[2020-11-06 04:38:02,191] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2020-11-06 04:38:02,223] multiqc [DEBUG ] Loading config settings from: /usr/lusers/samwhite/.multiqc_config.yaml [2020-11-06 04:38:02,223] multiqc [DEBUG ] Added to filename patterns: {'fastp': {'fn': '*report.json'}} [2020-11-06 04:38:02,223] multiqc [DEBUG ] New config 'hisat2': {'contents': 'HISAT2 summary stats:', 'shared': True} [2020-11-06 04:38:02,224] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2020-11-06 04:38:02,224] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc ../20201029_ssal_RNAseq_fastp_trimming/ ../20201103_ssal_RNAseq_hisat2_alignment/ [2020-11-06 04:38:03,603] multiqc [WARNING] MultiQC Version v1.9 now available! [2020-11-06 04:38:03,603] multiqc [INFO ] This is MultiQC v1.8 [2020-11-06 04:38:03,604] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc ../20201029_ssal_RNAseq_fastp_trimming/ ../20201103_ssal_RNAseq_hisat2_alignment/ [2020-11-06 04:38:03,604] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/samwhite/outputs/20201106_ssalar_multiqc_fastp-hisat2 [2020-11-06 04:38:03,604] multiqc [INFO ] Template : default [2020-11-06 04:38:03,604] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2020-11-06 04:38:03,605] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20201029_ssal_RNAseq_fastp_trimming [2020-11-06 04:38:03,605] multiqc [INFO ] Searching : /gscratch/scrubbed/samwhite/outputs/20201103_ssal_RNAseq_hisat2_alignment [2020-11-06 04:38:03,606] 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 [2020-11-06 04:38:03,606] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpfqnimaop [2020-11-06 04:38:04,439] multiqc [DEBUG ] Ignoring directory as matched fn_ignore_dirs: ../20201029_ssal_RNAseq_fastp_trimming/multiqc_data [2020-11-06 04:38:04,559] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: multiqc_report.html [2020-11-06 04:38:04,594] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_8_P_31_1.fastp-trim.20201029.fq.gz [2020-11-06 04:38:04,672] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20201029_ssal_RNAseq_fastp_trimming.sh [2020-11-06 04:38:04,674] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201029_ssal_RNAseq_fastp_trimming.sh [2020-11-06 04:38:04,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_8_P_31_2.fastp-trim.20201029.fq.gz [2020-11-06 04:38:04,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_16_P_31_2.fastp-trim.20201029.fq.gz [2020-11-06 04:38:04,686] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: raw_fastq_checksums.md5 [2020-11-06 04:38:04,713] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: program_options.log [2020-11-06 04:38:04,715] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: program_options.log [2020-11-06 04:38:04,745] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-426294.out [2020-11-06 04:38:04,747] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-426294.out [2020-11-06 04:38:04,760] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: trimmed_fastq_checksums.md5 [2020-11-06 04:38:04,760] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_16_P_31_2.fastp-trim.20201029.fq.gz [2020-11-06 04:38:04,769] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_16_P_31_1.fastp-trim.20201029.report.html [2020-11-06 04:38:04,770] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_8_P_31_1.fastp-trim.20201029.report.html [2020-11-06 04:38:04,770] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_8_P_31_1.fastp-trim.20201029.fq.gz [2020-11-06 04:38:04,770] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_16_P_31_1.fastp-trim.20201029.fq.gz [2020-11-06 04:38:04,770] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_16_P_31_1.fastp-trim.20201029.report.html [2020-11-06 04:38:04,770] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_8_P_31_1.fastp-trim.20201029.report.html [2020-11-06 04:38:04,771] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_8_P_31_2.fastp-trim.20201029.fq.gz [2020-11-06 04:38:04,771] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_16_P_31_1.fastp-trim.20201029.fq.gz [2020-11-06 04:38:04,785] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_8.sorted.bam [2020-11-06 04:38:04,798] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_16.sorted.bam [2020-11-06 04:38:04,874] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: program_options.log [2020-11-06 04:38:04,875] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: program_options.log [2020-11-06 