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[morecore] insufficient memory #33
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Hmm that is interesting. Firstly, yes you can still use ragoo.fasta. The SV calling step is independent. I am not sure why Minimap2 is running out of memory. For debugging, you can just run the same or similar command outside of RaGOO. What are you assembling? Thanks |
The reference is a plant genome and to assembled it we used for it PacBio and Hi-C data. On the other hand, the 'Contigs.txt` is a pure 50x Illumina assembly created by SparseAssembler. Additionally, I will run minimap2 manually. Michal |
At this point, if you would like to call SVs, I suggest you do your SV calling manually. You can either use minimap2/paftools or nucmer/assemblytics. If you use paftools, you might as well just write your minimap2 alignments to a PAF file rather than SAM format. I also have a wiki page about this here though you would have to generate your own alignments. |
Hi, The solution was to use Michal |
@malonge I am having a work at some of this in my fork (https://github.com/lucventurini/RaGOO), when I will be done, may I open a pull request? |
@mictadlo glad to hear you have resolved it. @lucventurini absolutely thanks so much for contributing. |
Hi, I'm wondering if the pull request as been done and so if it should work without problem on large genomes? C. |
Hi there, I am currently working on v2, which uses pysam to dramatically reduce the memory requirements. In fact, the memory for small and large genomes should be roughly the same. I am hoping to come out with v2 in the next month or so. I will reopen the issue so that I can send a note when the new version is ready. Thanks |
Hi there, RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag RagTag now uses pysam to query read coverage, so the memory requirement is dramatically reduced. Thanks, |
Hi,
The
Contigs.txt
andNbV1ChF.fasta
are 2.8 G and 2.6G. Minimap2 seems to run out of memory on 2TB machine.How important is the the allignment from
Aligning pseudomolecules to reference
or can ragoo.fasta been used? How much more memory do you think I would need?Thank you in advance,
Michal
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