Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/18e99a1be623ce1767644b9e7d4e23/HCC1395_BL.TsTv.count
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/4896a221e2ccbd7792862e636738b8/custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.qual
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/089071bea702f69476de73d2da1299/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.qual
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/d89916853f53b8b70da05b25872e30/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/e8dc79e6f8dce470fe715c170bd6f4/Sig_18_Blood.deconflicted_germline.FILTER.summary
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/e4/ce338f80f36c887d6250e8884344ae/workflow_summary_mqc.yaml
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/f105d8cae3e86a0cb39dd7b9079a38/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.qual
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/f5b7f0f7da9e730ed7dc1dc53b8347/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff.csv
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/a0ae88cdc258d53789913fccf3efd8/custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.qual
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/202956c18bc741bc3b142a55185eeb/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.count
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/26ef79d3cb1d0e89ace379b84587a5/Sig_18_Blood.deconflicted_germline.bcftools_stats.txt
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/1e31aeeae5c7a8312d88899a66e9bd/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.qual
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/b489e302e23d6c35491c03e3fbb2de/custom_Sig_18_tumor_normal.manta.somatic_sv.FILTER.summary
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/b8a156109ba4eeae8634e0ee625128/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff.csv
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/039cfc3207d29a2947016789c41ab3/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.FILTER.summary
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/f92a32afbbbc4d851cc3c5b1c6b544/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/bbebe43081da624132b9c77175c0cd/custom_Sig_18_tumor_normal.strelka.somatic_snvs.FILTER.summary
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/9c6442cbb58c733f9d76dad3273dbc/custom_Sig_18_tumor_normal.manta.somatic_sv.bcftools_stats.txt
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/652987422b525bae6bcc89f42a53f8/HCC1395_BL.deconflicted_germline.bcftools_stats.txt
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/f080c928d4109082b6031dd518b3b8/custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.count
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/9f63b8e53b8a9724142dd69a771ad1/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.qual
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/dbfce516f006a5d9292f311a18f2ba/Sig_18_tissue.mosdepth.region.dist.txt
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/99a8f59a170719ce35ea54ce1122a2/HCC1395_BL.mosdepth.global.dist.txt
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/4aa4a6a951c7e5a618b32b519527fa/Sig_18_Blood.deconflicted_germline.TsTv.count
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/79bb11703c880c12c14f8ea3de6eca/custom_Sig_18_tumor_normal.manta.diploid_sv.bcftools_stats.txt
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/eea7cffad6ad43857ee9a84a319300/.command.sh
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/9d2ebdc09ea454344befffb2060a44/custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.count
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/b4de810a6f18f26000ab5879536e9a/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.FILTER.summary
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/c451220e63e672dbfe7d19f3e5ebda/HCC1395_BL.bcftools_stats.txt
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/26b91dd6e78eb906aa1caebb67592a/custom_Sig_18_tumor_normal.strelka.somatic_indels.FILTER.summary
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/c1699626b50c157f277dabc2f8f639/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/4c1b6b591a290179b48fc1ac4724f1/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.count
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0afa6caa24e87f82df13515d184af1/HCC1395_tumor.mosdepth.region.dist.txt
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/432a0a78baccf0daa4917a914229be/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/62b211d7a00ca1835990508483246f/custom_Sig_18_tumor_normal.strelka.somatic_indels.bcftools_stats.txt
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/0afa6caa24e87f82df13515d184af1/HCC1395_tumor.mosdepth.global.dist.txt
