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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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docker run smc++: NotImplementedError: seek not implemented in files compressed by method 1 #244

Open xgdong opened 1 year ago

xgdong commented 1 year ago

I use docker to run smc++ , an error occurs as below, I don't konw what the problem is, anyone has suggestions? 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 4299, in pysam.libcbcf.VariantFile.open File "pysam/libchtslib.pyx", line 516, in pysam.libchtslib.HTSFile.tell NotImplementedError: seek not implemented in files compressed by method 1

xgdong commented 1 year ago

I use docker to run smc++ , an error occurs as below, I don't konw what the problem is, anyone has suggestions? 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 4299, in pysam.libcbcf.VariantFile.open File "pysam/libchtslib.pyx", line 516, in pysam.libchtslib.HTSFile.tell NotImplementedError: seek not implemented in files compressed by method 1

I have solved the issue, the error occurs because the VCF file needs compressed following the BGZF format (needed to be bgzip), not gzip.