Problem running mity - undefined symbol __intel_sse2_strcpy

[rkabiljo]

Hello,

I have installed mitt with pip3, python 3.7.4. The installation went fine, but it does not run:

$ mity --h
Traceback (most recent call last):
File "/home/skgtrk2/miniconda3/envs/py374/bin/mity", line 12, in
from mitylib import commands
File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/mitylib/init.py", line 2, in
from .commands import *
File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/mitylib/commands.py", line 13, in
from . import (call, normalise, report, merge)
File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/mitylib/call.py", line 6, in
from .util import tabix, check_missing_file, create_prefix, bam_get_mt_contig, bam_has_RG
File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/mitylib/util.py", line 8, in
import pysam
File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/pysam/init.py", line 4, in
from pysam.libchtslib import *
ImportError: /home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/pysam/libchtslib.cpython-37m-x86_64-linux-gnu.so: undefined symbol: __intel_sse2_strcpy

Have you seen this before?
Thank you

[drmjc]

Hi, I haven't seen this one. It looks related to this issue when using the Intel compiler: https://stackoverflow.com/questions/42611515/undefined-symbol-intel-sse2-strcpy Cheers

…

On Fri, 10 Nov 2023, 3:49 am Renata Kabiljo, ***@***.***> wrote: Hello, I have installed mitt with pip3, python 3.7.4. The installation went fine, but it does not run: $ mity --h Traceback (most recent call last): File "/home/skgtrk2/miniconda3/envs/py374/bin/mity", line 12, in from mitylib import commands File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/mitylib/ *init*.py", line 2, in from .commands import * File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/mitylib/commands.py", line 13, in from . import (call, normalise, report, merge) File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/mitylib/call.py", line 6, in from .util import tabix, check_missing_file, create_prefix, bam_get_mt_contig, bam_has_RG File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/mitylib/util.py", line 8, in import pysam File "/home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/pysam/ *init*.py", line 4, in from pysam.libchtslib import * ImportError: /home/skgtrk2/miniconda3/envs/py374/lib/python3.7/site-packages/pysam/ libchtslib.cpython-37m-x86_64-linux-gnu.so: undefined symbol: __intel_sse2_strcpy Have you seen this before? Thank you — Reply to this email directly, view it on GitHub <#32>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEQQM6RE3ECXTTHKK6HSHTYDUCR5AVCNFSM6AAAAAA7E357P6VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE4DMMBSHA3DONY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>