minia assembler - counting kmers 'gatb::core::system::Exception'

Question

[thackl]

Hi,

I'm trying to run minia-1.0.3 assemblies for 3Gbp plant genome. During "counting kmers" in dbgh5, I run into gatb::core::system::Exception. Any ideas, what might be the problem or where to look.

dbgh5 \
  -in il-01.fq,il-02.fq,il-03.fq,il-04.fq \
  -kmer-size 31 \
  -out mn-31 \
  -verbose 2 \
  -max-memory 50000 \
  -nb-cores 5

The same happened for -k51 and -k111

| Bank: fasta to binary                                                             |
[------------------------------------------------------ ----------------------------]
| counting kmers                                                                    |
[------terminate called after throwing an instance of 'gatb::core::system::Exception'
/tmp/slurmd/job11884/slurm_script: line 3: 12854 Aborted                 (core dumped) /software/minia/bin/dbgh5 $@

[lomereiter]

Where did you find the 1.0.3 version? The website http://minia.genouest.org/ has 1.6906, where the manual.pdf in the archive is dated October, 20, i.e. pretty recent.

[edrezen]

The current (and future) version of minia now relies on the GATB library, and minia can be downloaded here. The latest version is 1.0.4 (previously misnamed 0.0.1)

The 1.6906 version is in the previous SVN repository; some bugs correction may still be done in this repository but further improvements will be done only on the GATB basis.

[Rayan Chikhi]

Yeah, sorry for the confusion, we're transitioning Minia between the old and the new codebase. The website minia.genouest.org) will be updated shortly to point to the new codebase.

[edrezen]

Hi,

Could you try the 1.0.4 version of minia (20141207)? The 1.0.3 (20140417) is now quite old.

Moreover, v1.0.4 should provide more information if the exception still occurs.

[thackl]

Hi,

just to make sure - I downloaded minia-1.0.4-Linux.tar.gz from GATB website. It extracts to minia-0.1.1. This is the latest version?

[Rayan Chikhi]

Yes

Answer 1

[thackl]

Upgrading to the latest minia-1.0.4 (also referred to as minia-0.1.1) fixed the issue.

Thanks for your help