[2022-04-19 13:35:25,086] multiqc [DEBUG ] No MultiQC config found: /nfs/software/mi/el7.2/python_virtenvs2/.virtualenvs/multiqc/lib/python2.7/site-packages/multiqc_config.yaml [2022-04-19 13:35:25,086] multiqc [DEBUG ] No MultiQC config found: /users/jvalcarcel/emancini/.multiqc_config.yaml [2022-04-19 13:35:25,087] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2022-04-19 13:35:25,087] multiqc [DEBUG ] Command used: /nfs/software/mi/el7.2/python_virtenvs2/.virtualenvs/multiqc/bin/multiqc -p 03_align/ [2022-04-19 13:35:25,562] multiqc [WARNING] MultiQC Version v1.12 now available! [2022-04-19 13:35:25,562] multiqc [INFO ] This is MultiQC v1.6 [2022-04-19 13:35:25,562] multiqc [DEBUG ] Command : /nfs/software/mi/el7.2/python_virtenvs2/.virtualenvs/multiqc/bin/multiqc -p 03_align/ [2022-04-19 13:35:25,562] multiqc [DEBUG ] Working dir : /nfs/no_backup/jvalcarcel/emancini/anieto [2022-04-19 13:35:25,563] multiqc [INFO ] Template : default [2022-04-19 13:35:25,563] multiqc [INFO ] Searching '03_align/' [2022-04-19 13:35:25,563] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, 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, dedup, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, longranger, bbmap, bismark, 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, clusterflow, bcl2fastq, interop [2022-04-19 13:35:25,563] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpj2ftuq [2022-04-19 13:35:26,416] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_3_2.fastq.gz [2022-04-19 13:35:26,416] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_1.bam.bai [2022-04-19 13:35:27,676] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_1.bam [2022-04-19 13:35:28,557] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_3_1.fastq.gz [2022-04-19 13:35:28,557] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_1_2.fastq.gz [2022-04-19 13:35:30,430] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_1Aligned.out.sam [2022-04-19 13:35:30,430] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_1_1.fastq.gz [2022-04-19 13:35:30,432] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_3.bam.bai [2022-04-19 13:35:31,410] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_2.bam [2022-04-19 13:35:44,904] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_2_2.fastq.gz [2022-04-19 13:35:45,292] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_3_2.fastq.gz [2022-04-19 13:35:45,295] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_2.bam.bai [2022-04-19 13:35:45,296] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_1Aligned.out.sam [2022-04-19 13:35:45,297] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_3Aligned.out.sam [2022-04-19 13:35:45,297] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_2Aligned.out.sam [2022-04-19 13:35:46,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_3_2.fastq.gz [2022-04-19 13:35:46,764] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_1_2.fastq.gz [2022-04-19 13:35:46,765] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_3.bam.bai [2022-04-19 13:35:46,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_2.bam [2022-04-19 13:35:46,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_3_1.fastq.gz [2022-04-19 13:35:46,766] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_1_2.fastq.gz [2022-04-19 13:35:46,767] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_1_1.fastq.gz [2022-04-19 13:35:46,768] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_1.bam [2022-04-19 13:35:47,330] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_2.bam.bai [2022-04-19 13:35:57,344] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_2.bam [2022-04-19 13:35:57,346] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_3.bam.bai [2022-04-19 13:35:57,346] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_3Aligned.out.sam [2022-04-19 13:35:57,347] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_1.bam.bai [2022-04-19 13:35:57,348] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_1.bam.bai [2022-04-19 13:36:09,280] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_3Aligned.out.sam [2022-04-19 13:36:09,281] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_1.bam [2022-04-19 13:36:09,675] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_3.bam [2022-04-19 13:36:11,247] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_2_1.fastq.gz [2022-04-19 