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

Toni Hermoso Pulido toni.hermoso at crg.cat
Wed Jun 13 15:25:49 BST 2012


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

[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.



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