vg call: Found pileup for nonexistent edge

[ChriKub]

Hi, I'm trying to call variation from a flat vg graph using PacBio ccs reads, but the vg call fails:

Reading input graph Computing augmented graph terminate called after throwing an instance of 'std::runtime_error' what(): Found pileup for nonexistent edge {"from": 15592, "to": 15592, "from_start": true, "to_end": true}

Here are the commands I used:

vg index -x TAIR_flat_Chr1.xg -g TAIR_flat_Chr1.gcsa -t 40 -k 11 TAIR_flat_Chr1.vg vg map -t 40 -x TAIR_flat_Chr1.xg -g TAIR_flat_Chr1.gcsa -f errorRead.fastq > errorRead.gam vg pileup -p -t 20 -v TAIR_flat_Chr1.vg errorRead.gam > errorRead.gam.vgpu 2> errorRead.gam.vgpout vg call -v -p -t 40 -r TAIR_Chr1 TAIR_flat_Chr1.vg errorRead.gam.vgpu > errorRead.gam.call.vcf 2> errorRead.gam.call.vcout

I've packaged the raw graph and the single read fastq file to replicate this behaviour. It is available for download here The read is mapped as a repeat, although the original regions in the reference are not chimeric and thus the repeated alignment should get a worse alignment score.

Thanks for your help, Chris

[glennhickey]

Yeah, I can reproduce.

@ekg is this normal? where vg map aligns a read as a cycle on a node when the cycle edge is not in the graph?

In any case, vg call doesn't support calling copy number variants from cycles. You can use -U to ignore these edges and get around this error. Thanks for pointing it out though, we'll definitely have to clean it up a bit.

On Wed, Nov 15, 2017 at 1:41 PM, ChriKub notifications@github.com wrote:

Hi, I'm trying to call variation from a flat vg graph using PacBio ccs reads, but the vg call fails:

Reading input graph Computing augmented graph terminate called after throwing an instance of 'std::runtime_error' what(): Found pileup for nonexistent edge {"from": 15592, "to": 15592, "from_start": true, "to_end": true}

Here are the commands I used:

vg index -x TAIR_flat_Chr1.xg -g TAIR_flat_Chr1.gcsa -t 40 -k 11 TAIR_flat_Chr1.vg vg map -t 40 -x TAIR_flat_Chr1.xg -g TAIR_flat_Chr1.gcsa -f errorRead.fastq > errorRead.gam vg pileup -p -t 20 -v TAIR_flat_Chr1.vg errorRead.gam > errorRead.gam.vgpu 2> errorRead.gam.vgpout vg call -v -p -t 40 -r TAIR_Chr1 TAIR_flat_Chr1.vg errorRead.gam.vgpu > errorRead.gam.call.vcf 2> errorRead.gam.call.vcout

I've packaged the raw graph and the single read fastq file to replicate this behaviour. It is available for download here https://owncloud.tuebingen.mpg.de/index.php/s/xmqJJthZR2JVroB The read is mapped as a repeat, although the original regions in the reference are not chimeric and thus the repeated alignment should get a worse alignment score.

Thanks for your help, Chris

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[jeizenga]

It might be triggering the chunked version of the aligner, which can make paths that don't take extant edges. I'm not sure how that all is wired up these days.