04:38:04,898] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_16.sorted.bam.bai [2020-11-06 04:38:04,899] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_16.sorted.bam.bai [2020-11-06 04:38:04,899] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_16.sorted.bam [2020-11-06 04:38:04,904] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: hisat2_build.err [2020-11-06 04:38:04,947] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-443128.out [2020-11-06 04:38:04,949] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-443128.out [2020-11-06 04:38:04,980] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool32_8.sorted.bam.bai [2020-11-06 04:38:05,021] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 20201103_ssal_RNAseq_hisat2_alignment.sh [2020-11-06 04:38:05,023] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: 20201103_ssal_RNAseq_hisat2_alignment.sh [2020-11-06 04:38:05,041] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_8.sorted.bam [2020-11-06 04:38:05,093] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: GCF_000233375.1_ICSASG_v2.3.ht2 [2020-11-06 04:38:05,095] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: GCF_000233375.1_ICSASG_v2.3.ht2 [2020-11-06 04:38:05,095] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: GCF_000233375.1_ICSASG_v2.3.ht2 [2020-11-06 04:38:05,095] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: GCF_000233375.1_ICSASG_v2.3.ht2 [2020-11-06 04:38:05,095] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: GCF_000233375.1_ICSASG_v2.3.ht2 [2020-11-06 04:38:05,096] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: GCF_000233375.1_ICSASG_v2.3.ht2 [2020-11-06 04:38:05,103] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: fastq_checksums.md5 [2020-11-06 04:38:05,134] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: Pool26_8.sorted.bam.bai [2020-11-06 04:38:10,963] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2020-11-06 04:38:10,985] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2020-11-06 04:38:11,017] multiqc [DEBUG ] No samples found: custom_content [2020-11-06 04:38:11,080] multiqc [DEBUG ] No samples found: conpair [2020-11-06 04:38:11,162] multiqc [DEBUG ] No samples found: peddy [2020-11-06 04:38:11,221] multiqc [DEBUG ] No samples found: methylQA [2020-11-06 04:38:11,253] multiqc [DEBUG ] No samples found: phantompeakqualtools [2020-11-06 04:38:11,316] multiqc [DEBUG ] No samples found: qualimap [2020-11-06 04:38:11,356] multiqc [DEBUG ] No samples found: preseq [2020-11-06 04:38:11,397] multiqc [DEBUG ] No samples found: quast [2020-11-06 04:38:11,419] multiqc [DEBUG ] No samples found: qorts [2020-11-06 04:38:11,498] multiqc [DEBUG ] No samples found: rna_seqc [2020-11-06 04:38:11,567] multiqc [DEBUG ] No samples found: rsem [2020-11-06 04:38:11,672] multiqc [DEBUG ] No samples found: rseqc [2020-11-06 04:38:11,732] multiqc [DEBUG ] No samples found: busco [2020-11-06 04:38:11,811] multiqc [DEBUG ] No samples found: goleft_indexcov [2020-11-06 04:38:11,845] multiqc [DEBUG ] No samples found: disambiguate [2020-11-06 04:38:11,881] multiqc [DEBUG ] No samples found: supernova [2020-11-06 04:38:11,978] multiqc [DEBUG ] No samples found: deeptools [2020-11-06 04:38:12,028] multiqc [DEBUG ] No samples found: sargasso [2020-11-06 04:38:12,088] multiqc [DEBUG ] No samples found: verifybamid [2020-11-06 04:38:12,124] multiqc [DEBUG ] No samples found: mirtrace [2020-11-06 04:38:12,147] multiqc [DEBUG ] No samples found: happy [2020-11-06 04:38:12,213] multiqc [DEBUG ] No samples found: homer [2020-11-06 04:38:12,225] multiqc [DEBUG ] No samples found: macs2 [2020-11-06 04:38:12,235] multiqc [DEBUG ] No samples found: theta2 [2020-11-06 04:38:12,261] multiqc [DEBUG ] No samples found: snpeff [2020-11-06 04:38:12,302] multiqc [DEBUG ] No samples found: gatk [2020-11-06 04:38:12,311] multiqc [DEBUG ] No samples found: htseq [2020-11-06 04:38:12,340] multiqc [DEBUG ] No samples found: bcftools [2020-11-06 04:38:12,348] multiqc [DEBUG ] No samples found: featureCounts [2020-11-06 04:38:12,358] multiqc [DEBUG ] No samples found: fgbio [2020-11-06 04:38:12,365] multiqc [DEBUG ] No samples found: dedup [2020-11-06 04:38:12,401] multiqc [DEBUG ] No samples found: damageprofiler [2020-11-06 04:38:12,678] multiqc [DEBUG ] No samples found: biobambam2 [2020-11-06 04:38:12,699] multiqc [DEBUG ] No samples found: mtnucratio [2020-11-06 04:38:12,704] multiqc [DEBUG ] No samples found: picard [2020-11-06 04:38:12,738] multiqc [DEBUG ] No samples found: prokka [2020-11-06 04:38:12,747] multiqc [DEBUG ] No samples found: samblaster [2020-11-06 04:38:12,809] multiqc [DEBUG ] No samples found: samtools [2020-11-06 04:38:12,850] multiqc [DEBUG ] No samples found: sexdeterrmine [2020-11-06 04:38:12,900] multiqc [DEBUG ] No samples found: bamtools [2020-11-06 04:38:12,907] multiqc [DEBUG ] No samples found: jellyfish [2020-11-06 04:38:12,935] multiqc [DEBUG ] No samples found: vcftools [2020-11-06 04:38:12,954] multiqc [DEBUG ] No samples found: longranger [2020-11-06 04:38:12,979] multiqc [DEBUG ] No samples found: stacks [2020-11-06 04:38:13,063] multiqc [DEBUG ] No samples found: bbmap [2020-11-06 04:38:13,076] multiqc [DEBUG ] No samples found: bismark [2020-11-06 04:38:13,092] multiqc [DEBUG ] No samples found: biscuit [2020-11-06 04:38:13,114] multiqc [DEBUG ] No samples found: hicexplorer [2020-11-06 04:38:13,133] multiqc [DEBUG ] No samples found: hicup [2020-11-06 04:38:13,155] multiqc [DEBUG ] No samples found: hicpro [2020-11-06 04:38:13,162] multiqc [DEBUG ] No samples found: salmon [2020-11-06 04:38:13,179] multiqc [DEBUG ] No samples found: kallisto [2020-11-06 04:38:13,203] multiqc [DEBUG ] No samples found: slamdunk [2020-11-06 04:38:13,228] multiqc [DEBUG ] No samples found: star [2020-11-06 04:38:13,262] multiqc.modules.hisat2.hisat2 [INFO ] Found 4 reports [2020-11-06 04:38:13,288] multiqc [DEBUG ] No samples found: tophat [2020-11-06 04:38:13,305] multiqc [DEBUG ] No samples found: bowtie2 [2020-11-06 04:38:13,325] multiqc [DEBUG ] No samples found: bowtie1 [2020-11-06 04:38:13,332] multiqc [DEBUG ] No samples found: kat [2020-11-06 04:38:13,339] multiqc [DEBUG ] No samples found: leehom [2020-11-06 04:38:13,366] multiqc [DEBUG ] No samples found: adapterRemoval [2020-11-06 04:38:13,374] multiqc [DEBUG ] No samples found: clipandmerge [2020-11-06 04:38:13,384] multiqc [DEBUG ] No samples found: cutadapt [2020-11-06 04:38:13,392] multiqc [DEBUG ] No samples found: flexbar [2020-11-06 04:38:13,418] multiqc [DEBUG ] No samples found: trimmomatic [2020-11-06 04:38:13,433] multiqc [DEBUG ] No samples found: skewer [2020-11-06 04:38:13,440] multiqc [DEBUG ] No samples found: sortmerna [2020-11-06 04:38:13,481] multiqc [DEBUG ] No samples found: biobloomtools [2020-11-06 04:38:13,516] multiqc [DEBUG ] No samples found: fastq_screen [2020-11-06 04:38:13,548] multiqc [DEBUG ] No samples found: afterqc [2020-11-06 04:38:13,702] multiqc.modules.fastp.fastp [INFO ] Found 4 reports [2020-11-06 04:38:13,778] multiqc [DEBUG ] No samples found: fastqc [2020-11-06 04:38:13,806] multiqc [DEBUG ] No samples found: minionqc [2020-11-06 04:38:13,873] multiqc [DEBUG ] No samples found: mosdepth [2020-11-06 04:38:13,901] multiqc [DEBUG ] No samples found: clusterflow [2020-11-06 04:38:13,951] multiqc [DEBUG ] No samples found: bcl2fastq [2020-11-06 04:38:13,982] multiqc [DEBUG ] No samples found: interop [2020-11-06 04:38:14,035] multiqc [DEBUG ] No samples found: flash [2020-11-06 04:38:14,072] multiqc [DEBUG ] No samples found: seqyclean [2020-11-06 04:38:14,090] multiqc [INFO ] Compressing plot data [2020-11-06 04:38:14,451] multiqc [INFO ] Report : multiqc_report.html [2020-11-06 04:38:14,452] multiqc [INFO ] Data : multiqc_data [2020-11-06 04:38:14,475] multiqc [DEBUG ] Moving data file from '/tmp/tmpfqnimaop/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/samwhite/outputs/20201106_ssalar_multiqc_fastp-hisat2/multiqc_data' [2020-11-06 04:38:14,476] multiqc [DEBUG ] Moving data file from '/tmp/tmpfqnimaop/multiqc_data/multiqc_hisat2.txt' to '/gscratch/scrubbed/samwhite/outputs/20201106_ssalar_multiqc_fastp-hisat2/multiqc_data' [2020-11-06 04:38:14,476] multiqc [DEBUG ] Moving data file from '/tmp/tmpfqnimaop/multiqc_data/multiqc_fastp.txt' to '/gscratch/scrubbed/samwhite/outputs/20201106_ssalar_multiqc_fastp-hisat2/multiqc_data' [2020-11-06 04:38:14,477] multiqc [DEBUG ] Moving data file from '/tmp/tmpfqnimaop/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/samwhite/outputs/20201106_ssalar_multiqc_fastp-hisat2/multiqc_data' [2020-11-06 04:38:14,478] multiqc [DEBUG ] Moving data file from '/tmp/tmpfqnimaop/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/samwhite/outputs/20201106_ssalar_multiqc_fastp-hisat2/multiqc_data' [2020-11-06 04:38:14,479] multiqc [DEBUG ] Moving data file from '/tmp/tmpfqnimaop/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/samwhite/outputs/20201106_ssalar_multiqc_fastp-hisat2/multiqc_data' [2020-11-06 04:38:15,336] multiqc [INFO ] MultiQC complete