questions when using vcf2smc

[Yafei-Guo-coder]

hi dear @terhorst：
when i use the vcf2smc with your example.csv, with the commond below:
smc++ vcf2smc example.vcf.gz chr1.smc.gz pop1:msp_0,msp_1,msp_2,msp_3,msp_4
and it returns some error information:

Traceback (most recent call last):
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/bin/smc++", line 11, in
load_entry_point('smcpp==1.15.3', 'console_scripts', 'smc++')()
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/pkg_resources/init.py", line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/pkg_resources/init.py", line 2852, in load_entry_point
return ep.load()
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/pkg_resources/init.py", line 2443, in load
return self.resolve()
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/pkg_resources/init.py", line 2449, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/frontend/console.py", line 3, in
from .. import commands, logging, version, defaults, _smcpp
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/commands/init.py", line 1, in
from . import vcf2smc, estimate, split, chunk, cite, plot,
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/smcpp/commands/vcf2smc.py", line 7, in
from pysam import VariantFile, TabixFile
File "/data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/pysam/init.py", line 5, in
from pysam.libchtslib import *
ImportError: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /data1/home/yafei/Software/anaconda3/envs/smcpp/lib/python3.7/site-packages/pysam/libchtslib.cpython-37m-x86_64-linux-gnu.so)

and i can not get what they mean, so if it possible for you to nicely help me with this, thanks in advance!

Yafei

[terhorst]

Are you running smc++ on a different machine than the one you compiled it on?

[Fengyaa]

Hi, have you solved this? I met the same error.

[terhorst]

@Fengyaa The original poster never responded so I don't know what the issue is. There seem to be some other reports of similar bugs related to this package,for example kundajelab/atac_dnase_pipelines#33. You might try manually reinstalling the pysam package.

[Fengyaa]

@terhorst Thank you for the reply. I met the problem when after installing by conda.
"ImportError: /lib64/libm.so.6: version GLIBC_2.29' not found " I am using a cluster and I don't have too much experience to update the glibc library. So I tried with bash smcpp-1.15.2-Linux-x86_64.sh, then "ImportError: /lib64/libc.so.6: version GLIBC_2.14' not found" occurred when run vcf2smc. I loaded the glibc2.14 library, but it sleeps at the loading data stage like this:
19827 smcpp.analysis.base INFO theta: 0.000100
19829 smcpp.analysis.base INFO rho: 0.000100
19829 smcpp.data_filter INFO Loading data...

Finally, I tried installing a previous version (v1.13.1), it runs smoothly for now. But it sleeps after I load the glibc2.14 library. Maybe something incompatible with the glibc2.14?