[ensembl-dev] Problem with formatdb and several pep FASTA files

[Toni Hermoso Pulido]

Hello,

there seems to be a problem with a few FASTA pep files of some
organisms when performing a formatdb (2.2.25 and 2.2.26 tested):

$ blast/blast-2.2.26/bin/formatdb -i Mus_musculus.NCBIM37.67.pep.all.fa
[formatdb] WARNING: Cannot add sequence number 19278
(lcl|19278_Mus_musculus.NCBIM37.67.pep.all.) because it has
zero-length.

[formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.

This happens with empty FASTA, in this case:
>ENSMUSP00000118372 pep:known chromosome:NCBIM37:4:117507600:117515714:1 gene:ENSMUSG00000028542 transcript:ENSMUST00000151316 gene_biotype:protein_coding transcript_biotype:protein_coding

I haven't experienced a similar issue in the past.

Best,

Toni