.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (659_Mt-T1-TRNA-1_B23WHTKLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/4c46d740ad408a60ee60e1c58dc20d/.command.err
Size: 6.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (659_Mt-T1-TRNA-1_B23WHTKLT4_1)
Attempt
Content

+ mkdir 659_Mt-T1-TRNA-1_B23WHTKLT4_1
+ all_qc -bam 659_Mt-T1-TRNA-1_B23WHTKLT4_1.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 659_Mt-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.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: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai

0it [00:00, ?it/s]
163128it [00:00, 1630966.58it/s]
331544it [00:00, 1662222.65it/s]
509443it [00:00, 1715507.23it/s]
686902it [00:00, 1738810.82it/s]
865282it [00:00, 1754987.50it/s]
1045125it [00:00, 1769737.87it/s]
1222699it [00:00, 1771678.50it/s]
1399867it [00:00, 1767404.36it/s]
1576610it [00:00, 1762132.82it/s]
1754064it [00:01, 1765779.02it/s]
1934754it [00:01, 1778311.01it/s]
2113155it [00:01, 1780012.77it/s]
2293789it [00:01, 1787955.13it/s]
2472589it [00:01, 1781387.06it/s]
2652026it [00:01, 1785270.86it/s]
2831321it [00:01, 1787399.80it/s]
3010066it [00:01, 1776146.47it/s]
3189775it [00:01, 1782373.66it/s]
3368190it [00:01, 1782883.98it/s]
3546490it [00:02, 1746672.08it/s][W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai

3723304it [00:02, 1752989.83it/s]
3898728it [00:02, 1747303.67it/s]
4074950it [00:02, 1751710.06it/s]
4253942it [00:02, 1763067.92it/s]
4432358it [00:02, 1769340.37it/s]
4611146it [00:02, 1774850.26it/s]
4790190it [00:02, 1779495.76it/s]
4968163it [00:02, 1772885.26it/s]
5147861it [00:02, 1780060.97it/s]
5327500it [00:03, 1784926.54it/s]
5506564it [00:03, 1786617.41it/s]
5685236it [00:03, 1786318.19it/s]
5863875it [00:03, 1779109.87it/s][W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai

6041797it [00:03, 1774736.59it/s]
6219929it [00:03, 1776680.96it/s]
6397604it [00:03, 1772625.40it/s]
6574873it [00:03, 1764800.19it/s]
6751363it [00:03, 1752822.09it/s]
6926664it [00:03, 1732016.05it/s]
7099918it [00:04, 1709061.20it/s]
7270899it [00:04, 1699378.13it/s]
7442724it [00:04, 1704921.67it/s]
7622055it [00:04, 1731086.31it/s]
7801184it [00:04, 1748972.96it/s]
7980918it [00:04, 1763376.38it/s]
8104704it [00:04, 1761351.13it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.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: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23WHTKLT4_1.md.bai
+ merge_qc -folders 659_Mt-T1-TRNA-1_B23WHTKLT4_1/659_Mt-T1-TRNA-1_B23WHTKLT4_1.md -output 659_Mt-T1-TRNA-1_B23WHTKLT4_1/659_Mt-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv
+ head -n1 659_Mt-T1-TRNA-1_B23WHTKLT4_1/659_Mt-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_Mt-T1-TRNA-1_B23WHTKLT4_1/659_Mt-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv