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KolmogorovLab / hapdup

Pipeline to convert a haploid assembly into diploid
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--overwrite fails #21

Closed mattloose closed 1 year ago

mattloose commented 1 year ago

[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.

mikolmogorov commented 1 year ago

Oups! Will try to fix it soon.

mikolmogorov commented 1 year ago

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