.command.err - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (Sig_18_Blood)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/522fd43f74f0fa23f0133fd7dae56e/.command.err
Size: 1.5 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (Sig_18_Blood)
Attempt

Content

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recal.bam.bai
Deduplicated 15 probes with identical coordinates
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Loaded 4819 probes across 3366 contigs
Reads: 0 total, 0 skipped (flags/unmapped)
Fragments: 0 total (0 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 0 orphans, 0 too large [>5000 bp], 0 duplicates)
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Reads: 0 total, 0 skipped (flags/unmapped)
Fragments: 0 total (0 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 0 orphans, 0 too large [>5000 bp], 0 duplicates)
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
Reads: 0 total, 0 skipped (flags/unmapped)
Fragments: 0 total (0 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 0 orphans, 0 too large [>5000 bp], 0 duplicates)
Reads: 1685487 total, 159 skipped (flags/unmapped)
Fragments: 847166 total (846987 tlen-paired, 3 hash-paired, 13 singletons, 0 discordant, 163 orphans, 83 too large [>5000 bp], 130016 duplicates)