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