Permission Denied Error with convertInversion.py

[mdbjax]

I've tried to install this on (a) our research cluster, (b) inside a Singularity container, and (c) on my Macbook. All of these methods produce a similar error. I've tried installing this by Conda and from source, both produced the same error. Below is an example of a conda-based execution on my Macbook.

I run ~/miniconda3/envs/inversion/share/manta-1.6.0-0/libexec/convertInversion.py /Users/bradlma/miniconda3/envs/inversion/bin/ ./hg38.fa.gz candidateSV_1.vcf.gz

Traceback (most recent call last): File "/Users/bradlma/miniconda3/envs/inversion/share/manta-1.6.0-0/libexec/convertInversion.py", line 291, in convertInversions(samtools, refFasta, vcfFile, invMateDict) File "/Users/bradlma/miniconda3/envs/inversion/share/manta-1.6.0-0/libexec/convertInversion.py", line 175, in convertInversions vcfRec.chr, vcfRec.pos, vcfRec.pos) File "/Users/bradlma/miniconda3/envs/inversion/share/manta-1.6.0-0/libexec/convertInversion.py", line 121, in getReference samtoolsOut = check_output([samtools, "faidx", refFasta, region]) File "/Users/bradlma/miniconda3/envs/inversion/lib/python2.7/subprocess.py", line 216, in check_output process = Popen(stdout=PIPE, *popenargs, **kwargs) File "/Users/bradlma/miniconda3/envs/inversion/lib/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/Users/bradlma/miniconda3/envs/inversion/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 13] Permission denied

[YiBenqiu]

How did you finally solve this problem? I also encountered this problem with MANTA installed by conda.

[YiBenqiu]

OK, I know why this error occurred. convertInversion.py <samtools path> <reference fasta> <vcf file> The samtools path should contain the character samtools，i.e. /home/username/samtools_path/samtools