[2021-08-12 13:37:27,517] multiqc [DEBUG ] No MultiQC config found: /gscratch/srlab/programs/anaconda3/lib/python3.7/site-packages/multiqc_config.yaml [2021-08-12 13:37:27,520] multiqc [DEBUG ] No MultiQC config found: /usr/lusers/sr320/.multiqc_config.yaml [2021-08-12 13:37:27,520] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-08-12 13:37:27,520] multiqc [DEBUG ] Command used: /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-08-12 13:37:32,790] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2021-08-12 13:37:32,790] multiqc [INFO ] This is MultiQC v1.8 [2021-08-12 13:37:32,791] multiqc [DEBUG ] Command : /gscratch/srlab/programs/anaconda3/bin/multiqc . [2021-08-12 13:37:32,792] multiqc [DEBUG ] Working dir : /gscratch/scrubbed/sr320/071521-cvBS [2021-08-12 13:37:32,792] multiqc [INFO ] Template : default [2021-08-12 13:37:32,792] multiqc [DEBUG ] Running Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] [2021-08-12 13:37:32,792] multiqc [INFO ] Searching : /gscratch/scrubbed/sr320/071521-cvBS [2021-08-12 13:37:32,793] 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 [2021-08-12 13:37:32,793] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp8n6xkmsp [2021-08-12 13:37:33,352] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 64M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,366] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 53F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,367] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 29F_R1_val_1_fastqc.html [2021-08-12 13:37:33,368] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,370] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 39F_R1_val_1_fastqc.html [2021-08-12 13:37:33,371] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 19F_R1_val_1_fastqc.html [2021-08-12 13:37:33,372] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 12M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,373] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 23M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,375] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 77F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,380] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,381] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 31M_R2_val_2_fastqc.html [2021-08-12 13:37:33,382] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,409] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: bismark_summary_report.txt [2021-08-12 13:37:33,413] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: bismark_summary_report.txt [2021-08-12 13:37:33,436] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,436] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,437] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 9M_R2_val_2_fastqc.html [2021-08-12 13:37:33,437] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 39F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,437] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 35F_R2_val_2_fastqc.html [2021-08-12 13:37:33,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 29F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,438] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 23M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,439] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,439] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16F_R2_val_2_fastqc.html [2021-08-12 13:37:33,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 41F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 59M_R2_val_2_fastqc.html [2021-08-12 13:37:33,440] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 64M_R2_val_2_fastqc.html [2021-08-12 13:37:33,441] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,441] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 76F_R2_val_2_fastqc.html [2021-08-12 13:37:33,441] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 52F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,442] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 12M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,444] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 39F_R2_val_2_fastqc.html [2021-08-12 13:37:33,444] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 35F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,444] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 64M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,444] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 76F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,444] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 44F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,445] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 44F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,446] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 22F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,446] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 54F_R2_val_2_fastqc.html [2021-08-12 13:37:33,448] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 50F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,449] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 59M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,449] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 44F_R1_val_1_fastqc.html [2021-08-12 13:37:33,451] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 12M_R1_val_1_fastqc.html [2021-08-12 13:37:33,451] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,452] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,452] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 52F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,453] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,454] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 36F_R2_val_2_fastqc.html [2021-08-12 