prophyle_assignment: not enough values to unpack (expected 2, got 1)

[karel-brinda]

[prophyle] 2018-05-31 23:47:04 Shell command: make -j -s -C /home/kb219/miniconda/envs/p/lib/python3.6/site-packages/prophyle
klcp_loading    0.17s
Traceback (most recent call last):
  File "/home/kb219/miniconda/envs/p/bin/prophyle_assignment.py", line 11, in <module>
    load_entry_point('prophyle==0.3.2.0', 'console_scripts', 'prophyle_assignment.py')()
  File "/home/kb219/miniconda/envs/p/lib/python3.6/site-packages/prophyle/prophyle_assignment.py", line 812, in main
    kmer_lca=args.kmer_lca,
  File "/home/kb219/miniconda/envs/p/lib/python3.6/site-packages/prophyle/prophyle_assignment.py", line 719, in assign_all_reads
    assignment.process_read(krakline, form=form, measure=measure)
  File "/home/kb219/miniconda/envs/p/lib/python3.6/site-packages/prophyle/prophyle_assignment.py", line 105, in process_read
    self.krakline_parser.parse_krakline(krakline)
  File "/home/kb219/miniconda/envs/p/lib/python3.6/site-packages/prophyle/prophyle_assignment.py", line 637, in parse_krakline
    (ids, count) = block.split(":")
ValueError: not enough values to unpack (expected 2, got 1)

[rchikhi]

I get that bug too when trying to run prophyle giving a whole bacterial genome as input. This isn't a use case for the tool, right?

[karel-brinda]

How Rayan, could you please update to the commit b55e026? It should be fixed there.

[karel-brinda]

It's not a typical use case, but this is not the reason why it's crashing. There's a problem with fixed buffer sizes in one of the subprograms. The fix in b55e026 doesn't address the problem, but makes ProPhyle not crash when this happens.

[rchikhi]

Using that commit, no more crash. I can even confirm that the resulting classification of that long sequence is satisfactory. Thanks.