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Old 09-04-2011, 05:13 AM   #17
kwicher
Junior Member
 
Location: Cambridge

Join Date: Jan 2011
Posts: 7
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Thanks.
Here is how I converted the reference genome, indexed it and tried to make the alignment.
- converting genome
/mnt/fastfs/bin/bfast fasta2brg -A 1 -f refseq.fas

- INDEXING
qsub -q cb_quad -b y -e /mnt/fastfs/KW_Temp/bfast -o /mnt/fastfs/KW_Temp/bfast "/mnt/fastfs/bin/bfast index -f /mnt/fastfs/KW_Temp/bfast/refseq.fas -m <for each mask> -w 14 -A 1 -i <mask number>"

MASKS
M1 = 1111111111111111111111
M2 = 111110100111110011111111111
M3 = 10111111011001100011111000111111
M4 = 1111111100101111000001100011111011
M5 = 111111110001111110011111111
M6 = 11111011010011000011000110011111111
M7 = 1111111111110011101111111
M8 = 111011000011111111001111011111
M9 = 1111111111110011101111111
M10 = 1110110001011010011100101111101111

-ALIGNING:
qsub -q cb_quad -b y -e /mnt/fastfs/KW_Temp/bfast -o /mnt/fastfs/KW_Temp/bfast "/mnt/fastfs/bin/bfast match -f /mnt/fastfs/KW_Temp/bfast/refseq.fas -A 1 -r /mnt/fastfs/KW_Temp/input.fastq > /mnt/fastfs/KW_Temp/bfast/output.bmf"

I have done one test:
I extracted 5 seqs from fastq file and run test against this tiny file. It run without the problem.
It is really strange as using "-s 1 -e 5" options on full data set, so in fact providing the same sequences, causes the error reported earlier.

K
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