Flair align fails with pysam libcrypto.so.1.0.0 not found

[vpeddu]

Copy and paste the exact command you tried to run

Run command: flair align --mm_index hs1.mmi -r in.fastq.gz -t 64 --nvrna -o out.flair_align How did you install Flair? conda create -n flair -c conda-forge -c bioconda flair

What happened?

[WARNING] Indexing parameters (-k, -w or -H) overridden by parameters used in the prebuilt index.
[M::main::10.336*1.00] loaded/built the index for 25 target sequence(s)
[M::mm_mapopt_update::12.683*1.00] mid_occ = 892
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 25
[M::mm_idx_stat::13.773*1.00] distinct minimizers: 100277218 (38.70% are singletons); average occurrences: 5.856; average spacing: 5.308; total length: 3117292070
[M::worker_pipeline::73.962*37.82] mapped 378877 sequences
[M::worker_pipeline::85.409*37.91] mapped 158252 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -ax splice --secondary=no -uf -k14 -t 64 /private/groups/kimlab/vikas/refs/hs1.mmi /private/groups/kimlab/vikas/sree/hs1/01_02_18_R94_KRASKO_iPSC.fastq.gz
[M::main] Real time: 86.809 sec; CPU: 3239.415 sec; Peak RSS: 27.767 GB
Traceback (most recent call last):
  File "/private/groups/kimlab/vikas/sree/drna_flair/flair/src/flair/bam2Bed12.py", line 22, in <module>
    from samJuncs import SAM
  File "/private/groups/kimlab/vikas/miniconda/envs/flair/lib/python3.8/site-packages/flair/samJuncs.py", line 23, in <module>
    import pysam
  File "/private/groups/kimlab/vikas/miniconda/envs/flair/lib/python3.8/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
Traceback (most recent call last):
  File "flair/flair.py", line 1097, in <module>
    main()
  File "flair/flair.py", line 1015, in main
    status = align()
  File "flair/flair.py", line 98, in align
    subprocess.check_call(bed_conversion_cmd, stdout=open(args.o+'.bed', 'w'))
  File "/private/groups/kimlab/vikas/miniconda/envs/flair/lib/python3.8/subprocess.py", line 364, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/private/groups/kimlab/vikas/miniconda/envs/flair/bin/python3', '/private/groups/kimlab/vikas/sree/drna_flair/flair/src/flair/bam2Bed12.py', '-i', 'KRASKO.flai_align.bam']' returned non-zero exit status 1.

We know it's ugly but we promise it helps us solve problems faster.

What else do we need to know? It seems like this is an issue stemming from the conda pysam install. Would it be possible to update the pysam versions in the conda recipe?

[icemduru]

is libssl1.0.0 installed on your computer. If not, you can try:

sudo apt install libssl1.0.0

[Jeltje]

@vpeddu please respond to this ticket. The solution by @icemduru should work for you. If it does, please close this ticket. Thanks.