Error in BLASR 'name in reference not unique'

Question

[biomagician]

Dear all,

I've tried this:

blasr sx.fa.gz output/genome/ref/seq/celegans.fa.gz -out output/ -unaligned output/unaligned.txt

but got the following error:

[INFO] 2017-06-06T14:18:51 [blasr] started.
Error, reference with name "" in the reference genome is not unique

Can anyone help me, please?

Thanks.

C.

[GenoMax]

Have you checked the fasta headers in your file? Many program ignore text after first white space so may consider the headers non-unique. Replace the spaces with an "_" and see if that helps.

[biomagician]

I have checked the fasta headers in my file. There are exactly 7 fasta headers. They all start with the chromosome numbers:

"I" "II" "III" "IV" "MtDNA" "V" "X"

followed by a space and more text. For example, if I import my genome in R using genome = seqinr::read.fasta('genome.fa'), and type:

names(genome)

I get:

"I" "II" "III" "IV" "MtDNA" "V" "X"

[Brian Bushnell]

Sounds like a bug. Possibly, check to make sure you don't have unnecessary newlines in the middle of the file. But also grep for ">" to see how many there are.