File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/fe0e6f0b46b136ba5ae57554247de3/.command.err
Size
4.1 KB
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (rna_s1221_S42)
Attempt

Content

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+ mkdir rna_s1221_S42
+ all_qc -bam rna_s1221_S42.md.bam -beds Twist_rna_exome_AND_fusion_hg38.bed -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz -contamination_bed dbsnp_hg38_contam_sites.bed -output_folder rna_s1221_S42 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai

0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai

153541it [00:00, 1534994.26it/s]
320738it [00:00, 1615528.43it/s][W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai

460613it [00:00, 1627554.34it/s]
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.md.bai
+ merge_qc -folders rna_s1221_S42/rna_s1221_S42.md -output rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv
+ head -n1 rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed rna_s1221_S42/rna_s1221_S42_full_basic_stats.tsv