No samples found: busco [2023-05-19 14:21:41,586] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-19 14:21:41,594] multiqc [DEBUG ] No samples found: disambiguate [2023-05-19 14:21:41,603] multiqc [DEBUG ] No samples found: supernova [2023-05-19 14:21:41,615] multiqc [DEBUG ] No samples found: deeptools [2023-05-19 14:21:41,621] multiqc [DEBUG ] No samples found: sargasso [2023-05-19 14:21:41,627] multiqc [DEBUG ] No samples found: verifybamid [2023-05-19 14:21:41,632] multiqc [DEBUG ] No samples found: mirtrace [2023-05-19 14:21:41,637] multiqc [DEBUG ] No samples found: happy [2023-05-19 14:21:41,642] multiqc [DEBUG ] No samples found: homer [2023-05-19 14:21:41,647] multiqc [DEBUG ] No samples found: macs2 [2023-05-19 14:21:41,651] multiqc [DEBUG ] No samples found: theta2 [2023-05-19 14:21:41,656] multiqc [DEBUG ] No samples found: snpeff [2023-05-19 14:21:41,668] multiqc [DEBUG ] No samples found: gatk [2023-05-19 14:21:41,672] multiqc [DEBUG ] No samples found: htseq [2023-05-19 14:21:41,677] multiqc [DEBUG ] No samples found: bcftools [2023-05-19 14:21:41,681] multiqc [DEBUG ] No samples found: featureCounts [2023-05-19 14:21:41,686] multiqc [DEBUG ] No samples found: fgbio [2023-05-19 14:21:41,690] multiqc [DEBUG ] No samples found: dedup [2023-05-19 14:21:41,695] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-19 14:21:41,718] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-19 14:21:41,722] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-19 14:21:41,726] multiqc [DEBUG ] No samples found: picard [2023-05-19 14:21:41,730] multiqc [DEBUG ] No samples found: prokka [2023-05-19 14:21:41,735] multiqc [DEBUG ] No samples found: samblaster [2023-05-19 14:21:41,740] multiqc [DEBUG ] No samples found: samtools [2023-05-19 14:21:41,750] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-19 14:21:41,755] multiqc [DEBUG ] No samples found: bamtools [2023-05-19 14:21:41,759] multiqc [DEBUG ] No samples found: jellyfish [2023-05-19 14:21:41,764] multiqc [DEBUG ] No samples found: vcftools [2023-05-19 14:21:41,769] multiqc [DEBUG ] No samples found: longranger [2023-05-19 14:21:41,773] multiqc [DEBUG ] No samples found: stacks [2023-05-19 14:21:41,780] multiqc [DEBUG ] No samples found: bbmap [2023-05-19 14:21:41,784] multiqc [DEBUG ] No samples found: bismark [2023-05-19 14:21:41,813] multiqc [DEBUG ] No samples found: biscuit [2023-05-19 14:21:41,817] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-19 14:21:41,821] multiqc [DEBUG ] No samples found: hicup [2023-05-19 14:21:41,837] multiqc [DEBUG ] No samples found: hicpro [2023-05-19 14:21:41,841] multiqc [DEBUG ] No samples found: salmon [2023-05-19 14:21:41,845] multiqc [DEBUG ] No samples found: kallisto [2023-05-19 14:21:41,876] multiqc [DEBUG ] No samples found: slamdunk [2023-05-19 14:21:41,880] multiqc [DEBUG ] No samples found: star [2023-05-19 14:21:41,884] multiqc [DEBUG ] No samples found: hisat2 [2023-05-19 14:21:41,888] multiqc [DEBUG ] No samples found: tophat [2023-05-19 14:21:41,893] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-19 14:21:41,897] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-19 14:21:41,901] multiqc [DEBUG ] No samples found: kat [2023-05-19 14:21:41,906] multiqc [DEBUG ] No samples found: leehom [2023-05-19 14:21:41,910] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-19 14:21:41,914] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-19 14:21:41,933] multiqc [DEBUG ] No samples found: cutadapt [2023-05-19 14:21:41,937] multiqc [DEBUG ] No samples found: flexbar [2023-05-19 14:21:41,942] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-19 14:21:41,946] multiqc [DEBUG ] No samples found: skewer [2023-05-19 14:21:41,950] multiqc [DEBUG ] No samples found: sortmerna [2023-05-19 14:21:41,954] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-19 14:21:41,958] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-19 14:21:41,987] multiqc [DEBUG ] No samples found: afterqc [2023-05-19 14:21:41,995] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POC-50-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 14:21:41,999] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POC-57-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 14:21:42,003] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POC-53-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 14:21:42,016] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POC-48-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 14:21:42,045] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POC-47-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 14:21:42,046] multiqc.modules.fastp.fastp [INFO ] Found 5 reports [2023-05-19 14:21:44,259] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-19 14:21:44,466] multiqc [DEBUG ] No samples found: minionqc [2023-05-19 14:21:44,487] multiqc [DEBUG ] No samples found: mosdepth [2023-05-19 14:21:44,490] multiqc [DEBUG ] No samples found: clusterflow [2023-05-19 14:21:44,494] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-19 14:21:44,497] multiqc [DEBUG ] No samples found: interop [2023-05-19 14:21:44,501] multiqc [DEBUG ] No samples found: flash [2023-05-19 14:21:44,504] multiqc [DEBUG ] No samples found: seqyclean [2023-05-19 14:21:44,527] multiqc [INFO ] Compressing plot data [2023-05-19 14:21:44,999] multiqc [INFO ] Report : multiqc_report.html [2023-05-19 14:21:44,999] multiqc [INFO ] Data : multiqc_data [2023-05-19 14:21:45,000] multiqc [DEBUG ] Moving data file from '/tmp/tmples5gz1v/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-19 14:21:45,001] multiqc [DEBUG ] Moving data file from '/tmp/tmples5gz1v/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-19 14:21:45,002] multiqc [DEBUG ] Moving data file from '/tmp/tmples5gz1v/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-19 14:21:45,003] multiqc [DEBUG ] Moving data file from '/tmp/tmples5gz1v/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-19 14:21:45,003] multiqc [DEBUG ] Moving data file from '/tmp/tmples5gz1v/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-19 14:21:45,004] multiqc [DEBUG ] Moving data file from '/tmp/tmples5gz1v/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/multiqc_data' [2023-05-19 14:21:45,340] multiqc [INFO ] MultiQC complete