[2021-10-23 10:09:11,351] multiqc                                            [DEBUG  ]  No MultiQC config found: /opt/conda/envs/nf-core-sarek-2.7.1/lib/python2.7/site-packages/multiqc_config.yaml
[2021-10-23 10:09:11,359] multiqc                                            [DEBUG  ]  No MultiQC config found: /home/sigenae/.multiqc_config.yaml
[2021-10-23 10:09:11,367] multiqc                                            [DEBUG  ]  Loading config settings from: multiqc_config.yaml
[2021-10-23 10:09:11,367] multiqc                                            [DEBUG  ]  New config 'custom_logo_url': https://github.com/nf-core/sarek/
[2021-10-23 10:09:11,368] multiqc                                            [DEBUG  ]  New config 'report_comment': This report has been generated by the <a href="https://github.com/nf-core/sarek" target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://github.com/nf-core/sarek" target="_blank">documentation</a>.

[2021-10-23 10:09:11,368] multiqc                                            [DEBUG  ]  New config 'custom_logo_title': nf-core/sarek
[2021-10-23 10:09:11,368] multiqc                                            [ERROR  ]  Config 'custom_logo' path not found, skipping (../../../docs/images/nf-core_sarek_logo.png)
[2021-10-23 10:09:11,368] multiqc                                            [DEBUG  ]  New config 'export_plots': True
[2021-10-23 10:09:11,369] multiqc                                            [DEBUG  ]  New config 'top_modules': [{'fastqc': {'name': 'FastQC', 'path_filters_exclude': ['*trimmed_fastqc*']}}, {'fastqc': {'info': 'FastQC after applying TrimGalore.', 'name': 'FastQC after trimming', 'path_filters': ['*trimmed_fastqc*']}}, 'picard', 'gatk', 'samtools', 'qualimap', 'bcftools', 'vcftools', 'snpeff']
[2021-10-23 10:09:11,369] multiqc                                            [DEBUG  ]  New config 'report_section_order': {'software_versions': {'order': -1000}, 'nf-core-sarek-summary': {'order': -1001}}
[2021-10-23 10:09:11,370] multiqc                                            [DEBUG  ]  Command used: /opt/conda/envs/nf-core-sarek-2.7.1/bin/multiqc -f .
[2021-10-23 10:09:11,970] multiqc                                            [WARNING]  MultiQC Version v1.11 now available!
[2021-10-23 10:09:11,971] multiqc                                            [INFO   ]  This is MultiQC v1.8
[2021-10-23 10:09:11,971] multiqc                                            [DEBUG  ]  Command     : /opt/conda/envs/nf-core-sarek-2.7.1/bin/multiqc -f .
[2021-10-23 10:09:11,971] multiqc                                            [DEBUG  ]  Working dir : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0
[2021-10-23 10:09:11,971] multiqc                                            [INFO   ]  Template    : default
[2021-10-23 10:09:11,971] multiqc                                            [WARNING]  You are running MultiQC with Python 2.7.15
[2021-10-23 10:09:11,971] multiqc                                            [WARNING]  Please upgrade! MultiQC will soon drop support for Python < 3.6
[2021-10-23 10:09:11,972] multiqc                                            [INFO   ]  Searching   : /work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0
[2021-10-23 10:09:11,973] multiqc                                            [DEBUG  ]  Analysing modules: fastqc, fastqc, picard, gatk, samtools, qualimap, bcftools, vcftools, snpeff, custom_content, conpair, peddy, methylQA, phantompeakqualtools, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, homer, macs2, theta2, htseq, featureCounts, fgbio, dedup, damageprofiler, biobambam2, mtnucratio, prokka, samblaster, sexdeterrmine, bamtools, jellyfish, 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, minionqc, mosdepth, clusterflow, bcl2fastq, interop, flash, seqyclean
[2021-10-23 10:09:11,973] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /tmp/tmpSNQqk7
[2021-10-23 10:09:12,533] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: .command.run
[2021-10-23 10:09:12,541] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: .command.run
[2021-10-23 10:09:12,638] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: SRR7062654.recal.bam.samtools.stats.out
[2021-10-23 10:09:12,654] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: SRR7062654.recal.bam.samtools.stats.out
[2021-10-23 10:09:12,916] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: SRR7062655.recal.bam.samtools.stats.out
[2021-10-23 10:09:12,931] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: SRR7062655.recal.bam.samtools.stats.out
[2021-10-23 10:09:13,198] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: SRR7062655.bam.metrics
[2021-10-23 10:09:13,208] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: SRR7062655.bam.metrics
[2021-10-23 10:09:13,267] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: SRR7062654.bam.metrics
[2021-10-23 10:09:13,278] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: SRR7062654.bam.metrics
[2021-10-23 10:09:13,484] multiqc                                            [DEBUG  ]  Ignoring file as matched an ignore pattern: qualimapReport.html
[2021-10-23 10:09:13,592] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt
