Question: Segmentation fault (core dumped) during vg surject
0
gravatar for LilithElina
9 months ago by
LilithElina10
Germany
LilithElina10 wrote:

I tried to run vg surject on a GAM file I generated with vg map, but the call ended with "Segmentation fault (core dumped)" and the BAM file that was generated is truncated. I generated my graph from whole bacterial genomes and then did the following to index the graph and map my reads to it:

vg mod -X 32 graph.vg | vg mod -M 8 - | vg sort - > graph_mod.vg
vg index -x graph_mod.xg graph_mod.vg
vg prune -k 16 -e 3 graph_mod.vg > graph_prune.vg
vg index -g graph_mod.gcsa -k 16 graph_prune.vg
vg map -d graph_mod -f reads.fastq.gz > graph_reads.gam

This is the call that failed:

vg surject -x graph_mod.xg -b graph_reads.gam > graph_reads.bam

Should I use a different index for this?

vg • 315 views
ADD COMMENTlink modified 9 months ago by glenn.hickey170 • written 9 months ago by LilithElina10
2

Probably running out of memory. How much do you have? You may need to find a machine with more or utilize a high performance computing environment.

ADD REPLYlink written 9 months ago by jared.andrews077.9k

Thank you for the suggestion! I would hav thought that 94G overall would be enough, but maybe you're right and I should switch to the bigger cluster...

ADD REPLYlink written 9 months ago by LilithElina10

I am unfamiliar with the program, but usually most segfaults are the result of OOM errors assuming you've ensured your inputs are valid and the command is being called properly.. Does it say anything else in the error message other than the typical seg fault: core dumped?

ADD REPLYlink written 9 months ago by jared.andrews077.9k

No, sadly that's the whole message. I ran the same function with a different argument to generate a different output and that worked well, so I assume the input is fine.

ADD REPLYlink written 9 months ago by LilithElina10
1
gravatar for glenn.hickey
9 months ago by
glenn.hickey170
glenn.hickey170 wrote:

The commands look okay, so this could be a bug. If you are able to share your data, please raise an issue on Github https://github.com/vgteam/vg/issues/new?assignees=&labels=&template=report-a-bug.md&title= and we' should be able to fix it.

Other things to try: the very latest vg release (if you're not using it already), or having vg map output bam directly with the --surject-to bam option.

ADD COMMENTlink written 9 months ago by glenn.hickey170

The --surject-to bam option in vg map resulted iun exactly the same error. I've tried using a graph with less paths as reference and ended up with another problem, so I'm not sure if the size of the reference is the problem.

ADD REPLYlink written 8 months ago by LilithElina10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1093 users visited in the last hour