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feature request: read gzipped genomes #145
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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. |
thanks! I really appreciate the response & thanks again for mummer! |
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 it cannot read "gz files,how can i solve this problem ,thanks a lot. |
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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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)
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