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s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/f8c88c362ea6cc895eb8e5475ae69a/HCC1395_BL/HCC1395_BL.md/reads_per_target.altera_v3_targets_coding_postQC_hg38.bed.tsv ==> STAGING COMPLETE (406 inputs) /usr/local/lib/python3.13/site-packages/click/core.py:1223: UserWarning: The parameter --disable-seqtool-plugin is used more than once. Remove its duplicate as parameters should be unique. parser = self.make_parser(ctx) /usr/local/lib/python3.13/site-packages/click/core.py:1216: UserWarning: The parameter --disable-seqtool-plugin is used more than once. Remove its duplicate as parameters should be unique. self.parse_args(ctx, args) /// MultiQC v1.33 update_config | Report title: REGRESSION hooks | Running seqtool MultiQC Plugin v0.1.0 hooks | Running seqtool MultiQC Plugin v0.1.0 version_check | MultiQC Version v1.35 now available! file_search | Search path: /tmp/nxf.9D1HIcEtOi basic_stats | Found 4 full_basics_stats files depth_stats | Found 4 depth stats files for all_targets depth_stats | Found 4 depth stats files for all_probes depth_stats | Found 4 depth stats files for boosted_depth depth_stats | Found 4 depth stats files for coding_depth depth_stats | Found 4 depth stats files for noncoding_depth depth_stats | Found 4 depth stats files for non_boosted_depth depth_stats | Found 4 depth stats files for hotspot_depth depth_stats | Found 4 depth stats files for foresight_depth fragment_size | Found 4 fragment size files gc_bias | Found 4 GC bias files for all_targets gc_bias | Found 4 GC bias files for all_probes gc_bias | Found 4 GC bias files for boosted_depth gc_bias | Found 4 GC bias files for coding_depth gc_bias | Found 4 GC bias files for noncoding_depth gc_bias | Found 4 GC bias files for non_boosted_depth gc_bias | Found 4 GC bias files for hotspot_depth gc_bias | Found 4 GC bias files for foresight_depth mosdepth | Found reports for 4 samples picard | Found 4 AlignmentSummaryMetrics reports picard | Found 4 HsMetrics reports picard | Found 4 InsertSizeMetrics reports picard | Found 4 MarkDuplicates reports picard | Found 4 QualityByCycleMetrics reports picard | Found 4 QualityScoreDistributionMetrics reports samtools | Found 4 stats reports fastp | Found 32 reports bclconvert | Found RunInfo.xml file in 75 but no Demux Stats file, skipping bclconvert | Found RunInfo.xml file in 88 but no Demux Stats file, skipping bclconvert | Found RunInfo.xml file in 62 but no Demux Stats file, skipping bclconvert | Found RunInfo.xml file in 49 but no Demux Stats file, skipping bclconvert | Found RunInfo.xml file in 101 but no Demux Stats file, skipping bclconvert | Found RunInfo.xml file in 10 but no Demux Stats file, skipping bclconvert | Found RunInfo.xml file in 23 but no Demux Stats file, skipping bclconvert | Found RunInfo.xml file in 36 but no Demux Stats file, skipping bclconvert | Found Demux Stats file in 17 but no RunInfo.xml file, skipping bclconvert | Found Demux Stats file in 69 but no RunInfo.xml file, skipping bclconvert | Found Demux Stats file in 56 but no RunInfo.xml file, skipping bclconvert | Found Demux Stats file in 30 but no RunInfo.xml file, skipping bclconvert | Found Demux Stats file in 82 but no RunInfo.xml file, skipping bclconvert | Found Demux Stats file in 43 but no RunInfo.xml file, skipping bclconvert | Found Demux Stats file in 95 but no RunInfo.xml file, skipping bclconvert | Found Demux Stats file in 4 but no RunInfo.xml file, skipping write_results | Data : REGRESSION_multiqc_report_data write_results | Report : REGRESSION_multiqc_report.html multiqc | MultiQC complete /usr/local/lib/python3.13/site-packages/click/core.py:1223: UserWarning: The parameter --disable-seqtool-plugin is used more than once. Remove its duplicate as parameters should be unique. parser = self.make_parser(ctx) /usr/local/lib/python3.13/site-packages/click/core.py:1216: UserWarning: The parameter --disable-seqtool-plugin is used more than once. Remove its duplicate as parameters should be unique. self.parse_args(ctx, args)