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maickrau / GraphAligner

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Loading graph fail: 'std::out_of_range' #36

Closed Sebastien-Raguideau closed 3 years ago

Sebastien-Raguideau commented 3 years ago

Hello,

I'm trying to use GraphAligner and I get the following :

GraphAligner bioconda 1.0.12-
GraphAligner bioconda 1.0.12-
Load graph from spade_hybrid_assembly/assembly/assembly_graph_with_scaffolds.gfa
terminate called after throwing an instance of 'std::out_of_range'
  what():  stoi
/bin/bash: line 1: 12612 Aborted                 (core dumped) GraphAligner -g spade_hybrid_assembly/assembly/assembly_graph_with_scaffolds2.gfa -f /home/sebr/seb/Database/Fungus_DB/FRE_consensus_2_3_6_7.fas -a spade_hybrid_assembly/graphaligner/18S.gaf -t 100 -x dbg --high-memory

It looks like an issue with loading the graph. So some context, I'm using the conda install and the files from the test folder work. The graph is from a spade assembly and should be quite big, 1 of the component is at 5 millions contigs.

Any idea what could be make it work?

maickrau commented 3 years ago

Hi, could you please upload the graph?

Sebastien-Raguideau commented 3 years ago

Gfa file weight 8Gb, can you debug if I replace nuc sequences by 1 N, this makes the file only 1.3G. Here is a link for that : http://seb.s3.climb.ac.uk/no_seq.gfa I tested and I can replicate the issue with this file.

maickrau commented 3 years ago

GraphAligner had an issue with reading node IDs that are integers but too big to fit in 32 bits. Could you try again with commit ba87396?

maickrau commented 3 years ago

This should now work in version 1.0.13. If it happens again, please re-open or create a new issue.