[2021-10-23 10:09:13,603] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt
[2021-10-23 10:09:13,643] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:13,690] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:13,691] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:13,691] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:13,726] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:13,726] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:13,727] multiqc                                            [DEBUG  ]  File ignored by stacks/sumstats because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:16,008] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_clipping_profile.txt
[2021-10-23 10:09:16,046] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:16,091] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:16,091] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:16,092] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:16,126] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:16,126] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:18,286] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:18,332] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:18,332] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:18,332] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:18,366] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:18,366] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:20,602] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: jquery.js
[2021-10-23 10:09:20,614] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: jquery.js
[2021-10-23 10:09:20,680] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: websupport.js
[2021-10-23 10:09:20,692] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: websupport.js
[2021-10-23 10:09:20,852] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: pygments.css
[2021-10-23 10:09:20,886] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: doctools.js
[2021-10-23 10:09:20,896] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: doctools.js
[2021-10-23 10:09:20,955] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: searchtools.js
[2021-10-23 10:09:20,966] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: searchtools.js
[2021-10-23 10:09:21,053] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: underscore.js
[2021-10-23 10:09:21,062] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: underscore.js
[2021-10-23 10:09:21,096] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css
[2021-10-23 10:09:21,107] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css
[2021-10-23 10:09:21,180] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css
[2021-10-23 10:09:21,191] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css
[2021-10-23 10:09:21,275] multiqc                                            [DEBUG  ]  Ignoring file as matched an ignore pattern: qualimapReport.html
[2021-10-23 10:09:21,375] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt
[2021-10-23 10:09:21,385] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt
[2021-10-23 10:09:21,425] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:21,473] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:21,473] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:21,473] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:21,509] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:21,509] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:21,509] multiqc                                            [DEBUG  ]  File ignored by stacks/sumstats because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:23,814] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_clipping_profile.txt
[2021-10-23 10:09:23,853] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:23,898] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:23,898] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:23,898] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:23,932] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:23,932] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:26,096] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:26,143] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:26,143] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:26,143] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:26,177] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:26,177] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:28,456] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: jquery.js
[2021-10-23 10:09:28,467] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: jquery.js
[2021-10-23 10:09:28,533] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: websupport.js
[2021-10-23 10:09:28,544] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: websupport.js
[2021-10-23 10:09:28,703] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: pygments.css
[2021-10-23 10:09:28,737] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: doctools.js
[2021-10-23 10:09:28,747] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: doctools.js
[2021-10-23 10:09:28,806] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: searchtools.js
[2021-10-23 10:09:28,817] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: searchtools.js
