SAM to BAM conversion error

Question

[jitendoshi2006]

I am trying to convert SAM file to BAM file after genome alignment using bwa-mem on a cluster. I perform genome alignment on a cluster as well. The SAM file generated from bowtie2 works fine and I do not get error but there is problem when I use bwa-mem. I use following command to align my single end reads using bwa-mem

bwa mem –k 10 –v 3 bwa_index filtered_reads.fastq > SAM_output.sam

I run the following command for conversion of SAM to BAM file:

samtools view -b SAM_output.sam -o BAM_output.bam

It shows following error

[W::sam_read1] parse error at line 1
[main_samview] truncated file

I checked some answers from the similar questions but even then I was unable to solve the problem. Any help would be great.

[GenoMax]

Which version of samtools are you using?

[jitendoshi2006]

samtools version 1.2

[swbarnes2]

Shouldn't that bwa mem command line have a bit about where the reference genome is?

Answer 1

[Pierre Lindenbaum]

try

samtools view -Sb  -o BAM_output.bam SAM_output.sam

[jitendoshi2006]

Doesn't work. Gives the same error

[Pierre Lindenbaum]

what is the output of

head SAM_output.sam

[jitendoshi2006]

there is no output. when i run the command, following occurs Job <41483116> is submitted to queue <normal.4h>

when i check for job status bbjobs No jobs found for user_a

there is no output file generated in the directory

[GenoMax]

That means you don't have a file called SAM_output.sam in the directory where you ran the command. Is that file located somewhere else?

[jitendoshi2006]

the file is in the directory where i ran the command, i am sure about it. i just checked the size of the file SAM_output.sam, and it is just 50bytes so i guess there isnt anything inside the file. i do not think that is the size i expect. it should be a huge file. however, when i ran the genome alignment command earlier, the command ran for quite a while after which it generated SAM_output.sam, which is interesting. maybe my genome alignment command/tool has some issue.

[GenoMax]

I was going to ask if your alignment had worked right and it looks like it has not. So you need to go back and investigate that first.