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==> STAGING COMPLETE (14506 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: B23KGCJLT4
             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.aOdD5dyVuI
       basic_stats | Found 192 full_basics_stats files
       depth_stats | Found 192 depth stats files for all_targets
       depth_stats | Found 192 depth stats files for all_probes
       depth_stats | Found 192 depth stats files for boosted_depth
       depth_stats | Found 192 depth stats files for coding_depth
       depth_stats | Found 192 depth stats files for noncoding_depth
       depth_stats | Found 192 depth stats files for non_boosted_depth
       depth_stats | Found 192 depth stats files for hotspot_depth
       depth_stats | Found 192 depth stats files for foresight_depth
     fragment_size | Found 186 fragment size files
           gc_bias | Found 192 GC bias files for all_targets
           gc_bias | Found 192 GC bias files for all_probes
           gc_bias | Found 192 GC bias files for boosted_depth
           gc_bias | Found 192 GC bias files for coding_depth
           gc_bias | Found 192 GC bias files for noncoding_depth
           gc_bias | Found 192 GC bias files for non_boosted_depth
           gc_bias | Found 192 GC bias files for hotspot_depth
           gc_bias | Found 192 GC bias files for foresight_depth
          mosdepth | Found reports for 192 samples
            picard | Found 192 AlignmentSummaryMetrics reports
            picard | Found 192 HsMetrics reports
            picard | Found 195 InsertSizeMetrics reports
    MarkDuplicates | Skipping MarkDuplicates sample '659_ezg-N1-BDNA-1_B23KGCJLT4_1' as log contained no reads
    MarkDuplicates | Skipping MarkDuplicates sample '1136_181-N1-BDNA-1_B23KGCJLT4_1' as log contained no reads
            picard | Found 190 MarkDuplicates reports
            picard | Found 190 QualityByCycleMetrics reports
            picard | Found 190 QualityScoreDistributionMetrics reports
          samtools | Found 192 stats reports
             fastp | Found 1536 reports
        bclconvert | Found RunInfo.xml file in 23 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 10 but no Demux Stats file, skipping
        bclconvert | Found RunInfo.xml file in 75 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 36 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 62 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 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 56 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 17 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        : B23KGCJLT4_multiqc_report_data
     write_results | Report      : B23KGCJLT4_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)