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mummer4 / mummer

Mummer alignment tool
Artistic License 2.0
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feature request: read gzipped genomes #145

Open ctb opened 3 years ago

ctb commented 3 years ago

I've been working on running mummer from within a script (for #144) and it would be super nice if future versions of mummer could read gzipped files without me having to uncompress them first -- e.g. mashmap reads gzipped files natively! (not sure if it requires that the extension be .gz or not)

alekseyzimin commented 3 years ago

Thank you for your suggestion. Reading gzipped genomes is easy to incorporate, but it would break the downstream functionality, as the programs like delta-filter, dnadiff or mummerplot rely in unzipped fasta to be present at the location specified in delta file. It is possible to change all of the programs in the suite, I will look into that.

ctb commented 3 years ago

thanks! I really appreciate the response & thanks again for mummer!

Caiyulu-818 commented 2 years ago

so when i run dnadiff -p 10 ~/data1/LUCY/magdrep21077/SRR10159350bin.26.fa /home/ec2-user/data1/LUCY/refseq/undownr1/GCF_003988655.1_ASM398865v1_genomic.fna.gz Building alignments terminate called after throwing an instance of 'std::runtime_error' what(): Unsupported format ERROR: Failed to run nucmer, aborting.

it cannot read "gz files,how can i solve this problem ,thanks a lot.

alekseyzimin commented 2 years ago

Hello,

At this time mummer does not support gzipped genomes. Due to complications in integration with other software, this feature is not easy to incorporate and at this time it is not a priority. Please gunzip the fasta file and run mummer.

--Aleksey

On Wed, Apr 6, 2022 at 5:06 AM Caiyu @.***> wrote:

so when i run dnadiff -p 10 ~/data1/LUCY/magdrep21077/SRR10159350bin.26.fa /home/ec2-user/data1/LUCY/refseq/undownr1/GCF_003988655.1_ASM398865v1_genomic.fna.gz Building alignments terminate called after throwing an instance of 'std::runtime_error' what(): Unsupported format ERROR: Failed to run nucmer, aborting.

it cannot read "gz files,how can i solve this problem ,thanks a lot.

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