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/491ef6c5c51094e59d20c1774e845d/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/73a92fb4eca6ed410eeef2751f5ace/custom_Sig_18_tumor_normal.manta.diploid_sv.FILTER.summary
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/9deae44ce86f6f0547a0abd0b6c3e6/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.count
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/fc6486a9dedc22b30e424fd5f85c52/Sig_18_Blood_custom.ann_snpEff_VEP.ann.summary.html
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/401b3d6bf67198e539149454137a44/HCC1395_tumor_vs_HCC1395_BL.conpair.contamination.txt
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/982711cb76505f0186e322ea5d350c/HCC1395_BL.deconflicted_germline.FILTER.summary
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/052d657ee6e0a6cf167592bd87ab50/Sig_18_Blood.TsTv.qual
Downloading: s3://natera-rnd-pltf-dev-s3-gitlab-results/sarek/build2795358/regression-run/63486558/pipeline_info/nf_core_sarek_software_mqc_versions.yml
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/2db506627b730e68c0d1efd157990c/custom_Sig_18_tumor_normal.strelka.somatic_snvs.bcftools_stats.txt
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/d2274f2c415ede32cc0168335994ca/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.count
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/dc4c1964637351e68d73e6eb3cedb1/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/7f65e6bd9562b5d01fb8f4c9946679/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/8a3a99f58eec87e86afe393d443fe0/HCC1395_BL.FILTER.summary
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/205b6d048fbeba4a708e35bc52617f/HCC1395_BL.TsTv.qual
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/9133ba710b70be66a46311393abc6c/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.bcftools_stats.txt
==> STAGING COMPLETE (94 inputs)
/// MultiQC 🔍 v1.33
config | Loading config settings from: multiqc_config.yml
config | Config 'custom_logo' path not found, skipping (nf-core-sarek_logo_light.png)
version_check | MultiQC Version v1.35 now available!
file_search | Search path: /tmp/nxf.waPUHPNmJI
file_search | Only using modules: custom_content, fastqc, fastp, picard, samtools, mosdepth, gatk, bcftools, vcftools, snpeff, vep
custom_content | nf-core-sarek-methods-description: Found 1 sample (html)
custom_content | altera-sarek-summary: Found 1 sample (html)
samtools | Found 4 stats reports
mosdepth | Found reports for 4 samples
validation | mosdepth/mosdepth.py: warnings while parsing barplot.pconfig[id='mosdepth-coverage-per-contig-single'] {id: mosdepth-coverage-per-contig-single, title: Mosdepth: Coverage per contig, xlab: Sample, ylab: Average Coverage, tt_suffix: x, hide_zero_cats: False, categories: True}:
• 'categories': unrecognized field. Available fields: id, title, subtitle, anchor, height, width, square, logswitch, logswitch_active, logswitch_label, cpswitch, cpswitch_c_active, cpswitch_counts_label, cpswitch_percent_label, xlog, ylog, data_labels, xlab, ylab, xsuffix, ysuffix, tt_suffix, xlab_format, ylab_format, tt_label, x_decimals, y_decimals, tt_decimals, xmin, xmax, ymin, ymax, x_clipmin, x_clipmax, y_clipmin, y_clipmax, save_data_file, showlegend, x_minrange, y_minrange, x_bands, y_bands, x_lines, y_lines, series_label, flat_if_very_large, stacking, hide_zero_cats, sort_samples, cluster_samples, cluster_method, cluster_switch_clustered_active, use_legend, suffix, lab_format, sample_groups
bcftools | Found 12 stats reports
vcftools | Found 12 TsTv.count reports
vcftools | Found 12 TsTv.qual reports
snpeff | Found 12 reports
vep | Found 12 VEP summaries
file_search | Only using modules: samtools, mosdepth, bcftools, vcftools, snpeff, vep, nf-core-sarek-methods-description, altera-sarek-summary
write_results | Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set `export_plots: false` in config, or remove the `--export-plots` command line flag
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
mqc_colour | Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '55,126,184' to RGB: input #55,126,184 is not in #RRGGBB format
mqc_colour | Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
mqc_colour | Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
mqc_colour | Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
mqc_colour | Error converting color '77,175,74' to RGB: input #77,175,74 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '152,78,163' to RGB: input #152,78,163 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
mqc_colour | Error converting color '255,127,0' to RGB: input #255,127,0 is not in #RRGGBB format
write_results | Data : multiqc_data
write_results | Report : multiqc_report.html
write_results | Plots : multiqc_plots
multiqc | MultiQC complete