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Old 06-29-2011, 06:52 PM   #1
Junior Member
Location: Melbourne, Australia

Join Date: Feb 2011
Posts: 2
Default problem with indexing using bfast

I'm very new to next-gen sequencing and bioinformatics in general. I'm trying to use bfast to align solid4 colourspace reads to a cDNA sequence. I have completed the following steps:

1) fasta2brg -A 0 -f cDNA.fasta
2) fasta2brg -A 1 -f cDNA.fasta

It is when I attemp step 3 that I encounter a problem:

3) bfast index -A 1 -f cDNA.fa -m 1111111111111111111111 -w 14 -i 1
bfast index -A 1 -f cDNA.fa -m 111110100111110011111111111 -w 14 -i 2
bfast index -A 1 -f cDNA.fa -m 10111111011001100011111000111111 -w 14 -i 3
bfast index -A 1 -f cDNA.fa -m 1111111100101111000001100011111011 -w 14 -i 4
bfast index -A 1 -f cDNA.fa -m 111111110001111110011111111 -w 14 -i 5
bfast index -A 1 -f cDNA.fa -m 11111011010011000011000110011111111 -w 14 -i 6
bfast index -A 1 -f cDNA.fa -m 1111111111110011101111111 -w 14 -i 7
bfast index -A 1 -f cDNA.fa -m 111011000011111111001111011111 -w 14 -i 8
bfast index -A 1 -f cDNA.fa -m 1110110001011010011100101111101111 -w 14 -i 9
bfast index -A 1 -f cDNA.fa -m 111111001000110001011100110001100011111 -w 14 -i 10

The error message I get is:
Checking input parameters supplied by the user ...
Validating fastaFileName cDNA.fa.
Validating tmpDir path ./.
Input arguments look good!
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: cDNA.fa
space: [Color Space]
mask: 1111111111111111111111
depth: 0
hashWidth: 14
indexNumber: 1
repeatMasker: [Not Using]
startContig: 0
startPos: 0
endContig: 2147483647
endPos: 2147483647
exonsFileName: [Not Using]
numThreads: 1
tmpDir: ./
timing: [Not Using]
Reading in reference genome from cDNA.fa.cs.brg.
bfast: RGBinary.c:304: RGBinaryReadBinaryHeader: Assertion `rg->contigs[i].contigNameLength > 0' failed.
/var/spool/torque/mom_priv/jobs/ line 10: 4145 Aborted bfast index -A 1 -f cDNA.fa -m 1111111111111111111111 -w 14 -i 1

Is anyone able to suggest what I might be doing wrong? Any suggestions or assistance would be greatly appreciated.
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Old 06-29-2011, 10:33 PM   #2
Nils Homer
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Location: Boston, MA, USA

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Posts: 1,285

It looks like there is a problem with your input FASTA. Do you have empty lines or empty contigs? Could you post it somewhere for us to take a look?
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Old 06-30-2011, 06:19 PM   #3
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Location: Melbourne, Australia

Join Date: Feb 2011
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Ah, yes I had a gap in my fasta file between the > and the sample name but I have fixed this up and repeated the first 2 steps and now the third step worked. Thanks
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