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nghiavtr / FuSeq_WES

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TypeError: _open() got an unexpected keyword argument 'threads' #3

Open dhwani2410 opened 2 years ago

dhwani2410 commented 2 years ago

Hello,

I am trying to run the software using demo data, but it's showing an error.

python fuseq_wes.py --bam FuSeq_WES_testdata/test.bam --gtf UCSC_hg19_wes_contigSize3000_bigLen130000_r100/UCSC_hg19_wes_contigSize3000_bigLen130000_r100.json --outdir test_out/ Traceback (most recent call last): File "/nfs_master/dhwani/softwares/FuSeq_WES_v1.0.0/fuseq_wes.py", line 194, in samfile = pysam.AlignmentFile(args.bam, "rb", threads=8) File "pysam/calignmentfile.pyx", line 340, in pysam.calignmentfile.AlignmentFile.cinit File "pysam/calignmentfile.pyx", line 378, in pysam.calignmentfile.AlignmentFile._open TypeError: _open() got an unexpected keyword argument 'threads'

nghiavtr commented 2 years ago

Hi @dhwani2410,

Thank you for using FuSeq_WEs and I am sorry for the late reply.

We have not seen this error before. However, it is likely you have not installed pysam yet. If so, please install that package (https://pysam.readthedocs.io/en/latest/installation.html) before running.

Best, Nghia

dhwani2410 commented 2 years ago

@nghiavtr i am able to run the code now. The error was with pysam code, as it did not allowed multiple threads