Error when sorting a SAM file with samtools sort, sam file created with bwa mem

Question

[mpyle]

Hi, I created a .sam file using bwa mem, but when I try to sort the file using samtools sort I get this error:

[W::sam_read1] parse error at line 1
[bam_sort_core] truncated file. Aborting.

There is probably something worng with the header but I am not sure what. This is the first few lines of the sam file:

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 100378 sequences (10000099 bp)...
[M::process] read 100394 sequences (10000125 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 34952, 9, 3)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (175, 212, 292)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 526)
[M::mem_pestat] mean and std.dev: (235.46, 84.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 643)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 100378 reads in 43.264 CPU sec, 43.255 real sec
@SQ     SN:2L   LN:23513712
@SQ     SN:2R   LN:25286936
@SQ     SN:3L   LN:28110227

Please let me know if you see what the problem is so I can get past this. Thank you.

Answer 1

[Devon Ryan]

When you redirected the output of bwa mem, you redirected stderr to the same file as stdout. You want something like:

bwa mem ...stuff... > file.sam

Do not use 2>&1 anywhere, which appears to be what you did.

[mpyle]

I ran the bwa command as a job and so I never specified > file.sam at the end of the command because the sam file ends up just telling you the job number, this is the command I used:

sqsub -q serial -o aligned/drosophila2.sam -r 6h --mpp=16g bwa mem ref/drosophila_melanogaster_genome.fna reads/SRR3931619_1_val_1.fq.gz reads/SRR3931619_2_val_2.fq.gz

Instead I had to specify the output at the beginning

[Devon Ryan]

Perhaps you need a -e aligned/drosophila2.txtoption too. Either way, it's the fact that stderr is getting sent to stdout that's causing your problem.