error with BWA

[gigigou]

I try to use BWA to align some SOLiD reads.
1. I build the index
bwa index -c -a is ecoli.fa

2. I convert the csfasta and correspond qual file into fastq with solid2fastq.pl supplied by BWA(for test, very small, 50000 reads).

3. I try to align the reads to the ref
bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq map.sai
It gives some strange information as follow:

lane@LanePC[bwa] bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq map.sai
(here are some strange symbols)
(here are some strange symbols too)
[bwa_aln_core] calculate SA coordinate... 0.03 sec
[bwa_aln_core] write to the disk... ���� 0.01 sec
[bwa_aln_core] 25000 sequences have been processed.

But there is no output file.
The BWA version is 0.5.9-r16
Does anyone know why?
Thanks a lot.

[kaboroevich]

lane@LanePC[bwa] bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq map.sai
(here are some strange symbols)
(here are some strange symbols too)
[bwa_aln_core] calculate SA coordinate... 0.03 sec
[bwa_aln_core] write to the disk... ���� 0.01 sec
[bwa_aln_core] 25000 sequences have been processed.

Those "strange symbols" are your output. You need to direct stdout into the map.sai file

Try:

bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq [B]>[/B] map.sai

[TonyBrooks]

I've just started with BWA too.
I think you need to include a ">" in there somewhere. If you look at the BWA manual the command should be

bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc] [-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> > <out.sai>

So, maybe you could try to run

bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq > map.sai

I think your strange symbols are the data that should be going into the sai file but withouth the > they are being displayed in the terminal.

[gigigou]

I've just started with BWA too.
I think you need to include a ">" in there somewhere. If you look at the BWA manual the command should be

bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc] [-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> > <out.sai>

So, maybe you could try to run

bwa aln -n 3 -t 4 -M 3 -c ecoli.fa t_ecoli.fastq > map.sai

I think your strange symbols are the data that should be going into the sai file but withouth the > they are being displayed in the terminal.

YES!
You are right. I mistaken that ">" as the one quotes the file name which is unnecessary, so I didn't type it.
But there is another problem: I have 50000 reads, why did it only process 25000 reads? And in the final sam file no read is aligned. All the reads have a flag 4 which corresponds to unmapped.
Thank you!