[2021-10-23 10:09:28,904] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: underscore.js
[2021-10-23 10:09:28,929] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: underscore.js
[2021-10-23 10:09:28,962] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css
[2021-10-23 10:09:28,972] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css
[2021-10-23 10:09:29,047] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css
[2021-10-23 10:09:29,058] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css
[2021-10-23 10:09:29,142] multiqc                                            [DEBUG  ]  Ignoring file as matched an ignore pattern: qualimapReport.html
[2021-10-23 10:09:29,231] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt
[2021-10-23 10:09:29,238] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt
[2021-10-23 10:09:29,275] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:29,320] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:29,320] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:29,320] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:29,356] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:29,356] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:29,356] multiqc                                            [DEBUG  ]  File ignored by stacks/sumstats because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:31,636] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_clipping_profile.txt
[2021-10-23 10:09:31,671] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:31,713] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:31,713] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:31,713] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:31,747] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:31,747] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:33,921] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:33,964] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:33,965] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:33,965] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:33,999] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:33,999] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:36,234] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: jquery.js
[2021-10-23 10:09:36,244] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: jquery.js
[2021-10-23 10:09:36,305] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: websupport.js
[2021-10-23 10:09:36,315] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: websupport.js
[2021-10-23 10:09:36,461] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: pygments.css
[2021-10-23 10:09:36,493] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: doctools.js
[2021-10-23 10:09:36,501] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: doctools.js
[2021-10-23 10:09:36,556] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: searchtools.js
[2021-10-23 10:09:36,565] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: searchtools.js
[2021-10-23 10:09:36,647] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: underscore.js
[2021-10-23 10:09:36,654] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: underscore.js
[2021-10-23 10:09:36,684] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css
[2021-10-23 10:09:36,693] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css
[2021-10-23 10:09:36,763] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css
[2021-10-23 10:09:36,771] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css
[2021-10-23 10:09:36,851] multiqc                                            [DEBUG  ]  Ignoring file as matched an ignore pattern: qualimapReport.html
[2021-10-23 10:09:36,940] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt
[2021-10-23 10:09:36,948] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_nucleotide_content.txt
[2021-10-23 10:09:36,985] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:37,030] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:37,030] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:37,030] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:37,066] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:37,066] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:37,066] multiqc                                            [DEBUG  ]  File ignored by stacks/sumstats because it exceeded search pattern filesize limit: coverage_across_reference.txt
[2021-10-23 10:09:39,343] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapped_reads_clipping_profile.txt
[2021-10-23 10:09:39,378] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:39,420] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:39,420] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:39,420] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:39,454] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:39,454] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: mapping_quality_across_reference.txt
