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HaploKit / Strainline

Full-length de novo viral haplotype reconstruction from noisy long reads
GNU General Public License v3.0
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Segmentation fault #1

Closed dhcai21 closed 3 years ago

dhcai21 commented 3 years ago

Dear Xiao Luo,

I run Strainline on the data in the "example" folder with the following command:

./Strainline-master/src/strainline.sh -i ./Strainline-master/example/reads.fa -o test -p ont -t 128

But I encountered a problem shown as follow:

[V] using kmer range [8,8] [V] creating KmerLimit for k=8...done. [V] graph structures set up MemUsage(size=8516.46,rss=2419.07,peak=8625.32) ./Strainline-master/src/strainline.sh: line 331: 7834 Segmentation fault (core dumped) daccord -t$threads $las_file reads.dam >> corrected.0.fa

Could you please help me fix this problem?

Thanks!

Dehan

HaploKit commented 3 years ago

Hi, could you try to use fewer cores to run (for example, -t 32 or -t 8) on this small example dataset ? sometimes the read error correction tool 'daccord' causes 'segmentation fault' if using too many cores.

dhcai21 commented 3 years ago

Hi Xiao, Thanks for the reply! I have tried the tool using different numbers of cores, i.e. 1, and 8. But I still have the same problem, the "segmentation fault"

HaploKit commented 3 years ago

Hi, the reason is probably due to the version of daccord. You could have a look at the documentation(I have updated it) of using daccord. You should check your daccord version and make sure use daccord-0.0.10, so, please follow the new instructions and it should work.

dhcai21 commented 3 years ago

Hi Xiao, I reinstall the Daccord with version 0.0.10 according to your advice (I used version 0.0.14 previously). Now I can run the tool normally. Thanks!