13:37:33,454] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,455] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,456] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,456] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16F_R1_val_1_fastqc.html [2021-08-12 13:37:33,456] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6M_R2_val_2_fastqc.html [2021-08-12 13:37:33,457] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 31M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,457] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,457] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: bismark_summary_report.html [2021-08-12 13:37:33,457] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 48M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,458] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 77F_R1_val_1_fastqc.html [2021-08-12 13:37:33,458] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 77F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,458] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 52F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,459] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,459] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 76F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,459] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 41F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,460] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 13M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,460] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 53F_R2_val_2_fastqc.html [2021-08-12 13:37:33,460] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 41F_R1_val_1_fastqc.html [2021-08-12 13:37:33,461] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 31M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,461] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 23M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,461] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 64M_R1_val_1_fastqc.html [2021-08-12 13:37:33,462] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 54F_R1_val_1_fastqc.html [2021-08-12 13:37:33,462] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 36F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,463] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 50F_R1_val_1_fastqc.html [2021-08-12 13:37:33,469] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: job3.sh [2021-08-12 13:37:33,479] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 50F_R2_val_2_fastqc.html [2021-08-12 13:37:33,479] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 52F_R1_val_1_fastqc.html [2021-08-12 13:37:33,479] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 9M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:33,485] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: job2.sh [2021-08-12 13:37:33,494] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:33,494] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 59M_R1_val_1_fastqc.html [2021-08-12 13:37:33,494] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 23M_R1_val_1_fastqc.html [2021-08-12 13:37:33,495] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 77F_R2_val_2_fastqc.html [2021-08-12 13:37:33,495] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 35F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,495] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 16F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:33,560] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2101214.out [2021-08-12 13:37:33,562] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2101214.out [2021-08-12 13:37:33,562] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: slurm-2101214.out [2021-08-12 13:37:33,562] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: slurm-2101214.out [2021-08-12 13:37:33,562] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: slurm-2101214.out [2021-08-12 13:37:33,562] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: slurm-2101214.out [2021-08-12 13:37:33,593] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: slurm-2101214.out [2021-08-12 13:37:35,194] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 41F_R2_val_2_fastqc.html [2021-08-12 13:37:35,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 6M_R1_val_1_fastqc.html [2021-08-12 13:37:35,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 53F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:35,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 48M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:35,196] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 48M_R1_val_1_fastqc.html [2021-08-12 13:37:35,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 22F_R1_val_1_fastqc.html [2021-08-12 13:37:35,197] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 50F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:35,199] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3F_R1_val_1_fastqc.html [2021-08-12 13:37:35,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 9M_R1_val_1_fastqc.html [2021-08-12 13:37:35,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7M_R1_val_1_fastqc.html [2021-08-12 13:37:35,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 12M_R2_val_2_fastqc.html [2021-08-12 13:37:35,200] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 76F_R1_val_1_fastqc.html [2021-08-12 13:37:35,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7M_R2_val_2_fastqc.html [2021-08-12 13:37:35,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 13M_R1_val_1_fastqc.html [2021-08-12 13:37:35,201] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 44F_R2_val_2_fastqc.html [2021-08-12 13:37:35,202] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,202] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 35F_R1_val_1_fastqc.html [2021-08-12 13:37:35,203] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 53F_R1_val_1_fastqc.html [2021-08-12 13:37:35,203] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 