I am running bwa (0.5.0 (r1200)) on a linux box:
2.6.18-128.4.1.el5 (64)
gcc version 4.1.2
glib 2.5
I run it like this:
ref="./indexes/hsap.fasta"
reads="./fastqs/small.fastq"
align_out="align.sai"
bwa index -a bwtsw $ref
bwa dbwtsw -t 8 $ref $reads > $align_out
bwa samse $ref $align_out $reads > $sam_out
The first problem comes after generating the reference. Bwa is trying
to find:
hsap.fasta.nt.amb
hsap.fasta.nt.ann
hsap.fasta.nt.pac
But the index command generated:
hsap.fasta.amb
hsap.fasta.ann
hsap.fasta.pac
THat is easy to fix, but I would like to know why is doing that.
The other issue is more problematic. When trying to generate
the sam, bwa seems to stay in a loop and it doesn't generate anything.
When monitoring the process, it seems it is reading from a filedescriptor:
0.000000 [ 3bef0c5610] read(5, "", 4096) = 0
0.000106 [ 3bef0c5610] read(5, "", 2467500032) = 0
1.751992 [ 3bef0c5610] read(5, "", 4096) = 0
0.000095 [ 3bef0c5610] read(5, "", 2467500032) = 0
1.753771 [ 3bef0c5610] read(5, "", 4096) = 0
0.000094 [ 3bef0c5610] read(5, "", 2467500032) = 0
1.756972 [ 3bef0c5610] read(5, "", 4096) = 0
0.000092 [ 3bef0c5610] read(5, "", 2467500032) = 0
What do you think is happening?
2.6.18-128.4.1.el5 (64)
gcc version 4.1.2
glib 2.5
I run it like this:
ref="./indexes/hsap.fasta"
reads="./fastqs/small.fastq"
align_out="align.sai"
bwa index -a bwtsw $ref
bwa dbwtsw -t 8 $ref $reads > $align_out
bwa samse $ref $align_out $reads > $sam_out
The first problem comes after generating the reference. Bwa is trying
to find:
hsap.fasta.nt.amb
hsap.fasta.nt.ann
hsap.fasta.nt.pac
But the index command generated:
hsap.fasta.amb
hsap.fasta.ann
hsap.fasta.pac
THat is easy to fix, but I would like to know why is doing that.
The other issue is more problematic. When trying to generate
the sam, bwa seems to stay in a loop and it doesn't generate anything.
When monitoring the process, it seems it is reading from a filedescriptor:
0.000000 [ 3bef0c5610] read(5, "", 4096) = 0
0.000106 [ 3bef0c5610] read(5, "", 2467500032) = 0
1.751992 [ 3bef0c5610] read(5, "", 4096) = 0
0.000095 [ 3bef0c5610] read(5, "", 2467500032) = 0
1.753771 [ 3bef0c5610] read(5, "", 4096) = 0
0.000094 [ 3bef0c5610] read(5, "", 2467500032) = 0
1.756972 [ 3bef0c5610] read(5, "", 4096) = 0
0.000092 [ 3bef0c5610] read(5, "", 2467500032) = 0
What do you think is happening?
Comment