mahulchak
commented
5 years ago You can check if it is due to file size by running the command with
/usr/bin/time -v
It'll show you the memory usage for the two different assembly sizes.
Generally I don't recommend use of heterozygous assemblies for assembly merging. Better to use the assembly without haplotigs.
On Mon, Jul 22, 2019, 17:40 ViriatoII notifications@github.com wrote:
Hi,
I'm having segmentation fault at the quickmerger stage after using the merge_wrapper. Nucmer and everything before worked fine and created normal outputs, including oneline.fa files.
-rw-r--r-- 1 guerrer QGGP 2456765 Jul 22 13:23 anchor_summary_out.txt -rw-r--r-- 1 guerrer QGGP 1049205219 Jul 22 13:22 hybrid_oneline.fa -rw-r--r-- 1 guerrer QGGP 0 Jul 22 13:23 merged_out.fasta -rw-r--r-- 1 guerrer QGGP 91857760 Jul 22 13:22 out.delta -rw-r--r-- 1 guerrer QGGP 9563554 Jul 22 13:22 out.rq.delta -rw-r--r-- 1 guerrer QGGP 3982704 Jul 22 13:23 param_summary_out.txt -rw-r--r-- 1 guerrer QGGP 1343593069 Jul 22 13:22 self_oneline.fa
The quickmerge error must have to do with my input self_oneline.fa, it's the only new thing.
Now, instead of rerrunning the whole wrapper, I'm just running this command:
quickmerge -d out.rq.delta -q hybrid_oneline.fa -r self_oneline.fa -hco 5.0 -c 1.5 -l 0 -ml 5000 -p out
Results:
File size First line(fasta header) hybrid_oneline.fa 1049205219 >1 self_oneline.fa 845417800 >tig00035160 Success!
hybrid_oneline.fa 1049205219 >1 self_oneline.fa 1343593069 >tig00000003_pilon Segmentation fault (core dumped)
The only difference is the size and origin of the self file. The successful one is a canu assembly after using purge haplotigs to eliminate haplotigs (but without running pillon). The unsuccessful one is a piloned canu assembly but without using purge haplotigs (thus it is heterozygous).
Is my problem derived from the input sizes? Or maybe from heterozygosity?
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Hi,
I'm having segmentation fault at the quickmerger stage after using the merge_wrapper. Nucmer and everything before worked fine and created normal outputs, including oneline.fa files.
The quickmerge error must have to do with my input self_oneline.fa, it's the only new thing.
Now, instead of rerrunning the whole wrapper, I'm just running this command:
Results:
The only difference is the size and origin of the self file. The successful one is a canu assembly after using purge haplotigs to eliminate haplotigs (alternative diploid contigs ). The unsuccessful one is a canu assembly but without using purge haplotigs (thus it is heterozygous/diploid).
Is my problem derived from the input sizes? Or maybe from heterozygosity?