Segmentation fault (Core dumped)

[lborcard]

Dear authors,

Thank you for your work, I was testing your software on several datasets and I obtained this error message:

[raven::] loaded 9004 sequences 0.110631s
[raven::Graph::Construct] minimized 0 - 9004 / 9004 0.060756s
[raven::Graph::Construct] mapped sequences 77.204137s
[raven::Graph::Construct] annotated piles 0.150998s
[raven::Graph::Construct] removed contained sequences 0.000134s
Segmentation fault (core dumped)

I used your software with other datasets and it did not raise the same error. All datasets were from amplicons of sizes 400bp to 1200bp. Is it not adapted to small amplicons?

Is there any way to tweak the parameters to get it to work with such samples?

best,

Loïc

[monsanto-pinheiro]

I had the same problem, with datasets with sizes between [400-700]. The solution is proposed on #70 but, at the end, does not create any contig.

I tweak some values, "void Pile::FindValidRegion(std::uint16_t coverage)" and "kPSS" inside the code, but I'm not feeling confident about the results. With the decrease of coverage and kPSS, some contigs were created on this kind of datasets. Datasets: ERR4082025 and ERR4082026

[EricDeveaud]

same here with embeded dataset

rpm_maker:raven/raven-1.8.1 > make VERBOSE=x -C /opt/gensoft/tests/raven/1.8.1/
make: Entering directory '/opt/gensoft/tests/raven/1.8.1'
rm -f err out*  core.* in
sh test.sh
+ DAT=../../datas/raven
+ raven -h
+ raven ../../datas/raven/ERA476754.fastq.gz
+ raven ../../datas/raven/NC_001416.fasta.gz
test.sh: line 12:  7906 Segmentation fault      (core dumped) raven ${DAT}/NC_001416.fasta.gz > out 2> err
+ exit 1

and as @monsanto-pinheiro if #70 applied, no more egfault, but empty outpout

Eric

[EricDeveaud]

Hello,

same situation (segmentation fault) with tagged 1.8.3 version same with master

build-nv [rpm]:RavenTest/data > pwd
/opt/gensoft/src/raven/raven-1.8.3/RavenTest/data
build-nv [rpm]:RavenTest/data > raven NC_001416.fasta.gz
[raven::] loaded 1 sequences 0.001676s
[raven::Graph::Construct] minimized 0 - 1 / 1 0.045695s
[raven::Graph::Construct] mapped sequences 0.002303s
[raven::Graph::Construct] annotated piles 0.000020s
[raven::Graph::Construct] removed contained sequences 0.000004s
Segmentation fault