--overwrite fails

[mattloose]

[2022-11-03 20:16:22] INFO: Filtering alignments
Traceback (most recent call last):
File "/data/test_data/GIT/hapdup/hapdup.py", line 24, in
sys.exit(main())
File "/data/test_data/GIT/hapdup/hapdup/main.py", line 153, in main
filter_alignments_parallel(args.bam, filtered_bam, min(args.threads, 30),
File "/data/test_data/GIT/hapdup/hapdup/filter_misplaced_alignments.py", line 188, in filter_alignments_parallel
pysam.merge("-@", str(num_threads), bam_out, *bams_to_merge)
File "/home/plzmwl/anaconda3/envs/hapdup/lib/python3.8/site-packages/pysam/utils.py", line 69, in call
raise SamtoolsError(
pysam.utils.SamtoolsError: "samtools returned with error 1: stdout=, stderr=[bam_merge] File 'hapdup/filtered.bam' exists. Please apply '-f' to overwrite. Abort.\n"

Looks as though when you run with --overwrite the command is not being correctly passed through to sub processes.

[fenderglass]

Oups! Will try to fix it soon.

[fenderglass]

Just pushed a commit that should fix the problem. Haven't updated the docker image yet, but looks like you are using source builds.. Let me know if that works!

Misha