[2021-10-23 10:09:41,606] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:41,649] multiqc                                            [DEBUG  ]  File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:41,649] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:41,650] multiqc                                            [DEBUG  ]  File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:41,684] multiqc                                            [DEBUG  ]  File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:41,684] multiqc                                            [DEBUG  ]  File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: insert_size_across_reference.txt
[2021-10-23 10:09:43,910] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: jquery.js
[2021-10-23 10:09:43,928] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: jquery.js
[2021-10-23 10:09:44,023] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: websupport.js
[2021-10-23 10:09:44,035] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: websupport.js
[2021-10-23 10:09:44,180] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: pygments.css
[2021-10-23 10:09:44,212] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: doctools.js
[2021-10-23 10:09:44,220] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: doctools.js
[2021-10-23 10:09:44,275] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: searchtools.js
[2021-10-23 10:09:44,284] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: searchtools.js
[2021-10-23 10:09:44,367] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: underscore.js
[2021-10-23 10:09:44,374] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: underscore.js
[2021-10-23 10:09:44,408] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: agogo.css
[2021-10-23 10:09:44,417] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: agogo.css
[2021-10-23 10:09:44,487] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: basic.css
[2021-10-23 10:09:44,504] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: basic.css
[2021-10-23 10:09:44,630] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: 1.recal.table
[2021-10-23 10:09:44,640] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: 2.recal.table
[2021-10-23 10:09:44,644] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: HaplotypeCaller_SRR7062654.g.bcf.tools.stats.out
[2021-10-23 10:09:44,656] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: HaplotypeCaller_SRR7062654.g.bcf.tools.stats.out
[2021-10-23 10:09:44,834] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: HaplotypeCaller_SRR7062655.g.bcf.tools.stats.out
[2021-10-23 10:09:44,846] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: HaplotypeCaller_SRR7062655.g.bcf.tools.stats.out
[2021-10-23 10:09:45,027] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: HaplotypeCaller_SRR7062655.bcf.tools.stats.out
[2021-10-23 10:09:45,039] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: HaplotypeCaller_SRR7062655.bcf.tools.stats.out
[2021-10-23 10:09:45,217] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: FreeBayes_SRR7062655.bcf.tools.stats.out
[2021-10-23 10:09:45,230] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: FreeBayes_SRR7062655.bcf.tools.stats.out
[2021-10-23 10:09:45,406] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: HaplotypeCaller_SRR7062654.bcf.tools.stats.out
[2021-10-23 10:09:45,418] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: HaplotypeCaller_SRR7062654.bcf.tools.stats.out
[2021-10-23 10:09:45,596] multiqc                                            [DEBUG  ]  File ignored by hicexplorer because it exceeded search pattern filesize limit: FreeBayes_SRR7062654.bcf.tools.stats.out
[2021-10-23 10:09:45,609] multiqc                                            [DEBUG  ]  File ignored by longranger/invocation because it exceeded search pattern filesize limit: FreeBayes_SRR7062654.bcf.tools.stats.out
[2021-10-23 10:09:45,782] multiqc                                            [DEBUG  ]  Ignoring file as matched an ignore pattern: SRR7062655_1_R2_fastqc.html
[2021-10-23 10:09:45,783] multiqc                                            [DEBUG  ]  Ignoring file as matched an ignore pattern: SRR7062655_1_R1_fastqc.html
[2021-10-23 10:09:45,783] multiqc                                            [DEBUG  ]  Ignoring file as matched an ignore pattern: SRR7062654_1_R1_fastqc.html
[2021-10-23 10:09:45,784] multiqc                                            [DEBUG  ]  Ignoring file as matched an ignore pattern: SRR7062654_1_R2_fastqc.html
[2021-10-23 10:09:46,322] multiqc.plots.linegraph                            [DEBUG  ]  Using matplotlib version 2.2.5
[2021-10-23 10:09:46,323] multiqc.plots.bargraph                             [DEBUG  ]  Using matplotlib version 2.2.5
[2021-10-23 10:09:46,387] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 4 reports
[2021-10-23 10:09:51,606] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping 'SRR7062655_1_R1_fastqc.zip' as it didn't match the path_filters for 'FastQC after trimming'
[2021-10-23 10:09:51,606] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping 'SRR7062654_1_R2_fastqc.zip' as it didn't match the path_filters for 'FastQC after trimming'
[2021-10-23 10:09:51,606] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping 'SRR7062655_1_R2_fastqc.zip' as it didn't match the path_filters for 'FastQC after trimming'
