MaSuRCA runCA failed
0
0
Entering edit mode
3.4 years ago
mreijnders • 0

Hi there,

We are trying to assemble a genome using MaSuRCA and illumina reads + pacbio sequel reads. However, so far it results in over a 100k contigs, so obviously something is going wrong (the actual assembly part i suppose). When looking at the log file, the thing that stands out is the 'runCA failed' message, and a failure from 'consensus.sh' preceding it. We tried assembling it multiple times, and every time with the same error. We're at a loss. Any pointers as to where we might have to look would be greatly appreciated.

/scratch/cluster/monthly/mreijnde/assembly_04/CA.mr.41.15.17.0.029/8-consensus/genome_077 failed -- no .success. /scratch/cluster/monthly/mreijnde/assembly_04/CA.mr.41.15.17.0.029/8-consensus/genome_078 failed -- no .success. /scratch/cluster/monthly/mreijnde/assembly_04/CA.mr.41.15.17.0.029/8-consensus/genome_079 failed -- no .success.
================================================================================

runCA failed.

---------------------------------------- Stack trace:

 at /software/UHTS/Assembler/masurca/3.2.2/bin/../CA8/Linux-amd64/bin/runCA line 1592.
        main::caFailure("23 consensusAfterScaffolder jobs failed; remove /scratch/clus"..., undef) called at /software/UHTS/Assembler/masurca/3.2.2/bin/../CA8/Linux-amd64/bin/runCA line 5735
        main::postScaffolderConsensus() called at /software/UHTS/Assembler/masurca/3.2.2/bin/../CA8/Linux-amd64/bin/runCA line 6510

---------------------------------------- Failure message:

23 consensusAfterScaffolder jobs failed; remove /scratch/cluster/monthly/mreijnde/assembly_04/CA.mr.41.15.17.0.029/8-consensus/consensus.sh to try again
Assembly MaSuRCA • 922 views
ADD COMMENT

Login before adding your answer.

Traffic: 2795 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6