get_consensus_gfa.py error

ghost commented 8 years ago

After you having resolved #65 I get an error at last step (get_consensus_gfa.py):

user@myMachine:~/HINGE_all$ get_consensus_gfa.py $PWD pk pkid.G2.graphml pk.consensus.fasta 
Traceback (most recent call last):
  File "/home/bioinf/Software/HINGE/scripts/get_consensus_gfa.py", line 62, in <module>
    nodes_to_keep = [x for x in g.nodes() if consensus_contigs[g.node[x]['contig_id']] != '' ]
KeyError: 'contig_id'

AND I don't know what this means exactly and if it is related to this problem - HPC.daligner gives me after successful run:

...
# Check level 2 .las files jobs (1) (optional but recommended)
LAcheck -vS draft pk draft.pk
  **pk: Read indices out of range
  draft.pk: Read indices out of range**
# Remove level 1 .las files
rm L1.1.1.las L1.1.2.las L1.1. ...

govinda-kamath commented 8 years ago

Hi @MichaelsGITIGIT,

Can you give us the pkid.G2.graphml and draft_map.txt? Neither of these have any sequence information.

ghost commented 8 years ago

Here you go ...

draft_map.txt

pkid.G2.zip

govinda-kamath commented 8 years ago

It looks like the problem here is with pkid_draft.graphml. Could you give us that? It also contains no sequence information.

ghost commented 8 years ago

Here you go... I also provide you with draft_map.txt and pkid.G2.graphml again, since I did rerun everything:

error_hinge.zip

govinda-kamath commented 8 years ago

@ilanshom has fixed this in the latest version. Let us know if the problem persists!

HingeAssembler / HINGE

get_consensus_gfa.py error #75