13:36:11,249] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_2Aligned.out.sam [2022-04-19 13:36:38,193] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_2_2.fastq.gz [2022-04-19 13:36:38,195] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_3_1.fastq.gz [2022-04-19 13:36:39,009] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_2_1.fastq.gz [2022-04-19 13:36:39,011] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_2_1.fastq.gz [2022-04-19 13:36:39,012] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_1Aligned.out.sam [2022-04-19 13:36:48,869] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_3.bam [2022-04-19 13:36:48,870] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_3.bam [2022-04-19 13:36:58,485] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: LNB_1_1.fastq.gz [2022-04-19 13:36:58,864] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_2_2.fastq.gz [2022-04-19 13:36:58,865] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: ENB_2.bam.bai [2022-04-19 13:36:58,870] multiqc [DEBUG ] Ignoring file as matched an ignore pattern: NSC_2Aligned.out.sam [2022-04-19 13:37:13,245] multiqc [DEBUG ] No samples found: custom_content [2022-04-19 13:37:13,306] multiqc [DEBUG ] No samples found: conpair [2022-04-19 13:37:13,364] multiqc [DEBUG ] No samples found: peddy [2022-04-19 13:37:13,421] multiqc [DEBUG ] No samples found: methylQA [2022-04-19 13:37:13,520] multiqc [DEBUG ] No samples found: qualimap [2022-04-19 13:37:13,579] multiqc [DEBUG ] No samples found: preseq [2022-04-19 13:37:13,633] multiqc [DEBUG ] No samples found: quast [2022-04-19 13:37:13,699] multiqc [DEBUG ] No samples found: qorts [2022-04-19 13:37:13,781] multiqc [DEBUG ] No samples found: rna_seqc [2022-04-19 13:37:13,828] multiqc [DEBUG ] No samples found: rsem [2022-04-19 13:37:14,042] multiqc [DEBUG ] No samples found: rseqc [2022-04-19 13:37:14,103] multiqc [DEBUG ] No samples found: busco [2022-04-19 13:37:14,161] multiqc [DEBUG ] No samples found: goleft_indexcov [2022-04-19 13:37:14,214] multiqc [DEBUG ] No samples found: disambiguate [2022-04-19 13:37:14,270] multiqc [DEBUG ] No samples found: supernova [2022-04-19 13:37:14,419] multiqc [DEBUG ] No samples found: deeptools [2022-04-19 13:37:14,475] multiqc [DEBUG ] No samples found: sargasso [2022-04-19 13:37:14,528] multiqc [DEBUG ] No samples found: verifybamid [2022-04-19 13:37:14,580] multiqc [DEBUG ] No samples found: mirtrace [2022-04-19 13:37:14,641] multiqc [DEBUG ] No samples found: happy [2022-04-19 13:37:14,743] multiqc [DEBUG ] No samples found: homer [2022-04-19 13:37:14,821] multiqc [DEBUG ] No samples found: macs2 [2022-04-19 13:37:14,872] multiqc [DEBUG ] No samples found: theta2 [2022-04-19 13:37:14,923] multiqc [DEBUG ] No samples found: snpeff [2022-04-19 13:37:15,021] multiqc [DEBUG ] No samples found: gatk [2022-04-19 13:37:15,074] multiqc [DEBUG ] No samples found: htseq [2022-04-19 13:37:15,147] multiqc [DEBUG ] No samples found: bcftools [2022-04-19 13:37:15,206] multiqc [DEBUG ] No samples found: featureCounts [2022-04-19 13:37:15,272] multiqc [DEBUG ] No samples found: dedup [2022-04-19 13:37:15,599] multiqc [DEBUG ] No samples found: picard [2022-04-19 13:37:15,660] multiqc [DEBUG ] No samples found: prokka [2022-04-19 13:37:15,725] multiqc [DEBUG ] No samples found: samblaster [2022-04-19 13:37:15,843] multiqc [DEBUG ] No samples found: samtools [2022-04-19 13:37:15,927] multiqc [DEBUG ] No samples found: bamtools [2022-04-19 13:37:15,969] multiqc [DEBUG ] No samples found: jellyfish [2022-04-19 13:37:16,088] multiqc [DEBUG ] No samples found: vcftools [2022-04-19 13:37:16,137] multiqc [DEBUG ] No samples found: longranger [2022-04-19 13:37:16,436] multiqc [DEBUG ] No samples found: bbmap [2022-04-19 13:37:16,485] multiqc [DEBUG ] No samples found: bismark [2022-04-19 13:37:16,542] multiqc [DEBUG ] No samples found: hicexplorer [2022-04-19 13:37:16,611] multiqc [DEBUG ] No samples found: hicup [2022-04-19 13:37:16,662] multiqc [DEBUG ] No samples found: hicpro [2022-04-19 13:37:16,721] multiqc [DEBUG ] No samples found: salmon [2022-04-19 13:37:16,775] multiqc [DEBUG ] No samples found: kallisto [2022-04-19 13:37:16,829] multiqc [DEBUG ] No samples found: slamdunk [2022-04-19 13:37:17,490] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: ENB_2 [2022-04-19 13:37:17,910] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: NSC_1 [2022-04-19 13:37:18,327] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: