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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/338c684915aa27a98142f0d8b75ab8/1136_7OW-T1-TDNA-1_A23MHWWLT4_1/1136_7OW-T1-TDNA-1_A23MHWWLT4_1.md/gc_bias_qc.xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/736654f8f7baf50aef1775650430a3/NTC_0002_0015_A23MHWWLT4_1/NTC_0002_0015_A23MHWWLT4_1.md/reads_per_target.foresight_clarity_targets_hg38.bed.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/73f93c3777fd5d9e1cf37639afa9c4/1136_3WJ-T1-TDNA-1_A23MHWWLT4_1_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/b78cdcd32102ea2493c938beb2a4da/1136_253-T1-TDNA-1_A23MHWWLT4_1.md.metrics
==> STAGING COMPLETE (3706 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: A23MHWWLT4
             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.Jqsb0jNklH
       basic_stats | Found 48 full_basics_stats files
       depth_stats | Found 48 depth stats files for all_targets
       depth_stats | Found 48 depth stats files for all_probes
       depth_stats | Found 48 depth stats files for boosted_depth
       depth_stats | Found 48 depth stats files for coding_depth
       depth_stats | Found 48 depth stats files for noncoding_depth
       depth_stats | Found 48 depth stats files for non_boosted_depth
       depth_stats | Found 48 depth stats files for hotspot_depth
       depth_stats | Found 48 depth stats files for foresight_depth
     fragment_size | Found 48 fragment size files
           gc_bias | Found 48 GC bias files for all_targets
           gc_bias | Found 48 GC bias files for all_probes
           gc_bias | Found 48 GC bias files for boosted_depth
           gc_bias | Found 48 GC bias files for coding_depth
           gc_bias | Found 48 GC bias files for noncoding_depth
           gc_bias | Found 48 GC bias files for non_boosted_depth
           gc_bias | Found 48 GC bias files for hotspot_depth
           gc_bias | Found 48 GC bias files for foresight_depth
          mosdepth | Found reports for 48 samples
            picard | Found 48 AlignmentSummaryMetrics reports
            picard | Found 48 HsMetrics reports
            picard | Found 49 InsertSizeMetrics reports
            picard | Found 48 MarkDuplicates reports
            picard | Found 48 QualityByCycleMetrics reports
            picard | Found 48 QualityScoreDistributionMetrics reports
          samtools | Found 48 stats reports
             fastp | Found 384 reports
        bclconvert | Found RunInfo.xml file in 75 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 23 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 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 36 but no Demux Stats file, skipping
        bclconvert | Found RunInfo.xml file in 88 but no Demux Stats file, skipping
        bclconvert | Found Demux Stats file in 4 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 30 but no RunInfo.xml file, skipping
        bclconvert | Found Demux Stats file in 17 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 56 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
     write_results | Data        : A23MHWWLT4_multiqc_report_data
     write_results | Report      : A23MHWWLT4_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)