if locus name is too long, the extract step doesn't work

[Zachary-Muscavitch]

I submitted two fasta target files, both are identical except for the name of the sequence. I had longer "gene" names to be easily readable and it wouldn't work. I shortened the length of the gene names, and it seems to now work. I assume this is because no one expected someone to use such a long name. Perhaps consider adding a maximum length to the documentation?

Taxon-Contig_15_Locus_3_gene_B
Taxon-C15_L3_gene_B

best,
Zach

[edgardomortiz]

Hi @Zachary-Muscavitch ,

I can't replicate the issue, and I haven't met this limitation before. Perhaps you can send me the actual sample names you are trying, and maybe the target file too?

Edgardo

[Zachary-Muscavitch]

Sorry. The issue was the in the construction of the target file. It was late and I was changing many things, and thought it was the locus name.

Seems like the issue was an error when I extracted the CDS to make the target file. Some nucleotides were not extracted, in their place were ? characters. I ended up translating the nucleotides into aminoacid sequences. When in amino acid format, the ? in the target file did not throw any errors.

Sorry for the trouble.

Additionally, I have a question about why Ns are introduced into the sequences at the extraction step? Is there a flag I can add to prevent this? It seems to not be associated with the assembly process, as it happens when I use genomes with the FASTA option.