Error after while processing paralogs?

[bpeacock44]

Error after while processing paralogs?

[gtonkinhill]

Hi,

It looks like none of the gene sequences have made it to the clustering stage, as indicated by total seq: 0. This is leading to this error and the program crashing.

I would double check your annotation files and ensure they have CDS entries. These are the ones Panaroo makes use of.

[bpeacock44]

I just checked one of the gff files - I assume you mean entries like this one? NODE_1_length_305759_cov_60.148568 Protein Homology CDS 174 1322 . - 0 ID=cds-pgaptmp_001246;Parent=gene-pgaptmp_001246;Name=extdb:pgaptmp_001246;Ontology_term=GO:0006012,GO:0046835,GO:0004335,GO:0005524;gbkey=CDS;gene=galK;go_function=galactokinase activity|0004335||IEA,ATP binding|0005524||IEA;go_process=galactose metabolic process|0006012||IEA,carbohydrate phosphorylation|0046835||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_001713229.1;locus_tag=pgaptmp_001246;product=galactokinase;protein_id=extdb:pgaptmp_001246;transl_table=11

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On Sat, Jan 13, 2024 at 9:32 PM Gerry Tonkin-Hill ***@***.***> wrote: Hi, It looks like none of the gene sequences have made it to the clustering stage, as indicated by total seq: 0. This is leading to this error and the program crashing. I would double check your annotation files and ensure they have CDS entries. These are the ones Panaroo makes use of. — Reply to this email directly, view it on GitHub <#264 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHWZYN5BESONU4V7C3CUQOTYONGUXAVCNFSM6AAAAABBYSQPFSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJQHAZTKNBVGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[bpeacock44]

Just to make sure - I am using this as my input file, which is the gff file followed by the assembly file on each line. This is the correct input? Thank you again.

K12.gff K12.fna
LF_82.gff LF_82.fna
V3_2.gff V3_2.fna
V3_5.gff V3_5.fna

[gtonkinhill]

Hi,

That looks correct to me. There has not been extensive testing on the output of PGAP so it's possible there is a bug in the code.
If possible, it would be very helpful if you could attach a couple of input files (gff/fna pairs) to this issue to help with diagnosing the problem.

[bpeacock44]

Sure thing! I am new to genome annotation so I could very well have done something strange. I've put the files here.

[gtonkinhill]

Thanks very much for that. It looks like your fasta sequence names do not match those given in the gff file.
The sequence names in the fasta are prepended by >lcl|. To address this you can use sed. The following command can be used on your fasta file but note that it works inplace and thus will overwrite the originals.

sed -i 's/>lcl|/>/g' K12.fna

I will look at adding a more informative error message to Panaroo for the next release.

[bpeacock44]

Many thanks again!