error: GraphAligner maps reads to vg graph

[XuewenWangUGA]

I have a genome graph generated from pggb and then convert to vg graph using "vg convert" The vg graph is tested and works well for subsequent vg pipelines.

Then I tried to using GraphAligner to map reads to the gfa converted vg graph, but it gave an error : GraphAligner bioconda 1.0.12- Signal 11. Read: N^@^@^@^@^@^@^@ssing. Seed: 0+,0,0,0 /var/spool/slurmd/job5304653/slurm_script: line 172: 112982 Aborted (core dumped) GraphAligner -g $graph.vg -f $readir/$inseq -f $readir/$inseq2 -t $nthreadxw --seeds-mum-count -1 --bandwidth 100 -a $graph.$samp.${tag}.gam The command used for mapping is:

GraphAligner -g $graph.vg -f $readir/$inseq -f $readir/$inseq2 -t $nthreadxw --seeds-mum-count -1 --bandwidth 100 -a $graph.$samp.gam where inseq="sim.30x.r1.fq.gz" inseq2="sim.30x.r2.fq.gz" samp="sim" but when the Graphaligner mapping is successful if the input graph is .gfa before converting to vg graph using the same input reads.

Any suggestions or what caused this error? Thanks

[ekg]

Why not use the GFA from pggb directy?

On Thu, Dec 3, 2020 at 2:40 AM XuewenWangUGA notifications@github.com wrote:

I have a genome graph generated from pggb and then convert to vg graph using "vg convert" The vg graph is tested and works well for subsequent vg pipelines.

Then I tried to using GraphAligner to map reads to the gfa converted vg graph, but it gave an error : GraphAligner bioconda 1.0.12- Signal 11. Read: N^@^@^@^@^@^@^@ssing https://github.com/ssing. Seed: 0+,0,0,0 /var/spool/slurmd/job5304653/slurm_script: line 172: 112982 Aborted (core dumped) GraphAligner -g $graph.vg -f $readir/$inseq -f $readir/$inseq2 -t $nthreadxw --seeds-mum-count -1 --bandwidth 100 -a $graph.$samp.${tag}.gam The command used for mapping is:

GraphAligner -g $graph.vg -f $readir/$inseq -f $readir/$inseq2 -t $nthreadxw --seeds-mum-count -1 --bandwidth 100 -a $graph.$samp.gam

but when the Graphaligner mapping is successful if the input graph is .gfa before converting to vg graph using the same input reads.

Any suggestions or what caused this error? Thanks

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[XuewenWangUGA]

Erik,

I would like to call variance later from mapping results in .gam. Do you think vg or any other tool can call variance from .gam generated by GraphAligner? Thanks.

Xuewen

---

From: Erik Garrison notifications@github.com Sent: Thursday, December 3, 2020 10:13 AM To: maickrau/GraphAligner GraphAligner@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [maickrau/GraphAligner] error: GraphAligner maps reads to vg graph (#26)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Why not use the GFA from pggb directy?

On Thu, Dec 3, 2020 at 2:40 AM XuewenWangUGA notifications@github.com wrote:

I have a genome graph generated from pggb and then convert to vg graph using "vg convert" The vg graph is tested and works well for subsequent vg pipelines.

Then I tried to using GraphAligner to map reads to the gfa converted vg graph, but it gave an error : GraphAligner bioconda 1.0.12- Signal 11. Read: N^@^@^@^@^@^@^@ssing https://github.com/ssing. Seed: 0+,0,0,0 /var/spool/slurmd/job5304653/slurm_script: line 172: 112982 Aborted (core dumped) GraphAligner -g $graph.vg -f $readir/$inseq -f $readir/$inseq2 -t $nthreadxw --seeds-mum-count -1 --bandwidth 100 -a $graph.$samp.${tag}.gam The command used for mapping is:

GraphAligner -g $graph.vg -f $readir/$inseq -f $readir/$inseq2 -t $nthreadxw --seeds-mum-count -1 --bandwidth 100 -a $graph.$samp.gam

but when the Graphaligner mapping is successful if the input graph is .gfa before converting to vg graph using the same input reads.

Any suggestions or what caused this error? Thanks

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[ekg]

vg should be able to, but I'm not sure if it's been tested. @glennhickey ?

On Thu, Dec 3, 2020 at 4:30 PM XuewenWangUGA notifications@github.com wrote:

Erik,

I would like to call variance later from mapping results in .gam. Do you think vg or any other tool can call variance from .gam generated by GraphAligner? Thanks.

Xuewen

---

From: Erik Garrison notifications@github.com Sent: Thursday, December 3, 2020 10:13 AM To: maickrau/GraphAligner GraphAligner@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [maickrau/GraphAligner] error: GraphAligner maps reads to vg graph (#26)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Why not use the GFA from pggb directy?

On Thu, Dec 3, 2020 at 2:40 AM XuewenWangUGA notifications@github.com wrote:

I have a genome graph generated from pggb and then convert to vg graph using "vg convert" The vg graph is tested and works well for subsequent vg pipelines.

Then I tried to using GraphAligner to map reads to the gfa converted vg graph, but it gave an error : GraphAligner bioconda 1.0.12- Signal 11. Read: N^@^@^@^@^@^@^@ssing https://github.com/ssing. Seed: 0+,0,0,0 /var/spool/slurmd/job5304653/slurm_script: line 172: 112982 Aborted (core dumped) GraphAligner -g $graph.vg -f $readir/$inseq -f $readir/$inseq2 -t $nthreadxw --seeds-mum-count -1 --bandwidth 100 -a $graph.$samp.${tag}.gam The command used for mapping is:

GraphAligner -g $graph.vg -f $readir/$inseq -f $readir/$inseq2 -t $nthreadxw --seeds-mum-count -1 --bandwidth 100 -a $graph.$samp.gam

but when the Graphaligner mapping is successful if the input graph is .gfa before converting to vg graph using the same input reads.

Any suggestions or what caused this error? Thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maickrau/GraphAligner/issues/26, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AABDQEN2BYHRPOYZB47JTITSS3UBJANCNFSM4ULJMSYQ

.

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.

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[glennhickey]

We haven't used it much, to be honest. But we did do an experiment where we genotyped SVs using GraphAligner mappings of PacBio reads and were able to get much better accuracy than short reads from the same sample.

[maickrau]

Sounds like there is something weird going on with GraphAligner parsing the graph. Could you please upload the graph?