error: alignment contains sequences of unequal length

[rderelle]

Hi,

I have generated an alignment between 2 genomes using progressiveMauve (default parameters) and I'm now trying to extract SNPs using snp-sites.

My issue is that I get the error message: '' Alignment my_ali contains sequences of unequal length. Expected length is 42875 but got 42876 in sequence ''

However both sequences have a length of 42876, but both sequences have 1 indel '-'.

any idea about how to fix that ?

thanks
Romain

[dbrami]

I'm getting the same error while trying to extract SNPs from MAFFT alignments of coronavirus, courtesy of GISAID

(pangenomics) ubuntu@ip-172-31-29-49:~/covid19/vcf$ snp-sites -v -o GISAID0201 ../gisaid_hcov-19_2021_01_30_08.fasta.gz
Alignment ../gisaid_hcov-19_2021_01_30_08.fasta.gz contains sequences of unequal length. Expected length is 29766 but got 29768 in sequence hCoV-19/Japan/PG-9988/2020|EPI_ISL_902711|2020-07

Also, wasn't there an option to output a VCF per sample?

[Logan1x]

@rderelle @dbrami got any solution for this? any other tool or something?

[rderelle]

@Logan1x
I have abandoned Mauve, which doesn't seem to work well.
It is actually easy to get a list of SNPs from Minimap2 (using third party pgm provided in the same package) or GSalign (directly from the pgm).

cheers

[dbrami]

Sanger iInstitute doesn’t support this software and its the bug fix anymore and original authors left so no issue resolution in sight.

On Wed, Mar 24, 2021 at 9:08 AM romain derelle ***@***.***> wrote: @Logan1x <https://github.com/Logan1x> I have abandoned Mauve, which doesn't seem to work well. It is however easy to get a list of SNPs from Minimap2 (using third party pgm provided in the same package) or GSalign (directly from the pgm). cheers — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#101 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABH7W5ROJKPKAB2OU7SJNLTFIFAHANCNFSM4X6Y6E5Q> .

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[Albertzhuo123]

fxxk！

[ksw9]

Hi,
I'm wondering if folks might recommend a similar tool to extract SNPs from a multiple sequence alignment to generate an alignment of SNPs only? I am similarly running into errors with Expected length although I have confirmed that sequences are the same length.

Thank you in advance!

[ankeetkumar]

Hi,

Did anybody find solution?

Thanks

[Albertzhuo123]

Thank you for your prompt reply.I am no longer engaged in bioinformatics research. 获取Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: anamatgu ***@***.***> Sent: Monday, May 13, 2024 9:19:17 PM To: sanger-pathogens/snp-sites ***@***.***> Cc: Albertzhuo123 ***@***.***>; Comment ***@***.***> Subject: Re: [sanger-pathogens/snp-sites] error: alignment contains sequences of unequal length (#101) Hi, I've just come across the same issue and managed to solve it. When progressiveMauve outputs a multifasta it always adds the symbol '=' in the last line of the file. If this symbol is removed, snp-sites runs fine. Cheers ― Reply to this email directly, view it on GitHub<#101 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AVQATYDD256WKWAUHYZJWG3ZCC4VLAVCNFSM4X6Y6E52U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TEMJQG42TMMBSHE2Q>. You are receiving this because you commented.Message ID: ***@***.***>