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zengxi-hada / HIVID2

HIVID2 is a tool for detecting virus integration events in the host genome.
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Step 3 was killed after consuming too much memory #1

Open thestarocean opened 1 year ago

thestarocean commented 1 year ago

I was using HIVID2 to investigate virus integration and encountered this problem:

When running station.sh in step 3, the process was killed after a few hours of running.

The kill message displayed as follows:

[Wed Mar 22 21:17:52 2023] Out of memory: Killed process 26095 (perl) total-vm:224358716kB, anon-rss:224333264kB, file-rss:0kB, shmem-rss:0kB, UID:1000 pgtables:439124kB oom_score_adj:0

It seems that new_HBCV_human_soap.pl consumes too much memory. Is there a workaround to avoid this?

zengxi-hada commented 1 year ago

Hi,

In this case, you can split your fastq file into several parts, then run each parts seprately till step3. Then merge the outputs of step3 from each part for each item. Note that do not run step4 at this stage, otherwise the outputs of step3 will be deleted. Here is the output files of step3 you should use in the step4: "reads_assemble/*/trimmo.paired" and "reads_unassemble*/*/*unpaired". When you look at the first couple of lines at the shell script of step4, you will get more sense for this operation (bwa_mem_and_call_integration_sites.sh).

Feel free to continue to post your feedback at here. We will follow-up.

Best,