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AntonBankevich / LJA

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Crash during "Export to GFA and compressed contigs" step #36

Open YannDussert opened 1 year ago

YannDussert commented 1 year ago

Hi,

First, thanks for developing LJA!

I am trying to run LJA on my HiFi data, using the command: lja -o lja_defPars --diploid -t 30 --reads hifi.fastq.gz

The program crashes at the "Export to GFA and compressed contigs" step, with the following error: terminate called after throwing an instance of 'std::out_of_range' what(): map::at

This looks similar to the crash described by @peterdfields in issue #4 but I am not sure how it was resolved. Unfortunately, I cannot share the raw data. I tried to attach the gzipped dbg.log file, but it is too large for github.

Best regards, Yann

MrTomRod commented 3 months ago

Dear Anton and Yann

I ran into the same issue and can share my raw data!

What is nice is that it's a bacterial genome dataset: only 116 MB of data, so quick to work with.

stdout:

...
00:00:30 28Mb  INFO: Exporting remaining active transitions
00:00:30 28Mb  INFO: Export to Dot
00:00:30 28Mb  INFO: Export to GFA and compressed contigs
Child process crashed

stderr:

terminate called after throwing an instance of 'std::out_of_range'
  what():  map::at

Best, Thomas