Sam to Bam Conversion Failing ****

[AnushaC]

Hi All ,
Can any one please clarify why samtools view is failing .
I am writing shell script like this

#!/bin/bash
#PBS -l nodes=2pn=2
for files in *.sra
do
OUT=(${files%.sra}.bam)
ref=($"/raid/references-and-indexes/hg19/bwa/hg19.fa")
fq=$(fastq-dump $files)
# Main code

bwa aln -t 8 $ref $fq|bwa samse $ref - $fq -|samtools view -bSh - /raid/development/anusha/python_test/shelltest/fetalbrain_bam/$OUT
done
I tried different combination for view like -bS
-Shu
by using the option -o still is failing
the code is working pretty fine till point of samtools view
I am getting following error many times and creating empty bam files
bwa_seq_open] fail to open file 'Written' : No such file or directory
[fread] Unexpected end of file
[samopen] no @SQ lines in the header.
[main_samview] random alignment retrieval only works for indexed BAM files.

[bam_header_read] EOF marker is absent. The input is probably truncated.

I am not understanding why this is failing

Thanks in advance ,
Anusha.Ch

[gringer]

samtools view -bSh -  /raid/development/anusha/python_test/shelltest/fetalbrain_bam/$OUT

Assuming BWA is producing a properly-formatted SAM file as output (which I'm doubtful of, given the error messages), it looks like you're not specifying the input/output files correctly. Samtools view takes a single non-option parameter (the input file name, or '-' for standard input), and the output (default to standard out) can be redirected to a different file using the '-o' parameter.

So, there are two ways to output to a file (instead of standard out):

samtools view [options] <input> -o <output> # redirect using samtools 
samtools view [options] <input> > <output> # redirect using the shell

Subsituting in the bits from your code for these two options:

samtools view -bSh  - -o /raid/development/anusha/python_test/shelltest/fetalbrain_bam/$OUT # note two dashes separated by a space
samtools view -bSh  - > /raid/development/anusha/python_test/shelltest/fetalbrain_bam/$OUT

Of course, that all assumes your other options are correct. If you're sending output to a binary BAM file (option -b), then you don't need to include the SAM header (option -h), because you can't have a BAM file without a header.