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bihealth / seasnap-pipeline

SeA-SnaP: (Se)q (A)nalysis (Sna)kemake (P)ipeline
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mapping pipeline fails at infer experiment rule due to missing pysam libraries #15

Open mmilek opened 2 years ago

mmilek commented 2 years ago

Current conda_env.yaml installs samtools 1.3.1 and does not handle the shared library libcrypto.so.1.0.0. correctly with pysam.

+ infer_experiment.py -r /fast/projects/cubit/18.12/static_data/annotation/GENCODE/M12/GRCm38/gencode.vM12.chr_scaff.annotation.bed -i mapping/star/P1153_wt3.all_mates/out/star.P1153_wt3.all_mates.bam -q 255
Traceback (most recent call last):
  File "/data/gpfs-1/users/milekm_c/work/miniconda/envs/sea_snap/bin/infer_experiment.py", line 53, in <module>
    from qcmodule import SAM
  File "/data/gpfs-1/users/milekm_c/work/miniconda/envs/sea_snap/lib/python3.9/site-packages/qcmodule/SAM.py", line 22, in <module>
    import pysam
  File "/data/gpfs-1/users/milekm_c/work/miniconda/envs/sea_snap/lib/python3.9/site-packages/pysam/__init__.py", line 5, in <module>
    from pysam.libchtslib import *
ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

Workaround: create environment with conda_env_mapping_sc.yaml in development branch. This will install samtools 1.9 and the proper libraries.