19F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:35,204] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,204] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,205] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,205] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 22F_R2_val_2_fastqc.html [2021-08-12 13:37:35,206] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 29F_R2_val_2_fastqc.html [2021-08-12 13:37:35,238] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2089584.out [2021-08-12 13:37:35,239] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2089584.out [2021-08-12 13:37:35,239] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: slurm-2089584.out [2021-08-12 13:37:35,239] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: slurm-2089584.out [2021-08-12 13:37:35,239] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: slurm-2089584.out [2021-08-12 13:37:35,239] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: slurm-2089584.out [2021-08-12 13:37:35,246] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: slurm-2089584.out [2021-08-12 13:37:35,640] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 52F_R2_val_2_fastqc.html [2021-08-12 13:37:35,641] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 19F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:35,641] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 39F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:35,642] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,643] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,647] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: job.sh [2021-08-12 13:37:35,654] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 23M_R2_val_2_fastqc.html [2021-08-12 13:37:35,655] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 3F_R2_val_2_fastqc.html [2021-08-12 13:37:35,655] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,656] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 22F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:35,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 59M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:35,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 36F_R1_val_1_fastqc.html [2021-08-12 13:37:35,657] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 36F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:35,658] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 13M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:35,658] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 54F_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:35,659] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam [2021-08-12 13:37:35,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 48M_R2_val_2_fastqc.html [2021-08-12 13:37:35,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 31M_R1_val_1_fastqc.html [2021-08-12 13:37:35,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 19F_R2_val_2_fastqc.html [2021-08-12 13:37:35,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 9M_R1_val_1_bismark_bt2_PE_report.html [2021-08-12 13:37:35,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 13M_R2_val_2_fastqc.html [2021-08-12 13:37:35,660] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 29F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:35,661] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 7M_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:35,661] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: 54F_R1_val_1_bismark_bt2_pe.bam [2021-08-12 13:37:35,729] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: slurm-2121097.out [2021-08-12 13:37:35,730] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: slurm-2121097.out [2021-08-12 13:37:35,730] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: slurm-2121097.out [2021-08-12 13:37:35,730] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: slurm-2121097.out [2021-08-12 13:37:35,730] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: slurm-2121097.out [2021-08-12 13:37:35,730] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: slurm-2121097.out [2021-08-12 13:37:35,777] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: slurm-2121097.out [2021-08-12 13:37:43,095] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 2.2.4 [2021-08-12 13:37:43,112] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 2.2.4 [2021-08-12 13:37:43,143] multiqc [DEBUG ] No samples found: custom_content [2021-08-12 13:37:43,186] multiqc [DEBUG ] No samples found: conpair [2021-08-12 13:37:43,251] multiqc [DEBUG ] No samples found: peddy [2021-08-12 13:37:43,323] multiqc [DEBUG ] No samples found: methylQA [2021-08-12 13:37:43,343] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-08-12 13:37:43,497] multiqc [DEBUG ] No samples found: qualimap [2021-08-12 13:37:43,525] multiqc [DEBUG ] No samples found: preseq [2021-08-12 13:37:43,574] multiqc [DEBUG ] No samples found: quast [2021-08-12 13:37:43,586] multiqc [DEBUG ] No samples found: qorts [2021-08-12 13:37:43,653] multiqc [DEBUG ] No samples found: rna_seqc [2021-08-12 13:37:43,676] multiqc [DEBUG ] No samples found: rsem [2021-08-12 13:37:43,817] multiqc [DEBUG ] No samples found: rseqc [2021-08-12 13:37:43,855] multiqc [DEBUG ] No samples found: busco [2021-08-12 13:37:43,909] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-08-12 13:37:43,923] multiqc [DEBUG ] No samples found: disambiguate [2021-08-12 13:37:43,963] multiqc [DEBUG ] No samples found: supernova [2021-08-12 13:37:44,044] multiqc [DEBUG ] No samples found: deeptools [2021-08-12 13:37:44,091] multiqc [DEBUG ] No samples found: sargasso [2021-08-12 13:37:44,164] multiqc [DEBUG ] No samples found: verifybamid [2021-08-12 13:37:44,180] multiqc [DEBUG ] No samples found: mirtrace [2021-08-12 13:37:44,202] multiqc [DEBUG ] No samples found: happy [2021-08-12 13:37:44,233] multiqc [DEBUG ] No samples