"Error creating sorted mer list" with progressiveMauve

Question

[sebastien.letort]

Hi everybody,

First try with progressiveMauve, and I got this error.

I'm trying to align two de novo assembly genome of Brassica napus on its reference (850 MB). It seems that something goes wrong on the first steps.

./progressiveMauve --seed-family --seed-weight 41 $REF_FASTA $ASS_PATH/aviso.fa $ASS_PATH/tower.fa > run.log 2> run.err

This list makes reference to memory or version pb for this error. I launched the command on a cluster with a lot of memory.

./progressiveMauve --version
progressiveMauve  build date Feb 13 2015 at 05:57:13

I tried with default size for seed-weight, it didn't change the error.

Any help ?

---

run.log

Storing raw sequence at /tmp/rawseq11609.000
Sequence loaded successfully.
Brassica_napus_v4.1.chromosomes.fasta 850292103 base pairs.
Storing raw sequence at /tmp/rawseq11609.001
Sequence loaded successfully.
aviso.fa 699132284 base pairs.
Storing raw sequence at /tmp/rawseq11609.002
Sequence loaded successfully.
tower.fa 690335263 base pairs.
Creating sorted mer list

---

run.err

Error creating sorted mer list
terminate called after throwing an instance of 'genome::gnException'

(code error 134)

Answer 1

[Sissi]

I know it's been a while but maybe it could help someone else.. I got the same error and then I noticed that I was working as user in a folder with root permission. Moved my folder into my home and everything worked well. Cheers.