[2023-05-19 13:36:50,741] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2023-05-19 13:36:50,750] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2023-05-19 13:36:50,750] multiqc [DEBUG ] New config 'star': {'fn': '*Log.final.out'} [2023-05-19 13:36:50,750] multiqc [DEBUG ] New config 'star/genecounts': {'fn': '*ReadsPerGene.out.tab'} [2023-05-19 13:36:50,750] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2023-05-19 13:36:50,750] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2023-05-19 13:36:50,751] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2023-05-19 13:36:50,751] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 13:36:56,124] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2023-05-19 13:36:56,124] multiqc [INFO ] This is MultiQC v1.8 [2023-05-19 13:36:56,125] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2023-05-19 13:36:56,125] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed [2023-05-19 13:36:56,125] multiqc [INFO ] Template : default [2023-05-19 13:36:56,125] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2023-05-19 13:36:56,125] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed [2023-05-19 13:36:56,126] 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 13:36:56,126] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp9xe670oh [2023-05-19 13:36:56,479] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 13:36:56,480] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,480] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,480] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 13:36:56,480] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,480] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,480] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,481] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,481] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,481] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,482] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,482] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,482] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 13:36:56,482] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2023-05-19 13:36:56,483] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,483] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,483] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 13:36:56,483] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,483] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,483] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-71-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,483] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,483] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2_R2_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,484] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-73-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:56,484] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-79-S1-TP2_R1_001.fastp-trim.20230519_fastqc.html [2023-05-19 13:36:56,484] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-76-S1-TP2.fastp-trim.20230519.report.html [2023-05-19 13:36:56,485] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: RNA-POR-82-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz [2023-05-19 13:36:58,921] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 13:36:58,922] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2023-05-19 13:36:58,924] multiqc [DEBUG ] No samples found: custom_content [2023-05-19 13:36:58,933] multiqc [DEBUG ] No samples found: conpair [2023-05-19 13:36:58,964] multiqc [DEBUG ] No samples found: peddy [2023-05-19 13:36:58,973] multiqc [DEBUG ] No samples found: methylQA [2023-05-19 13:36:58,983] multiqc [DEBUG ] No samples found: phantompeakqualtools [2023-05-19 13:36:59,035] multiqc [DEBUG ] No samples found: qualimap [2023-05-19 13:36:59,043] multiqc [DEBUG ] No samples found: preseq [2023-05-19 13:36:59,052] multiqc [DEBUG ] No samples found: quast [2023-05-19 13:36:59,063] multiqc [DEBUG ] No samples found: qorts [2023-05-19 13:36:59,072] multiqc [DEBUG ] No samples found: rna_seqc [2023-05-19 13:36:59,080] multiqc [DEBUG ] No samples found: rsem [2023-05-19 13:36:59,094] multiqc [DEBUG ] No samples found: rseqc [2023-05-19 13:36:59,102] multiqc [DEBUG ] No samples found: busco [2023-05-19 13:36:59,120] multiqc [DEBUG ] No samples found: goleft_indexcov [2023-05-19 13:36:59,129] multiqc [DEBUG ] No samples found: disambiguate [2023-05-19 13:36:59,184] multiqc [DEBUG ] No samples found: supernova [2023-05-19 13:36:59,198] multiqc [DEBUG ] No samples found: deeptools [2023-05-19 13:36:59,207] multiqc [DEBUG ] No samples found: sargasso [2023-05-19 13:36:59,215] multiqc [DEBUG ] No samples found: verifybamid [2023-05-19 13:36:59,223] multiqc [DEBUG ] No samples found: mirtrace [2023-05-19 13:36:59,230] multiqc [DEBUG ] No samples found: happy [2023-05-19 13:36:59,236] multiqc [DEBUG ] No samples found: homer [2023-05-19 13:36:59,241] multiqc [DEBUG ] No samples found: macs2 [2023-05-19 13:36:59,246] multiqc [DEBUG ] No samples found: theta2 [2023-05-19 13:36:59,251] multiqc [DEBUG ] No samples found: snpeff [2023-05-19 13:36:59,269] multiqc [DEBUG ] No samples found: gatk [2023-05-19 13:36:59,274] multiqc [DEBUG ] No samples found: htseq [2023-05-19 13:36:59,279] multiqc [DEBUG ] No samples found: bcftools [2023-05-19 13:36:59,283] multiqc [DEBUG ] No samples found: featureCounts [2023-05-19 13:36:59,288] multiqc [DEBUG ] No samples found: fgbio [2023-05-19 13:36:59,292] multiqc [DEBUG ] No samples found: dedup [2023-05-19 13:36:59,297] multiqc [DEBUG ] No samples found: damageprofiler [2023-05-19 13:36:59,320] multiqc [DEBUG ] No samples found: biobambam2 [2023-05-19 13:36:59,325] multiqc [DEBUG ] No samples found: mtnucratio [2023-05-19 13:36:59,329] multiqc [DEBUG ] No samples found: picard [2023-05-19 13:36:59,352] multiqc [DEBUG ] No samples found: prokka [2023-05-19 13:36:59,356] multiqc [DEBUG ] No samples found: samblaster [2023-05-19 13:36:59,362] multiqc [DEBUG ] No samples found: samtools [2023-05-19 13:36:59,378] multiqc [DEBUG ] No samples found: sexdeterrmine [2023-05-19 13:36:59,383] multiqc [DEBUG ] No samples found: bamtools [2023-05-19 13:36:59,387] multiqc [DEBUG ] No samples found: jellyfish [2023-05-19 13:36:59,393] multiqc [DEBUG ] No samples found: vcftools [2023-05-19 13:36:59,397] multiqc [DEBUG ] No samples found: longranger [2023-05-19 13:36:59,402] multiqc [DEBUG ] No samples found: stacks [2023-05-19 13:36:59,409] multiqc [DEBUG ] No samples found: bbmap [2023-05-19 13:36:59,414] multiqc [DEBUG ] No samples found: bismark [2023-05-19 13:36:59,431] multiqc [DEBUG ] No samples found: biscuit [2023-05-19 13:36:59,435] multiqc [DEBUG ] No samples found: hicexplorer [2023-05-19 13:36:59,440] multiqc [DEBUG ] No samples found: hicup [2023-05-19 13:36:59,457] multiqc [DEBUG ] No samples found: hicpro [2023-05-19 13:36:59,462] multiqc [DEBUG ] No samples found: salmon [2023-05-19 13:36:59,487] multiqc [DEBUG ] No samples found: kallisto [2023-05-19 13:36:59,522] multiqc [DEBUG ] No samples found: slamdunk [2023-05-19 13:36:59,534] multiqc [DEBUG ] No samples found: star [2023-05-19 13:36:59,538] multiqc [DEBUG ] No samples found: hisat2 [2023-05-19 13:36:59,543] multiqc [DEBUG ] No samples found: tophat [2023-05-19 13:36:59,548] multiqc [DEBUG ] No samples found: bowtie2 [2023-05-19 13:36:59,552] multiqc [DEBUG ] No samples found: bowtie1 [2023-05-19 13:36:59,557] multiqc [DEBUG ] No samples found: kat [2023-05-19 13:36:59,561] multiqc [DEBUG ] No samples found: leehom [2023-05-19 13:36:59,566] multiqc [DEBUG ] No samples found: adapterRemoval [2023-05-19 13:36:59,570] multiqc [DEBUG ] No samples found: clipandmerge [2023-05-19 13:36:59,594] multiqc [DEBUG ] No samples found: cutadapt [2023-05-19 13:36:59,599] multiqc [DEBUG ] No samples found: flexbar [2023-05-19 13:36:59,629] multiqc [DEBUG ] No samples found: trimmomatic [2023-05-19 13:36:59,634] multiqc [DEBUG ] No samples found: skewer [2023-05-19 13:36:59,638] multiqc [DEBUG ] No samples found: sortmerna [2023-05-19 13:36:59,643] multiqc [DEBUG ] No samples found: biobloomtools [2023-05-19 13:36:59,647] multiqc [DEBUG ] No samples found: fastq_screen [2023-05-19 13:36:59,672] multiqc [DEBUG ] No samples found: afterqc [2023-05-19 13:36:59,680] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POR-73-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 13:36:59,685] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POR-79-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 13:36:59,689] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POR-76-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 13:36:59,711] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POR-71-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 13:36:59,730] multiqc.modules.fastp.fastp [DEBUG ] No duplication rate plot data: RNA-POR-82-S1-TP2.fastp-trim.20230519.report.json [2023-05-19 13:36:59,731] multiqc.modules.fastp.fastp [INFO ] Found 5 reports [2023-05-19 13:37:01,989] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2023-05-19 13:37:02,308] multiqc [DEBUG ] No samples found: minionqc [2023-05-19 13:37:02,356] multiqc [DEBUG ] No samples found: mosdepth [2023-05-19 13:37:02,359] multiqc [DEBUG ] No samples found: clusterflow [2023-05-19 13:37:02,367] multiqc [DEBUG ] No samples found: bcl2fastq [2023-05-19 13:37:02,370] multiqc [DEBUG ] No samples found: interop [2023-05-19 13:37:02,374] multiqc [DEBUG ] No samples found: flash [2023-05-19 13:37:02,377] multiqc [DEBUG ] No samples found: seqyclean [2023-05-19 13:37:02,399] multiqc [INFO ] Compressing plot data [2023-05-19 13:37:02,869] multiqc [INFO ] Report : multiqc_report.html [2023-05-19 13:37:02,869] multiqc [INFO ] Data : multiqc_data [2023-05-19 13:37:02,870] multiqc [DEBUG ] Moving data file from '/tmp/tmp9xe670oh/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-19 13:37:02,871] multiqc [DEBUG ] Moving data file from '/tmp/tmp9xe670oh/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-19 13:37:02,871] multiqc [DEBUG ] Moving data file from '/tmp/tmp9xe670oh/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-19 13:37:02,872] multiqc [DEBUG ] Moving data file from '/tmp/tmp9xe670oh/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-19 13:37:02,873] multiqc [DEBUG ] Moving data file from '/tmp/tmp9xe670oh/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-19 13:37:02,874] multiqc [DEBUG ] Moving data file from '/tmp/tmp9xe670oh/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/multiqc_data' [2023-05-19 13:37:03,396] multiqc [INFO ] MultiQC complete