Error batch-file-temp - Segmentation fault (core dumped)

[Former user]

Hi, I am facing the following error:

Reading inputfile: /tmp/scratch/xxxxx-static/tania/scaffolds_filtered.fasta

Total time used for DB loading: 77.08 s.

...

Score collection done

Sort, output and select k-mer alignments.

Total time for sorting and outputting KMA alignment 0.31 s.

Doing local assemblies of found templates, and output results

/tmp/tmp.XXXiEkrrN/batch-file-temp: line 82: 183 Segmentation fault (core dumped) kma -i /tmp/scratch/xxxxtania/scaffolds_filtered.fasta -o teste_scaffolds.kmaout -t_db access-vpc-cromwell-sxxxxx/db/compress_ncbi_nt_no_env_11jun2019/ncbi_nt_no_env_11jun2019 -t 12 -1t1 -mem_mode -ef

The multifasta input file (approximatelly 11MB) has 545 scaffolds. The largest one's size is 536704 and the smallest one's size is 200. The machine has 250 GB RAM. The KMA version is 1.3.23.

Anybody could help to understand why this error is happening. Thanks a lot.

[ptlcc]

Hi Tania

It might be an error that has been fixed in a later version, there has been some refinement of the code since 1.3.23. The newest version is 1.4.6, can I get you to try that.

Unrelated to the error, I would recommend adding the “-ca” option for long input sequences. As this will allow circular alignments in the cases where the sequences span e.g. oriT.

Best,
Philip