Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/183e490a94643caffa4aac4dd1ea46/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/183e490a94643caffa4aac4dd1ea46/.command.run
  Downloading: s3://natera-platform-sandbox/platform-users/sgreer/pipeline-output/sarek_tools_a77_snv_indel__380c4714--20260524-002943/variant_calling/snv_indel/1136_8ER-T1-TDNA-1_A23MCVNLT4_1_vs_1136_8ER-N1-BDNA-1_A23NLN3LT4_1/1136_8ER-T1-TDNA-1_A23MCVNLT4_1_vs_1136_8ER-N1-BDNA-1_A23NLN3LT4_1.snv_indel.phased.vep.final.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/altera_harmonize/liftover/hg38ToHg19.over.chain.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz
==> STAGING COMPLETE (6 inputs)

WARNING: The directory '/home/mambauser/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
INFO: Loaded 550680 positions from pon_tnseq_42_curated_v4.vcf.gz
INFO: Loaded 545 positions from aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
[E::idx_find_and_load] Could not retrieve index file for '1136_8ER-T1-TDNA-1_A23MCVNLT4_1_vs_1136_8ER-N1-BDNA-1_A23NLN3LT4_1.snv_indel.phased.vep.final.vcf.gz'
INFO: Using tumor sample: 1136_8ER-T1-TDNA-1_A23MCVNLT4_1
WARNING: Liftover failed for chr7:100966290 (G>C)
WARNING: Liftover failed for chrX:316900 (C>T)
INFO: 1136_8ER — 29867 records scanned, 29410 skipped (non-PASS), 16 skipped (indel/other), 2 liftover failures, 442 variants written