miniasm segmentation fault about miniasm HOT 8 OPEN

Forgot to mention the version of miniasm is 0.2-r128

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Update:

I used the new version 0.3_r179. It seem like when data use small memory, such as 80GB, it works fine. However, when data needs big memory, it still fail with segmentation fault. And I was able to repeat the error and noticed that both time the error happened when memory usage reach to about 120GB, yet I have total 240GB memory.

......
[M::main] CMD: minimap2 -x ava-pb -t 28 /efs/fasta/merged_BAC_PACBIO.filtered.fasta /efs/fasta/merged_BAC_PACBIO.filtered.fasta
[M::main] Real time: 30832.901 sec; CPU: 674449.293 sec
31699 Segmentation fault (core dumped) /home/biodocker/miniasm//miniasm -f /efs/fasta/merged_BAC_PACBIO.filtered.fasta /efs/fasta//miniasm/BAC_corn.paf.gz -Rc2 > /efs/fasta/miniasm/BAC_corn.gfa 2> /efs/fasta//miniasm/step2.err

Is there any other way to decrease the memory useage?

Best,
Xin

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I run into same error when using miniasm with large datasets. In case, it consistently fails around 256GB memory beyond a certain file size.

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same here, I get the Segmentation fault error when the process uses about half of the total memory (in my case ~65 GB out of 126). My version is 0.3-r179 as well.

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@lh3 does miniasm have a upper limitation of what it can actually read? I am trying to assemble a gzipped 4Tb PAF file and it looks there is a hard cap at around 2Tb memory usage.

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We are experiencing this as well. we have 1TB of RAM and the segfault consistently occurs around the halfway point like others here; which is around of 550GB used for us. We also use a gzipped paf file. We were using 0.2-r168-dirty and updated to the current release and the issue still occurs.

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@mr--white set -m to something between 1000-2000 during your minimap2 overlap. Resulting PAF file should much smaller and miniasm run through.

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am having the same problem anyone tried out what at @mr--white suggested to see if it worked?
am working with a 734 GB .paf.gz file, wouldnt want to repeat this step if it doesent work.

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