found: homer [2021-08-12 13:37:44,243] multiqc [DEBUG ] No samples found: macs2 [2021-08-12 13:37:44,253] multiqc [DEBUG ] No samples found: theta2 [2021-08-12 13:37:44,265] multiqc [DEBUG ] No samples found: snpeff [2021-08-12 13:37:44,316] multiqc [DEBUG ] No samples found: gatk [2021-08-12 13:37:44,327] multiqc [DEBUG ] No samples found: htseq [2021-08-12 13:37:44,353] multiqc [DEBUG ] No samples found: bcftools [2021-08-12 13:37:44,364] multiqc [DEBUG ] No samples found: featureCounts [2021-08-12 13:37:44,376] multiqc [DEBUG ] No samples found: fgbio [2021-08-12 13:37:44,386] multiqc [DEBUG ] No samples found: dedup [2021-08-12 13:37:44,399] multiqc [DEBUG ] No samples found: damageprofiler [2021-08-12 13:37:44,563] multiqc [DEBUG ] No samples found: biobambam2 [2021-08-12 13:37:44,573] multiqc [DEBUG ] No samples found: mtnucratio [2021-08-12 13:37:44,579] multiqc [DEBUG ] No samples found: picard [2021-08-12 13:37:44,593] multiqc [DEBUG ] No samples found: prokka [2021-08-12 13:37:44,603] multiqc [DEBUG ] No samples found: samblaster [2021-08-12 13:37:44,658] multiqc [DEBUG ] No samples found: samtools [2021-08-12 13:37:44,682] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-08-12 13:37:44,728] multiqc [DEBUG ] No samples found: bamtools [2021-08-12 13:37:44,738] multiqc [DEBUG ] No samples found: jellyfish [2021-08-12 13:37:44,789] multiqc [DEBUG ] No samples found: vcftools [2021-08-12 13:37:44,833] multiqc [DEBUG ] No samples found: longranger [2021-08-12 13:37:44,849] multiqc [DEBUG ] No samples found: stacks [2021-08-12 13:37:44,943] multiqc [DEBUG ] No samples found: bbmap [2021-08-12 13:37:45,112] multiqc.modules.bismark.bismark [INFO ] Found 26 bismark alignment reports [2021-08-12 13:37:45,115] multiqc.modules.bismark.bismark [INFO ] Found 26 bismark dedup reports [2021-08-12 13:37:45,116] multiqc.modules.bismark.bismark [INFO ] Found 26 bismark methextract reports [2021-08-12 13:37:45,188] multiqc [DEBUG ] No samples found: biscuit [2021-08-12 13:37:45,210] multiqc [DEBUG ] No samples found: hicexplorer [2021-08-12 13:37:45,258] multiqc [DEBUG ] No samples found: hicup [2021-08-12 13:37:45,266] multiqc [DEBUG ] No samples found: hicpro [2021-08-12 13:37:45,273] multiqc [DEBUG ] No samples found: salmon [2021-08-12 13:37:45,295] multiqc [DEBUG ] No samples found: kallisto [2021-08-12 13:37:45,318] multiqc [DEBUG ] No samples found: slamdunk [2021-08-12 13:37:45,336] multiqc [DEBUG ] No samples found: star [2021-08-12 13:37:45,383] multiqc [DEBUG ] No samples found: hisat2 [2021-08-12 13:37:45,410] multiqc [DEBUG ] No samples found: tophat [2021-08-12 13:37:45,422] multiqc [DEBUG ] No samples found: bowtie2 [2021-08-12 13:37:45,472] multiqc [DEBUG ] No samples found: bowtie1 [2021-08-12 13:37:45,483] multiqc [DEBUG ] No samples found: kat [2021-08-12 13:37:45,492] multiqc [DEBUG ] No samples found: leehom [2021-08-12 13:37:45,528] multiqc [DEBUG ] No samples found: adapterRemoval [2021-08-12 13:37:45,538] multiqc [DEBUG ] No samples found: clipandmerge [2021-08-12 13:37:45,609] multiqc [DEBUG ] No samples found: cutadapt [2021-08-12 13:37:45,619] multiqc [DEBUG ] No samples found: flexbar [2021-08-12 13:37:45,646] multiqc [DEBUG ] No samples found: trimmomatic [2021-08-12 13:37:45,680] multiqc [DEBUG ] No samples found: skewer [2021-08-12 13:37:45,690] multiqc [DEBUG ] No samples found: sortmerna [2021-08-12 13:37:45,700] multiqc [DEBUG ] No samples found: biobloomtools [2021-08-12 13:37:45,729] multiqc [DEBUG ] No samples found: fastq_screen [2021-08-12 13:37:45,762] multiqc [DEBUG ] No samples found: afterqc [2021-08-12 13:37:45,773] multiqc [DEBUG ] No samples found: fastp [2021-08-12 13:38:00,247] multiqc.modules.fastqc.fastqc [INFO ] Found 52 reports [2021-08-12 13:38:01,244] multiqc [DEBUG ] No samples found: minionqc [2021-08-12 13:38:01,265] multiqc [DEBUG ] No samples found: mosdepth [2021-08-12 13:38:01,317] multiqc [DEBUG ] No samples found: clusterflow [2021-08-12 13:38:01,343] multiqc [DEBUG ] No samples found: bcl2fastq [2021-08-12 13:38:01,365] multiqc [DEBUG ] No samples found: interop [2021-08-12 13:38:01,380] multiqc [DEBUG ] No samples found: flash [2021-08-12 13:38:01,395] multiqc [DEBUG ] No samples found: seqyclean [2021-08-12 13:38:01,495] multiqc [INFO ] Compressing plot data [2021-08-12 13:38:02,616] multiqc [INFO ] Report : multiqc_report.html [2021-08-12 13:38:02,616] multiqc [INFO ] Data : multiqc_data [2021-08-12 13:38:02,617] multiqc [DEBUG ] Moving data file from '/tmp/tmp8n6xkmsp/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/gscratch/scrubbed/sr320/071521-cvBS/multiqc_data' [2021-08-12 13:38:02,618] multiqc [DEBUG ] Moving data file from '/tmp/tmp8n6xkmsp/multiqc_data/multiqc_bismark_alignment.txt' to '/gscratch/scrubbed/sr320/071521-cvBS/multiqc_data' [2021-08-12 13:38:02,620] multiqc [DEBUG ] Moving data file from '/tmp/tmp8n6xkmsp/multiqc_data/multiqc_bismark_dedup.txt' to '/gscratch/scrubbed/sr320/071521-cvBS/multiqc_data' [2021-08-12 13:38:02,620] multiqc [DEBUG ] Moving data file from '/tmp/tmp8n6xkmsp/multiqc_data/multiqc_bismark_methextract.txt' to '/gscratch/scrubbed/sr320/071521-cvBS/multiqc_data' [2021-08-12 13:38:02,621] multiqc [DEBUG ] Moving data file from '/tmp/tmp8n6xkmsp/multiqc_data/multiqc_fastqc.txt' to '/gscratch/scrubbed/sr320/071521-cvBS/multiqc_data' [2021-08-12 13:38:02,622] multiqc [DEBUG ] Moving data file from '/tmp/tmp8n6xkmsp/multiqc_data/multiqc_general_stats.txt' to '/gscratch/scrubbed/sr320/071521-cvBS/multiqc_data' [2021-08-12 13:38:02,623] multiqc [DEBUG ] Moving data file from '/tmp/tmp8n6xkmsp/multiqc_data/multiqc_sources.txt' to '/gscratch/scrubbed/sr320/071521-cvBS/multiqc_data' [2021-08-12 13:38:02,624] multiqc [DEBUG ] Moving data file from '/tmp/tmp8n6xkmsp/multiqc_data/multiqc_data.json' to '/gscratch/scrubbed/sr320/071521-cvBS/multiqc_data' [2021-08-12 13:38:03,421] multiqc [INFO ] MultiQC complete