[2021-10-23 10:09:51,606] multiqc.modules.base_module                        [DEBUG  ]  fastqc/zip - Skipping 'SRR7062654_1_R1_fastqc.zip' as it didn't match the path_filters for 'FastQC after trimming'
[2021-10-23 10:09:51,606] multiqc                                            [DEBUG  ]  No samples found: fastqc
[2021-10-23 10:09:52,768] multiqc.modules.picard.picard                      [INFO   ]  Found 2 MarkDuplicates reports
[2021-10-23 10:09:52,834] multiqc.modules.gatk.base_recalibrator             [INFO   ]  Found 2 BaseRecalibrator reports
[2021-10-23 10:09:55,008] multiqc.modules.samtools.samtools                  [INFO   ]  Found 2 stats reports
[2021-10-23 10:09:55,166] multiqc.modules.qualimap.QM_BamQC                  [DEBUG  ]  Using default Qualimap thresholds: 1, 5, 10, 30, 50
[2021-10-23 10:09:58,034] multiqc.modules.qualimap.qualimap                  [INFO   ]  Found 4 BamQC reports
[2021-10-23 10:10:14,445] multiqc.modules.bcftools.bcftools                  [INFO   ]  Found 6 stats reports
[2021-10-23 10:10:15,123] multiqc.modules.vcftools.vcftools                  [INFO   ]  Found 6 TsTv.count reports
[2021-10-23 10:10:16,258] multiqc.modules.vcftools.vcftools                  [INFO   ]  Found 4 TsTv.qual reports
[2021-10-23 10:10:16,263] multiqc                                            [DEBUG  ]  No samples found: snpeff
[2021-10-23 10:10:16,278] multiqc.modules.custom_content.custom_content      [INFO   ]  software_versions: Found 1 sample (html)
[2021-10-23 10:10:16,278] multiqc.modules.custom_content.custom_content      [INFO   ]  software_versions: Found 1249 samples (html)
[2021-10-23 10:10:16,278] multiqc.modules.custom_content.custom_content      [INFO   ]  sarek-summary: Found 1 sample (html)
[2021-10-23 10:10:16,278] multiqc.modules.custom_content.custom_content      [INFO   ]  sarek-summary: Found 3073 samples (html)
[2021-10-23 10:10:16,282] multiqc                                            [DEBUG  ]  No samples found: conpair
[2021-10-23 10:10:16,287] multiqc                                            [DEBUG  ]  No samples found: peddy
[2021-10-23 10:10:16,291] multiqc                                            [DEBUG  ]  No samples found: methylQA
[2021-10-23 10:10:16,295] multiqc                                            [DEBUG  ]  No samples found: phantompeakqualtools
[2021-10-23 10:10:16,300] multiqc                                            [DEBUG  ]  No samples found: preseq
[2021-10-23 10:10:16,305] multiqc                                            [DEBUG  ]  No samples found: quast
[2021-10-23 10:10:16,309] multiqc                                            [DEBUG  ]  No samples found: qorts
[2021-10-23 10:10:16,313] multiqc                                            [DEBUG  ]  No samples found: rna_seqc
[2021-10-23 10:10:16,316] multiqc                                            [DEBUG  ]  No samples found: rsem
[2021-10-23 10:10:16,322] multiqc                                            [DEBUG  ]  No samples found: rseqc
[2021-10-23 10:10:16,327] multiqc                                            [DEBUG  ]  No samples found: busco
[2021-10-23 10:10:16,331] multiqc                                            [DEBUG  ]  No samples found: goleft_indexcov
[2021-10-23 10:10:16,336] multiqc                                            [DEBUG  ]  No samples found: disambiguate
[2021-10-23 10:10:16,341] multiqc                                            [DEBUG  ]  No samples found: supernova
[2021-10-23 10:10:16,346] multiqc                                            [DEBUG  ]  No samples found: deeptools
[2021-10-23 10:10:16,350] multiqc                                            [DEBUG  ]  No samples found: sargasso
[2021-10-23 10:10:16,355] multiqc                                            [DEBUG  ]  No samples found: verifybamid
[2021-10-23 10:10:16,360] multiqc                                            [DEBUG  ]  No samples found: mirtrace
[2021-10-23 10:10:16,364] multiqc                                            [DEBUG  ]  No samples found: happy
[2021-10-23 10:10:16,369] multiqc                                            [DEBUG  ]  No samples found: homer
[2021-10-23 10:10:16,374] multiqc                                            [DEBUG  ]  No samples found: macs2
[2021-10-23 10:10:16,378] multiqc                                            [DEBUG  ]  No samples found: theta2
[2021-10-23 10:10:16,382] multiqc                                            [DEBUG  ]  No samples found: htseq
[2021-10-23 10:10:16,388] multiqc                                            [DEBUG  ]  No samples found: featureCounts
[2021-10-23 10:10:16,392] multiqc                                            [DEBUG  ]  No samples found: fgbio
[2021-10-23 10:10:16,396] multiqc                                            [DEBUG  ]  No samples found: dedup
[2021-10-23 10:10:16,401] multiqc                                            [DEBUG  ]  No samples found: damageprofiler
[2021-10-23 10:10:16,405] multiqc                                            [DEBUG  ]  No samples found: biobambam2
[2021-10-23 10:10:16,410] multiqc                                            [DEBUG  ]  No samples found: mtnucratio
