I'm trying to run bwa (0.5.8a, the last version on SourceForge) on a 64-bit box running Enterprise Oracle Linux with colorspace data (using this guide) & am getting an obviously bogus result. These reads are known to align with Bowtie; here is one
First I indexed hg18 in colorspace
Which produced STDERR output which seemed to indicate success
Then I have this code
with the usual sort of STDERR output
with the rather peculiar SAM output of everything looking like the below (i.e. nothing aligned)
Any clue what I did wrong?
Code:
@SRR040290.24278 VAB_ugc_85__100_137__138_121__123_bc_Frag50_solid0032_20090715_ugc_121__1232_543_1118 length=50 T32310003110000202001010330012330302002022323210221 +SRR040290.24278 VAB_ugc_85__100_137__138_121__123_bc_Frag50_solid0032_20090715_ugc_121__1232_543_1118 length=50 !:8>>;=6=<9<9>>799;>::9:7<<=<<<7<:=8;7;:;/,81<)9;:&
Code:
bwa index -a bwtsw -c hg18.fasta > build-cs.sh.out
Code:
[bwa_index] Pack nucleotide FASTA... 41.87 sec [bwa_index] Convert nucleotide PAC to color PAC... 16.71 sec [bwa_index] Reverse the packed sequence... 11.21 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 1675.10 seconds elapse. [bwa_index] Construct BWT for the reverse packed sequence... [bwa_index] 1658.72 seconds elapse. [bwa_index] Update BWT... 12.65 sec [bwa_index] Update reverse BWT... 11.94 sec [bwa_index] Construct SA from BWT and Occ... 616.15 sec [bwa_index] Construct SA from reverse BWT and Occ... 618.90 sec
Code:
bwa aln -c -t 8 ./hg18.fasta test-reads.fastq > test-reads.sai bwa samse ./hg18.fasta test-reads.sai test-reads.fastq > test-reads.sam
Code:
[bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... 0.00 sec [bwa_aln_core] write to the disk... 0.00 sec [bwa_aln_core] 482 sequences have been processed. [bwa_aln_core] convert to sequence coordinate... 3.14 sec [bwa_aln_core] refine gapped alignments... 1.45 sec [bwa_aln_core] print alignments... 0.00 sec [bwa_aln_core] 482 sequences have been processed.
Code:
SRR040290.24278 4 * 0 0 * * 0 0 TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN !:8>>;=6=<9<9>>799;>::9:7<<=<<<7<:=8;7;:;/,81<)9;:& SRR040290.113515 4 * 0 0 * * 0 0 TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN !5;2.25:15/2//77*:.48:9466195.<7949.:9)4)/-,1*1/4,4 SRR040290.129188 4 * 0 0 * * 0 0 TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN !796878778;:<:8:5::95;<331:=397A;7;998)4:<;/,936&9. SRR040290.182661 4 * 0 0 * * 0 0 TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN !:==?A><8>>?<9>>>/>:<?/)?7>3:<<<)3=<>/;::<,<:31<282 SRR040290.188969 4 * 0 0 * * 0 0 TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN !:<:<:?:>>9<<;<<(:57=2@<<<689>>8<<>=9:):8*4)7</<8&,
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