.command.err - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (HCC1395_tumor)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/5e01897dbbce7422dac82047cf5120/.command.err
Size: 1.5 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_PROBE_COUNTS (HCC1395_tumor)
Attempt

Content

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recal.bam.bai
The index file is older than the data file: HCC1395_tumor.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recal.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HCC1395_tumor.recal.bam.bai
Deduplicated 15 probes with identical coordinates
Deduplicated 15 probes with identical coordinates
Loaded 4819 probes across 3366 contigs
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)
Reads: 0 total, 0 skipped (flags/unmapped)
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)
Fragments: 0 total (0 tlen-paired, 0 hash-paired, 0 singletons, 0 discordant, 0 orphans, 0 too large [>5000 bp], 0 duplicates)
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: 3618686 total, 765 skipped (flags/unmapped)
Fragments: 1817976 total (1817315 tlen-paired, 110 hash-paired, 19 singletons, 0 discordant, 532 orphans, 225 too large [>5000 bp], 765992 duplicates)