Entering edit mode
4.6 years ago
nsapoval
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10
I have a fasta file consisting of 5 concatenated E.coli genomes. I then simulate paired end reads with wgsim aiming for 25x coverage. Hence I get about 690K+ reads in total. Now, when I run abyss-pe (I am using ABySS 2.0.2) on this dataset as
abyss-pe name=test k=50 in='seq.read1.fq seq.read2.fq'
My run fails after about 7 minutes with the following error message:
abyss-scaffold: scaffold.cc:504: bool isOverlap(const DistanceEst&): Assertion 'd.distance < 0' failed.
I have ran on smaller read datasets, up to 625K reads, and ABySS seemed to handle those perfectly fine. I have also tried changing k-mer size to 75, but I get exactly the same error. Has anyone seen this before or has any ideas how to go around this issue?
Is there any specific reason for using ~3 years old version of the tool? Could you try the same assembly with the latest version of the tool?
I have upgraded to ABySS 2.2.3 and rerun the scenario. The original error went away, but the run still fails, with the following message.
error: no edge 7515- -> 40850+warning: the head of 40850+ does not match the tail of the previous contigAlthough the issues with running in the default mode persisted, I was able to successfully generate unitigs by using
abyss-pe name=test k=50 in='seq.read1.fq seq.read2.fq' unitigsSince this was the original goal for which I was using ABySS, I am closing this question.
Hello nsapoval!
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Resolved the issue as far as I was concerned. The original issue still remains open.
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