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_8DJ-T1-TDNA-1_B23KCHGLT4_1_vs_1136_8DJ-N1-BDNA-1_B23MHTGLT4_1.snv_indel.phased.vep.final.vcf.gz'
INFO: Using tumor sample: 1136_8DJ-T1-TDNA-1_B23KCHGLT4_1
WARNING: Liftover failed for chr1:1649441 (G>A)
WARNING: Liftover failed for chr1:205992745 (G>A)
WARNING: Liftover failed for chr1:248745334 (G>A)
WARNING: Liftover failed for chr3:57366785 (C>T)
WARNING: Liftover failed for chr3:57368202 (C>T)
WARNING: Liftover failed for chr3:57380323 (C>T)
WARNING: Liftover failed for chr3:57386614 (G>A)
WARNING: Liftover failed for chr3:57387092 (G>C)
WARNING: Liftover failed for chr3:57394282 (G>A)
WARNING: Liftover failed for chr7:100957927 (G>A)
WARNING: Liftover failed for chr7:100966592 (G>A)
WARNING: Liftover failed for chr8:143865359 (G>A)
WARNING: Liftover failed for chr9:130320872 (C>T)
WARNING: Liftover failed for chr9:130325895 (G>A)
WARNING: Liftover failed for chr9:130341084 (C>T)
WARNING: Liftover failed for chr9:130341113 (C>T)
WARNING: Liftover failed for chr9:136281593 (C>T)
WARNING: Liftover failed for chr9:136286530 (C>T)
WARNING: Liftover failed for chr11:1174925 (C>T)
WARNING: Liftover failed for chr11:1174926 (C>T)
WARNING: Liftover failed for chr11:1178730 (G>A)
WARNING: Liftover failed for chr11:1181200 (C>T)
WARNING: Liftover failed for chr11:1182156 (C>T)
WARNING: Liftover failed for chr11:1184331 (G>A)
WARNING: Liftover failed for chr11:1184683 (C>T)
WARNING: Liftover failed for chr11:1187818 (C>T)
WARNING: Liftover failed for chr11:1188365 (C>T)
WARNING: Liftover failed for chr11:50033328 (G>A)
WARNING: Liftover failed for chr11:50033508 (C>T)
WARNING: Liftover failed for chr11:71075195 (C>T)
WARNING: Liftover failed for chr17:36457049 (C>T)
INFO: 1136_8DJ — 99360 records scanned, 75895 skipped (non-PASS), 116 skipped (indel/other), 31 liftover failures, 23845 variants written