Open AFrolicOfFerns opened 3 years ago
I am also having a repeated problem with segmentation fault occurring, but for me, it occurs at purge_dups instead of after get_seqs has started.
FWIW, my genome size is about the same as @AFrolicOfFerns (1.27GB, Aedes aegypti in this case) and heterozygosity might be quite high -- I do not have an estimate. I'm working on getting that.
I have tried running this on two different compute systems, and gotten a segmentation fault on both of them. Is it running out of memory? Or something like that?
Hi there, this is still happening to me on a different assembly. I get "segmentation fault (core dumped) during purge_dups and the dups.bed file does not get written.
Heterozygosity is estimated by kmer analysis to be 1.6% in this species. Repetitive DNA is 65% of the genome.
Here is the coverage graph from the current assembly that this happened on:
And here is the error log from purge_dups: [M::main] finish parsing params [M::main] finish reading hits [M::main] finish reading cutoffs [M::main] finish reading coverages
System: Dell OptiPlex 5070 32 Gb RAM 8-core CPU (9th gen intel core i7-9700 @ 3.00Ghz)
Operating system: Ubuntu 20.04 on Windows Subsystem for Linux 2 - Windows 10
@fishercera I switched to using pseudohaploid and it worked quickly with no issues. I never figured out what was going on here!
Hi @fishercera did you end up switching to pseudo haploid as well or were you able to solve the issue as well?
Hello, I am trying to use purge_dupes on my Nanopore-based genome assembly. Heterozygosity is estimated (using GenomeScope and Illumina data) to be ~3% in this organism, which has a 1C genome size of 1.27Gb. The commands I used are included below - everything ran fine except for get_seqs, which triggered the error message:
Commands used:
And here is the coverage plot, if that helps:![PB covV2](https://user-images.githubusercontent.com/51330684/122117435-d8ec2100-cdf4-11eb-93f5-bd0edfebaa78.png)
It looks to me like hap.fa and purged.fa are started correctly, but they are not completed/ have very small file sizes. Any idea what's going on here? Thanks!