Segmentation fault

[luciaalvarez95]

Hi!
I am trying to run racon (v1.4.22) to correct the assembly of some nanopore reads (coverage x5). So far I have done the following:

minimap2 -ax map-ont -t 8 reads.fq.gz reads.fq.gz | gzip -1 > reads.paf.gz
miniasm -f reads.fq reads.paf.gz > reads.gfa
awk '$1 ~/S/ {print ">"$2"\n"$3}' reads.gfa > reads.fasta
minimap2 -t 8 reads.fasta reads.fq > reads.gfa1.paf

No problem here, however when I run racon I get this error:

racon -t 8 reads.fq reads.gfa1.paf reads.fasta reads.racon1.fasta
[racon::Polisher::initialize] loaded target sequences 5.985872 s
[racon::Polisher::initialize] loaded sequences 335.045284 s
[racon::Polisher::initialize] loaded overlaps 5.728979 s
[racon::Polisher::initialize] aligning overlaps [===================>] 1939.807444 s

[racon::Polisher::initialize] aligning overlaps [====================] 2037.413755 s
[racon::Polisher::initialize] transformed data into windows 125.536970 s
Segmentation fault (core dumped) nsensus [===========>        ] 813.410991 s

I have increased the threads and I still get the same error. The data I am using is this big:

• reads.fq.gz - 29Gb
• reads.fasta - 2.4Gb
• reads.gfa1.paf - 600Mb

is it a memory issue?

Many thanks

Lucía

[rvaser]

Hi Lucia,
not sure what is causing the problem, can you try v1.4.20 from bioconda? Is there a chance for you to share your data?

Best regards,
Robert