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popgenmethods / smcpp

SMC++ infers population history from whole-genome sequence data.
GNU General Public License v3.0
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PermissionError: [Errno 13] could not open variant (vcf) file #254

Open chenchengaaaaa opened 11 months ago

chenchengaaaaa commented 11 months ago

I wanna tranfer the vcf file to the smc file, however i met a errno 13 siad that the smc can't open the vcf file due to have no permmission, so what should i do to sovle this error? my conmand and log were shown at below.

$docker run --rm -v $PWD:/mnt terhorst/smcpp:latest vcf2smc 95.vcf.gz trans LG01 BJ:BJCP_F10

1036 smcpp.commands.vcf2smc WARNING Neither missing cutoff (-c) or mask (-m) has been specified. This means that stretches of the chromosome that do not have any VCF entries (for example, centromeres) will be interpreted as homozygous recessive. 1036 smcpp.commands.vcf2smc INFO Population 1: 1036 smcpp.commands.vcf2smc INFO Distinguished lineages: BJCP_F10:0, BJCP_F10:1 1036 smcpp.commands.vcf2smc INFO Undistinguished lineages: [E::hts_open_format] Failed to open file "95.vcf.gz" : Permission denied Traceback (most recent call last): File "/usr/local/bin/smc++", line 11, in load_entry_point('smcpp==1.15.4.dev18+gca077da.d20210316', 'console_scripts', 'smc++')() File "/usr/local/lib/python3.8/dist-packages/smcpp-1.15.4.dev18+gca077da.d20210316-py3.8-linux-x86_64.egg/smcpp/frontend/console.py", line 26, in main cmds[args.command].main(args) File "/usr/local/lib/python3.8/dist-packages/smcpp-1.15.4.dev18+gca077da.d20210316-py3.8-linux-x86_64.egg/smcpp/commands/vcf2smc.py", line 128, in main vcf = VariantFile(args.vcf) File "pysam/libcbcf.pyx", line 4036, in pysam.libcbcf.VariantFile.init File "pysam/libcbcf.pyx", line 4261, in pysam.libcbcf.VariantFile.open PermissionError: [Errno 13] could not open variant file b'95.vcf.gz': Permission denied

terhorst commented 11 months ago

I think this is an issue with your Docker configuration, see https://stackoverflow.com/questions/24288616/permission-denied-on-accessing-host-directory-in-docker.