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kishwarshafin / pepper

PEPPER-Margin-DeepVariant
MIT License
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ImportError #159

Closed BrendaLee1 closed 2 years ago

BrendaLee1 commented 2 years ago

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 commented 2 years ago

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.