seqan::UnexpectedEnd

[eldariont]

Hi Jongkyu,

when I run Vaquita:
vaquita -cg hg19.fa input.bam > output.vcf

I'm getting the following exception:

[2017-3-2 15:15:51] [START] Split-read analysis
[2017-3-2 15:15:57] [END] Split-read analysis (6 seconds.)
[2017-3-2 15:15:57] [START] Paired-end analysis
[2017-3-2 15:15:57] [END] Paired-end analysis (0 seconds.)
[2017-3-2 15:15:57] [START] Clipped-read analysis
[2017-3-2 15:15:57] [END] Clipped-read analysis (0 seconds.)
[2017-3-2 15:15:57] [END] BREAKPOINT IDENTIFICATION (0 seconds.)
[2017-3-2 15:15:57] Found breakpoints
[2017-3-2 15:15:57] 24428 from split-read evidences.
[2017-3-2 15:15:57] 0 from read-pair evidences.
[2017-3-2 15:15:57] 1708878 from soft-clipped evidences.
[2017-3-2 15:15:57] [START] BREAKPOINT MERGING
[2017-3-2 15:15:57] [START] From split-read evidences.
[2017-3-2 15:15:57] [END] From split-read evidences. (0 seconds.)
[2017-3-2 15:15:57] [START] From read-pair evidences.
[2017-3-2 15:15:57] [END] From read-pair evidences. (0 seconds.)
[2017-3-2 15:15:57] [START] From soft-clipped evidences.
terminate called after throwing an instance of 'seqan::UnexpectedEnd'
  what():  Unexpected end of input.
Aborted

I already tried with different input files and recreated hg19.fa.fai but all with the same result. Any idea why this is happening? 🙂

[xenigmax]

Hi David, thank you for the reporting.

What I think weird is this part since it's not possible.

[2017-3-2 15:15:57] 0 from read-pair evidences

What kind of dataset did you use?
Vaquita needs short & paired-end dataset.
eg. The current version does not support long-reads dataset.

hg19.fa must contain all the reference sequences that were used in making .bam files.
Sometimes it can be different. For example, one can consider mitochondrial genome in alignment while your hg19 does not contain it.

[xenigmax]

Regarding 2 you can check it like this

shell > samtools view -H input.bam

@hd VN:1.5 SO:coordinate
@sq SN:chr10 LN:135534747
@sq SN:chr11 LN:135006516
@sq SN:chr11_gl000202_random LN:40103
.
.
@sq SN:chrX LN:155270560
@sq SN:chrY LN:59373566
@rg ID:1 LB:lib1 PL:illumina SM:20 PU:unit1

All the name after "SN" should be listed like this.

shell> cat hg19.fa | grep ">"
>chr10
>chr11
>chr11_gl000202_random
.
.
>chrX
>chrY

[eldariont]

Thanks for the super quick reply!
Yeah, the cause of the error is that I used long read data. I didn't catch that Vaquita isn't for long reads just yet. So I will try again with short paired end reads.

Thanks again!