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mahulchak / quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
GNU General Public License v3.0
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Is there a way to run quickmerge wrapper in multi-threads? #49

Open ShuChen1986 opened 4 years ago

ShuChen1986 commented 4 years ago

Hi,

I am dealing with a large genome and therefore running quickmerge took a very long time, is there a way to run the quickmerge wrapper in multi-thread to accelerate the process? I check the wrapper and nucmer help manuals, there seems no option for multi-thread.

Shu

mahulchak commented 4 years ago

You can use mummer 4 which uses multi threading. You can run quickmerge manually after that.

On Thu, Nov 21, 2019, 18:15 ShuChen1986 notifications@github.com wrote:

Hi,

I am dealing with a large genome and therefore running quickmerge took a very long time, is there a way to run the quickmerge wrapper in multi-thread to accelerate the process? I check the wrapper and nucmer help manuals, there seems no option for multi-thread.

Shu

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ShuChen1986 commented 4 years ago

You can use mummer 4 which uses multi threading. You can run quickmerge manually after that. … On Thu, Nov 21, 2019, 18:15 ShuChen1986 @.***> wrote: Hi, I am dealing with a large genome and therefore running quickmerge took a very long time, is there a way to run the quickmerge wrapper in multi-thread to accelerate the process? I check the wrapper and nucmer help manuals, there seems no option for multi-thread. Shu — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#49?email_source=notifications&email_token=ABZQH2DOUHMVKI3DONIJFATQU46ANA5CNFSM4JQKWSEKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H3IRY7Q>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZQH2DIOU7YWU4G4LFNMITQU46ANANCNFSM4JQKWSEA .

I used to mummer 4, but multi thread can only used when output format is sam file. Then I used a script sam2delta.py ( https://gist.github.com/malonge/a05da7f99e651ea55e8a4e57a5c4aab1) to convert sam file to delta file, but it gave me the following error:

Traceback (most recent call last):
  File "./sam2delta.py", line 239, in <module>
    write_delta(alns, sam_file + '.delta')
  File "./sam2delta.py", line 140, in write_delta
    f.write('>%s %s %r %r\n' % (aln[0], aln[1], ref_chr_lens[aln[0]], query_len))
KeyError: '001005F'

Could you give me some suggestion on this?

mahulchak commented 4 years ago

sorry for the late response. MUMmer v4 supports multi-threading for both sam and delta. run nucmer like this - nucmer --threads 4 --prefix foo ref.fasta query.fasta [assuming that you are using 4 threads]