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rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes
GNU General Public License v3.0
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Running trycylcer cluster under python3.7 #32

Closed AmyNjaaye closed 1 year ago

AmyNjaaye commented 2 years ago

Hi, I’m @AmyNjaaye and curently testing trycycler cluster. I encounter the following error at the Building distance matrix:

Traceback (most recent call last):
  File "/usr/bin/trycycler", line 11, in <module>
    load_entry_point('Trycycler==0.5.3', 'console_scripts', 'trycycler')()
  File "/usr/lib/python3/dist-packages/trycycler/__main__.py", line 41, in main
    cluster(args)
  File "/usr/lib/python3/dist-packages/trycycler/cluster.py", line 41, in cluster
    matrix = distance_matrix(seqs, seq_names, args.distance)
  File "/usr/lib/python3/dist-packages/trycycler/cluster.py", line 234, in distance_matrix
    mash_matrix = get_mash_dist_matrix(seq_names, seqs, distance, indent=False)
  File "/usr/lib/python3/dist-packages/trycycler/mash.py", line 28, in get_mash_dist_matrix
    pos_sketches, neg_sketches = make_mash_sketches(seq_names, seqs, temp_dir)
  File "/usr/lib/python3/dist-packages/trycycler/mash.py", line 69, in make_mash_sketches
    str(fasta_pos)], stderr=dev_null)
  File "/usr/lib/python3.7/subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "/usr/lib/python3.7/subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mash', 'sketch', '-n', '-o', '/tmp/tmpgmibvfqh/A_contig_1_pos.msh', '/tmp/tmpgmibvfqh/A_contig_1_pos.fasta']' died with <Signals.SIGSEGV: 11>.

It seems to be related with the python version. I used the great datasets available on the wiki for testing. Any idea about that error ? Thank you for your response.

Aminata

rrwick commented 2 years ago

Hi Amy,

I don't think the Python version is the problem - 3.7 should be fine. It looks like something has gone wrong when Trycycler tried to run mash sketch, specifically sketching contig_1 of your first assembly. Can you double check that mash works on your system if you run it outside Trycycler? E.g. Just run mash sketch anything.fasta and see if that works. If you get an error, then the problem is with mash and it might need to be reinstalled.

Ryan