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

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/74a06117e6dd03e8f50c0de5d7c1e9/.command.err
Size: 6.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:SEQTOOL_QC (659_cRB-T1-TRNA-1_B23WHTKLT4_1)
Attempt
Content

+ mkdir 659_cRB-T1-TRNA-1_B23WHTKLT4_1
+ all_qc -bam 659_cRB-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_cRB-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_cRB-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_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-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_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai

0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai

143090it [00:00, 1410618.03it/s]
296095it [00:00, 1480420.26it/s]
449818it [00:00, 1506251.73it/s]
612766it [00:00, 1554706.69it/s]
779010it [00:00, 1593466.63it/s]
951365it [00:00, 1637633.17it/s]
1125107it [00:00, 1670213.47it/s]
1297858it [00:00, 1688423.82it/s]
1469585it [00:00, 1697060.07it/s]
1642442it [00:01, 1706757.22it/s]
1813123it [00:01, 1702097.73it/s]
1985234it [00:01, 1707852.58it/s]
2157555it [00:01, 1712446.70it/s]
2333240it [00:01, 1725822.81it/s]
2508427it [00:01, 1733646.54it/s]
2685151it [00:01, 1743730.87it/s]
2859528it [00:01, 1741121.54it/s]
3033644it [00:01, 1736302.31it/s]
3209518it [00:01, 1742997.62it/s]
3383823it [00:02, 1728221.87it/s]
3556675it [00:02, 1713730.22it/s]
3728087it [00:02, 1710898.42it/s]
3899202it [00:02, 1709280.64it/s]
4070147it [00:02, 1704590.78it/s]
4243501it [00:02, 1713192.26it/s]
4414834it [00:02, 1707326.92it/s]
4588200it [00:02, 1715159.02it/s]
4761050it [00:02, 1719118.79it/s]
4934300it [00:02, 1723095.26it/s]
5106618it [00:03, 1710566.21it/s]
5277700it [00:03, 1696005.29it/s]
5450703it [00:03, 1706076.53it/s]
5628039it [00:03, 1726089.02it/s]
5805342it [00:03, 1740071.15it/s]
5980643it [00:03, 1743912.97it/s]
6155578it [00:03, 1745481.84it/s]
6332086it [00:03, 1751246.00it/s]
6508037it [00:03, 1753687.35it/s]
6683416it [00:03, 1746031.63it/s][W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai

6858034it [00:04, 1695466.26it/s]
7027895it [00:04, 1691695.16it/s]
7197279it [00:04, 1661457.94it/s]
7363648it [00:04, 1653935.37it/s]
7535984it [00:04, 1674295.99it/s]
7708790it [00:04, 1690159.50it/s]
7885454it [00:04, 1712821.52it/s]
8059696it [00:04, 1721492.16it/s]
8233617it [00:04, 1726760.15it/s]
8409561it [00:04, 1736500.84it/s]
8584161it [00:05, 1739320.04it/s]
8758127it [00:05, 1728692.42it/s]
8931034it [00:05, 1717660.28it/s]
9102837it [00:05, 1702611.61it/s]
9276609it [00:05, 1712995.37it/s]
9450239it [00:05, 1719869.20it/s]
9622262it [00:05, 1704699.00it/s]
9792780it [00:05, 1696580.50it/s]
9966244it [00:05, 1707852.46it/s]
10139586it [00:05, 1715305.98it/s][W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai

10312319it [00:06, 1718839.37it/s]
10486276it [00:06, 1725013.48it/s]
10662966it [00:06, 1737464.83it/s]
10837157it [00:06, 1738616.38it/s]
11012663it [00:06, 1743520.66it/s]
11185169it [00:06, 1707905.83it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-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_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cRB-T1-TRNA-1_B23WHTKLT4_1.md.bai
+ merge_qc -folders 659_cRB-T1-TRNA-1_B23WHTKLT4_1/659_cRB-T1-TRNA-1_B23WHTKLT4_1.md -output 659_cRB-T1-TRNA-1_B23WHTKLT4_1/659_cRB-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv
+ head -n1 659_cRB-T1-TRNA-1_B23WHTKLT4_1/659_cRB-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_cRB-T1-TRNA-1_B23WHTKLT4_1/659_cRB-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv