Hello,

I am currently working on a de novo large genome assembly. In this context I would like to use JELLYFISH.

I have an Error with JELLYFISH:

/data/DataSet/DeNovo/Softs/jellyfish-1.1.11/bin/jellyfish count -m 14 -o /data/DataSet/DeNovo/Softs/pipeline/tempmodif/Preassembly/Quake_annexe/jellyfishCount -c 2 -s 71326 -t 16 /data/DataSet/DeNovo/Softs/pipeline/donneestest/frag_1.fastq /data/DataSet/DeNovo/Softs/pipeline/donneestest/frag_2.fastq
/data/DataSet/DeNovo/Softs/jellyfish-1.1.11/bin/jellyfish dump -c -o /data/DataSet/DeNovo/Softs/pipeline/tempmodif/Preassembly/Quake_annexe/columnformat /data/DataSet/DeNovo/Softs/pipeline/tempmodif/Preassembly/Quake_annexe/jellyfishCount
terminate called after throwing an instance of 'jellyfish::compacted_hash::ErrorReading'
  what():  '/data/DataSet/DeNovo/Softs/pipeline/tempmodif/Preassembly/Quake_annexe/jellyfishCount': File truncated
make: *** [Quake] Abandon (vidange mémoire)

I know that the commands are good because I've already used previously

This means that the problem is related to the program or cluster on which I work.

Do you have a solution or indication to correct this problem?

Cordially

A. GUYOMARD

France