samtools mpileup Aborted (Core dumped)

Question: samtools mpileup Aborted (Core dumped)

4.1 years ago by

Colombia

I'm just trying to use samtools mpileup and it is aborting with out showing any error for some bacterial genomes, with the file given there are two variants and the program dies.

The error is just:

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Aborted (core dumped)

The reference file (indexed with bwa) is: https://drive.google.com/file/d/0BzPjZ1hM-XWPMmxucnpDUjdpUFE/view?usp=sharing
The sorted bam file is: https://drive.google.com/file/d/0BzPjZ1hM-XWPUWw4NkdhM0E3Vm8/view?usp=sharing

The call is:
samtools mpileup -uf SaureusTCH1516_nt_genome.fasta 446.srt.bam

To obtained the sorted bam file:
First I trimmed pair end reads by quality and if adapters were found.
Second the trimmed reads are splitted in two different files, one for each end of the sequencing data, resulting in files without quality information.
Third I aligned the reads files to the reference with bwa aln and bwa sampe
Fourth I created the sam file with samtools view | sort
And finally i indexed the sorted bam file resulting in the file given in the link.

The version of samtools i'm using is 1.1 using htslib 1.1

Any hints on what i could be doing wrong, or what may be happening?

Thanks in advance

snp samtools • 2.8k views

ADD COMMENT • link •

modified 18 months ago by Biostar ♦♦ 20 • written 4.1 years ago by rafa.rios.50 • 50

4.1 years ago by

Devon Ryan ♦ 88k

Freiburg, Germany

Devon Ryan ♦ 88k wrote:

You have a corrupted alignment (for read #1 of HISEQ:185:HBB8WADXX:2:1105:8685:78337). I haven't determined what's actually wrong with its encoding (well, it's with the auxiliary tags), but you can simply avoid the problem with

samtools mpileup -Ruf SaureusTCH1516_nt_genome.fasta 446.srt.bam

ADD COMMENT • link written 4.1 years ago by Devon Ryan ♦ 88k

This is the 64th read in the file, and I believe the preceding reads were just lucky. I think the problem occurs due to the QUAL being * and that Rafa has encountered bug #320/BAQ recalculation corrupts records without base qualities, which can alternatively be worked around by disabling BAQ recalculation (if appropriate) with -B.

ADD REPLY • link written 4.1 years ago by John Marshall • 1.5k

Interesting, I guess I've never looked at the code for BAQ (I just noticed that the core dumps due to an assert in skip_aux when it's looking for the RG tag).

ADD REPLY • link written 4.1 years ago by Devon Ryan ♦ 88k

Indeed. Like I alluded to in the samtools-help thread linked from bug #320, tracking this down involved quite a lot of not-fun with the debugger :-)

ADD REPLY • link modified 4.1 years ago • written 4.1 years ago by John Marshall • 1.5k

3.1 years ago by

vaibhav.vsk • 0

vaibhav.vsk • 0 wrote:

I did bwa mem human alignment with single end fasta file. I tried running samtools mpileup & i'm getting same error as mentioned in thread as :Aborted (core dumped)

Command used was :
samtools mpileup -g -u -f /hg19/referenceFile/genome.fa MDS03_T_DRR001284_1111_small_fasta-quality_checked.bam > MDS03_T_DRR001284_1111_small_fasta-quality_checked__mpileup

There's no such exact error cause displayed on stdout.I tried solutions & I could get rid of this error using -R and -B options both independently. However there's difference between the variants obtained in vcf file after bcftools.
How to debug the exact cause and which fix to be used either -B or -R?

ADD COMMENT • link written 3.1 years ago by vaibhav.vsk • 0

You can debug this by running the command in gdb. This requires that you be familiar with C, though.

ADD REPLY • link written 3.1 years ago by Devon Ryan ♦ 88k

Are you sure that you have enough Memory for running samtools with this reference? This may be caused simply by the lack of PC resources. Have you previously successfully performed mpileup with this reference on your PC/server?

ADD REPLY • link written 3.1 years ago by Max Ivon • 110

Please log in to add an answer.

Similar posts • Search »