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wshuai294 / PStrain

Pstrain profiles strains in metagenomics data. It infers strain abundance and genotype for each species. Also, it has a single species mode; where given a BAM and VCF, it can phase the variants for any species.
MIT License
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Auto detection of dependenies #6

Closed yuxiangtan closed 3 years ago

yuxiangtan commented 3 years ago

I put the db and packages into the PStrain folder and it worked for the test.

However, when I was running my own folders, it failed. Especially it will give me error messages began with:

Error! numpy python library not detected!! rm: cannot remove ‘PS_out/C1_WGSerr_r0//metaphlan2//bowtie.out.bz2’: No such file or directory Could not build fai index PS_out/C1_WGSerr_r0//ref//merged_ref.fa.fai

I am very confused about why it worked for test but not any other samples. Could the guideline be more precise in the readme?

Thank you!

Yuxiang

yuxiangtan commented 3 years ago

I fixed this by modify the python2 metaphlan2 to python metaphlan2, because my python2 do not have the required dependencies which were listed in readme only for python3