[2021-10-23 10:10:16,414] multiqc                                            [DEBUG  ]  No samples found: prokka
[2021-10-23 10:10:16,419] multiqc                                            [DEBUG  ]  No samples found: samblaster
[2021-10-23 10:10:16,423] multiqc                                            [DEBUG  ]  No samples found: sexdeterrmine
[2021-10-23 10:10:16,428] multiqc                                            [DEBUG  ]  No samples found: bamtools
[2021-10-23 10:10:16,432] multiqc                                            [DEBUG  ]  No samples found: jellyfish
[2021-10-23 10:10:16,436] multiqc                                            [DEBUG  ]  No samples found: longranger
[2021-10-23 10:10:16,441] multiqc                                            [DEBUG  ]  No samples found: stacks
[2021-10-23 10:10:16,447] multiqc                                            [DEBUG  ]  No samples found: bbmap
[2021-10-23 10:10:16,451] multiqc                                            [DEBUG  ]  No samples found: bismark
[2021-10-23 10:10:16,455] multiqc                                            [DEBUG  ]  No samples found: biscuit
[2021-10-23 10:10:16,460] multiqc                                            [DEBUG  ]  No samples found: hicexplorer
[2021-10-23 10:10:16,465] multiqc                                            [DEBUG  ]  No samples found: hicup
[2021-10-23 10:10:16,469] multiqc                                            [DEBUG  ]  No samples found: hicpro
[2021-10-23 10:10:16,473] multiqc                                            [DEBUG  ]  No samples found: salmon
[2021-10-23 10:10:16,478] multiqc                                            [DEBUG  ]  No samples found: kallisto
[2021-10-23 10:10:16,482] multiqc                                            [DEBUG  ]  No samples found: slamdunk
[2021-10-23 10:10:16,487] multiqc                                            [DEBUG  ]  No samples found: star
[2021-10-23 10:10:16,491] multiqc                                            [DEBUG  ]  No samples found: hisat2
[2021-10-23 10:10:16,495] multiqc                                            [DEBUG  ]  No samples found: tophat
[2021-10-23 10:10:16,500] multiqc                                            [DEBUG  ]  No samples found: bowtie2
[2021-10-23 10:10:16,504] multiqc                                            [DEBUG  ]  No samples found: bowtie1
[2021-10-23 10:10:16,509] multiqc                                            [DEBUG  ]  No samples found: kat
[2021-10-23 10:10:16,513] multiqc                                            [DEBUG  ]  No samples found: leehom
[2021-10-23 10:10:16,517] multiqc                                            [DEBUG  ]  No samples found: adapterRemoval
[2021-10-23 10:10:16,521] multiqc                                            [DEBUG  ]  No samples found: clipandmerge
[2021-10-23 10:10:16,525] multiqc                                            [DEBUG  ]  No samples found: cutadapt
[2021-10-23 10:10:16,530] multiqc                                            [DEBUG  ]  No samples found: flexbar
[2021-10-23 10:10:16,534] multiqc                                            [DEBUG  ]  No samples found: trimmomatic
[2021-10-23 10:10:16,539] multiqc                                            [DEBUG  ]  No samples found: skewer
[2021-10-23 10:10:16,542] multiqc                                            [DEBUG  ]  No samples found: sortmerna
[2021-10-23 10:10:16,547] multiqc                                            [DEBUG  ]  No samples found: biobloomtools
[2021-10-23 10:10:16,551] multiqc                                            [DEBUG  ]  No samples found: fastq_screen
[2021-10-23 10:10:16,556] multiqc                                            [DEBUG  ]  No samples found: afterqc
[2021-10-23 10:10:16,559] multiqc                                            [DEBUG  ]  No samples found: fastp
[2021-10-23 10:10:16,564] multiqc                                            [DEBUG  ]  No samples found: minionqc
[2021-10-23 10:10:16,568] multiqc                                            [DEBUG  ]  No samples found: mosdepth
[2021-10-23 10:10:16,573] multiqc                                            [DEBUG  ]  No samples found: clusterflow
[2021-10-23 10:10:16,578] multiqc                                            [DEBUG  ]  No samples found: bcl2fastq
[2021-10-23 10:10:16,583] multiqc                                            [DEBUG  ]  No samples found: interop
[2021-10-23 10:10:16,588] multiqc                                            [DEBUG  ]  No samples found: flash
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  No samples found: seqyclean
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'FastQC'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'FastQC'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Picard'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'Picard'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'GATK'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'GATK'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Samtools'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'Samtools'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'QualiMap'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'QualiMap'.
[2021-10-23 10:10:16,593] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'Bcftools'.
[2021-10-23 10:10:16,594] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'Bcftools'.
[2021-10-23 10:10:16,594] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'VCFTools'.
[2021-10-23 10:10:16,594] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'VCFTools'.
[2021-10-23 10:10:16,594] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/sarek Workflow Summary'.
[2021-10-23 10:10:16,594] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'nf-core/sarek Workflow Summary'.
[2021-10-23 10:10:16,594] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'software_versions' not found for module 'nf-core/sarek software versions'.
[2021-10-23 10:10:16,594] multiqc                                            [DEBUG  ]  Reordering sections: anchor 'nf-core-sarek-summary' not found for module 'nf-core/sarek software versions'.
[2021-10-23 10:10:16,632] multiqc                                            [INFO   ]  Compressing plot data
[2021-10-23 10:10:18,401] multiqc                                            [INFO   ]  Report      : multiqc_report.html
[2021-10-23 10:10:18,401] multiqc                                            [INFO   ]  Data        : multiqc_data
[2021-10-23 10:10:18,403] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/multiqc_general_stats.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,404] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,405] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_qualimap_coverage_histogram_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,406] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,406] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_vcftools_tstv_by_count_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,407] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,408] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/multiqc_picard_dups.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,409] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_bcftools-stats-subtypes_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,410] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_qualimap_insert_size_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,411] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,412] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/multiqc_data.json' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,418] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_qualimap_gc_content_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,419] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_bcftools_stats_indel-lengths_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,419] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,420] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/multiqc_sources.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,421] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,422] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_bcftools_stats_vqc_Count_Transitions.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,423] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_bcftools_stats_vqc_Count_Indels.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,424] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_bcftools_stats_depth_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,425] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_vcftools_tstv_by_qual_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,426] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_qualimap_genome_fraction_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,427] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_bcftools_stats_vqc_Count_SNP.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,428] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,429] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,430] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_picard_deduplication_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,431] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,431] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/multiqc_bcftools_stats.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,432] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_bcftools_stats_vqc_Count_Transversions.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,433] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/multiqc_samtools_stats.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,434] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_samtools_alignment_plot_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,434] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/mqc_fastqc_sequence_counts_plot_1.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,435] multiqc                                            [DEBUG  ]  Moving data file from '/tmp/tmpSNQqk7/multiqc_data/multiqc_fastqc.txt' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_data'
[2021-10-23 10:10:18,436] multiqc                                            [INFO   ]  Plots       : multiqc_plots
[2021-10-23 10:10:18,437] multiqc                                            [DEBUG  ]  Moving plots directory from '/tmp/tmpSNQqk7/multiqc_plots/png' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_plots'
[2021-10-23 10:10:18,460] multiqc                                            [DEBUG  ]  Moving plots directory from '/tmp/tmpSNQqk7/multiqc_plots/pdf' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_plots'
[2021-10-23 10:10:18,480] multiqc                                            [DEBUG  ]  Moving plots directory from '/tmp/tmpSNQqk7/multiqc_plots/svg' to '/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/multiqc_plots'
[2021-10-23 10:10:18,635] multiqc                                            [INFO   ]  MultiQC complete