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==> 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.JHcCMZkDxZ
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 23 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 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)