NSC_2 [2022-04-19 13:37:18,741] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: LNB_3 [2022-04-19 13:37:19,113] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: ENB_3 [2022-04-19 13:37:19,433] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: LNB_1 [2022-04-19 13:37:19,774] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: NSC_3 [2022-04-19 13:37:20,126] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: ENB_1 [2022-04-19 13:37:20,452] multiqc.modules.star.star [DEBUG ] Duplicate ReadsPerGene sample name found! Overwriting: LNB_2 [2022-04-19 13:37:20,453] multiqc.modules.star.star [INFO ] Found 9 reports and 9 gene count files [2022-04-19 13:37:31,922] multiqc [DEBUG ] No samples found: hisat2 [2022-04-19 13:37:31,973] multiqc [DEBUG ] No samples found: tophat [2022-04-19 13:37:32,021] multiqc [DEBUG ] No samples found: bowtie2 [2022-04-19 13:37:32,072] multiqc [DEBUG ] No samples found: bowtie1 [2022-04-19 13:37:32,119] multiqc [DEBUG ] No samples found: kat [2022-04-19 13:37:32,166] multiqc [DEBUG ] No samples found: leehom [2022-04-19 13:37:32,229] multiqc [DEBUG ] No samples found: adapterRemoval [2022-04-19 13:37:32,283] multiqc [DEBUG ] No samples found: clipandmerge [2022-04-19 13:37:32,334] multiqc [DEBUG ] No samples found: cutadapt [2022-04-19 13:37:32,392] multiqc [DEBUG ] No samples found: flexbar [2022-04-19 13:37:32,448] multiqc [DEBUG ] No samples found: trimmomatic [2022-04-19 13:37:32,501] multiqc [DEBUG ] No samples found: skewer [2022-04-19 13:37:32,555] multiqc [DEBUG ] No samples found: sortmerna [2022-04-19 13:37:32,617] multiqc [DEBUG ] No samples found: biobloomtools [2022-04-19 13:37:32,677] multiqc [DEBUG ] No samples found: fastq_screen [2022-04-19 13:37:32,733] multiqc [DEBUG ] No samples found: afterqc [2022-04-19 13:37:32,785] multiqc [DEBUG ] No samples found: fastp [2022-04-19 13:37:32,842] multiqc [DEBUG ] No samples found: fastqc [2022-04-19 13:37:32,900] multiqc [DEBUG ] No samples found: clusterflow [2022-04-19 13:37:32,951] multiqc [DEBUG ] No samples found: bcl2fastq [2022-04-19 13:37:33,005] multiqc [DEBUG ] No samples found: interop [2022-04-19 13:37:33,023] multiqc [INFO ] Compressing plot data [2022-04-19 13:37:33,102] multiqc [INFO ] Report : multiqc_report.html [2022-04-19 13:37:33,102] multiqc [INFO ] Data : multiqc_data [2022-04-19 13:37:33,122] multiqc [DEBUG ] Moving data file from '/tmp/tmpj2ftuq/multiqc_data/multiqc_star.txt' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_data' [2022-04-19 13:37:33,170] multiqc [DEBUG ] Moving data file from '/tmp/tmpj2ftuq/multiqc_data/mqc_star_gene_counts_Same_Stranded.txt' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_data' [2022-04-19 13:37:33,195] multiqc [DEBUG ] Moving data file from '/tmp/tmpj2ftuq/multiqc_data/mqc_star_alignment_plot_1.txt' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_data' [2022-04-19 13:37:33,203] multiqc [DEBUG ] Moving data file from '/tmp/tmpj2ftuq/multiqc_data/mqc_star_gene_counts_Reverse_Stranded.txt' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_data' [2022-04-19 13:37:33,217] multiqc [DEBUG ] Moving data file from '/tmp/tmpj2ftuq/multiqc_data/multiqc_data.json' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_data' [2022-04-19 13:37:33,227] multiqc [DEBUG ] Moving data file from '/tmp/tmpj2ftuq/multiqc_data/mqc_star_gene_counts_Unstranded.txt' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_data' [2022-04-19 13:37:33,235] multiqc [DEBUG ] Moving data file from '/tmp/tmpj2ftuq/multiqc_data/multiqc_sources.txt' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_data' [2022-04-19 13:37:33,243] multiqc [DEBUG ] Moving data file from '/tmp/tmpj2ftuq/multiqc_data/multiqc_general_stats.txt' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_data' [2022-04-19 13:37:33,253] multiqc [INFO ] Plots : multiqc_plots [2022-04-19 13:37:33,254] multiqc [DEBUG ] Moving plots directory from '/tmp/tmpj2ftuq/multiqc_plots/svg' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_plots' [2022-04-19 13:37:33,330] multiqc [DEBUG ] Moving plots directory from '/tmp/tmpj2ftuq/multiqc_plots/pdf' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_plots' [2022-04-19 13:37:33,399] multiqc [DEBUG ] Moving plots directory from '/tmp/tmpj2ftuq/multiqc_plots/png' to '/nfs/no_backup/jvalcarcel/emancini/anieto/multiqc_plots' [2022-04-19 13:37:34,342] multiqc [INFO ] MultiQC complete