ImportError

[BrendaLee1]

Hi!
I tried the following commands：
singularity exec --bind /usr/lib/locale/
pepper_deepvariant_r0.8.sif
run_pepper_margin_deepvariant call_variant
-b "${INPUT_DIR}/${BAM}"
-f "${INPUT_DIR}/${REF}"
-o "${OUTPUT_DIR}"
-p "${OUTPUT_PREFIX}"
-t "${THREADS}"
--ont_r9_guppy5_sup
There were no output and the error information like below:
from pysam.libchtslib import *
ImportError: /soft/anaconda3/lib/python3.8/site-packages/pysam/../../../././libssl.so.1.1: undefined symbol: EVP_idea_cbc, version OPENSSL_1_1_0
CentOS Linux release 7.6.1810 (Core)

I tried to install openssl independently, but seems not work. Would you please give me some suggestion about this problem?

Thanks!

Best,
BL

[kishwarshafin]

hi @BrendaLee1 ,

Can you please try to install pysam independently to see if you can install pysam?

python3 -m pip install pysam

If this doesn't work due to permission, please try:

python3 -m pip install pysam --user

And please put the full log here so I can help you debug this issue.