Bam and Sam don't like my fasta file

[mindlessbrain]

Hello all,

I have a sequence from the yeast s. cerevisiae containing at least 1 SNP. I formatted it into a fasta file using fastx formatter. Its fine if I use it with StandAloneBlast. I get an alignment, and its all fine. Then when I throw it into BAM/SAM, I don't seem to get anything. I tried it out on MAQ, and instead of doing the easyrun I broke it down step by step. When it was time to read in this file it could make the index file, but i got a message saying 0 sequences were loaded, and aborted on the next run. So I think I'm having the same problem with both SAM/BAM and MAQ.

jill@jill-desktop:~/maq/scripts$ maq fasta2bfa /home/jill/maq/Project/yeast.nt /home/jill/maq/Project/yeast.nt.bfa
-- 17 sequences have been converted.
jill@jill-desktop:~/maq/scripts$ maq fastq2bfq /home/jill/maq/Project/yeast.fasta  /home/jill/maq/Project/yeast.fasta.bfq
-- finish writing file '/home/jill/maq/Project/yeast.fasta.bfq'
-- 0 sequences were loaded.
jill@jill-desktop:~/maq/scripts$ maq match /home/jill/maq/Project/yeast.map /home/jill/maq/Project/yeast.nt.bfa /home/jill/maq/Project/yeast.fasta.bfq
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] 0*2 reads loaded.
[ma_longread2read] encoding reads... 0 sequences processed.
maq: match.cc:569: int ma_match(int, char**): Assertion `size_l >= 12 && (size_r == 0 || size_r >= 12)' failed.
Aborted

yeast.fasta is my query, and yeast.nt is my reference.

Here's the first bit of my yeast.fasta

>Yeast
NAGTTGTCATCCAGCTTCCATTACATCCGNNNNNNNNATGCAACTGGATGGAGAATGGCA
AAATANNNNNNNNAGCATAAATTAAAATGAAGGAAATAACACNNNNNNNATACATTCCTA
ATCATTTTTGTTTATTTCNNNNNNNGATCAACTTTTTATTTTTATTTTTATTTTNNNNNN
NGTGTAATGCGGCAAAATGTTAGTGCAGGANNNNNNNTGTTCTTCAAAAAGGCGGAGTGG
CTATGGAANNNNNGAGAATCTATGTTGGTTTATGTTCCGGAAGCNNNNNATCCATCCTTG
TACGATCTGTATGTTTACTCNNNNNATTGCTTTACCTTTTGCATTTTCTTACTGGGNNNN
NACGAAATAAACGCCACATAACAGTATAATGTNNNNNGTCCTGTTCAGACAAATTTTGAG
CGATGCCGNNNNNGCCTATCATTACTGGCCCAATCGGCTTGTTTNNNNNAGGTTATCATC
ACGTATATTGGAGATAATATNNNNNATGTCACTATTATCAACCTATCGATATCGAANNNN
NCAACAATCAGCAAAACTACCAGCAATACAGCCNNNNAGACAATAATTGAACAAATCTTA
TCCTTCTTACCTNATACAATACTGAGCATGAAGTTGCATAGCTTAAGCNATTTCAAGGTT
TTGAATCCGTCGATAGTCTCATCANGTTC

Any hints for me? I've been scratching my head over what the problem could be, and I got nothing.

Thanks so much!

[maubp]

Are you trying to use fastq2bfq on a fasta file?

[sklages]

Have you tried removing the whitespaces in the sequence? This is, by definition, not a sequence base ..