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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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empty gfa file #32

Open rthapa1 opened 3 years ago

rthapa1 commented 3 years ago

Hi,I am trying to create a graph file using multiple files. I used the following command but got an empty gfa output. Could you provide any suggestions? Thanks

minigraph -xggs -t16 reference.fa sample1.fa sample2.fa sample3.fa sample4.fa sample5.fa sample6.fa> out.gfa

rthapa1 commented 3 years ago

If I use only two query samples at a time, it works and I got gfa output. But the bed file with structural variants looks weird.

Screen Shot 2021-01-26 at 4 37 14 PM
lh3 commented 3 years ago

The BED file looks ok.

What is the log message when you run for multiple input fasta files? Thanks.

rthapa1 commented 3 years ago

Thank you, how could we know if there is deletion and translocation? Is the position in bed file corresponding to position in genome assembly?

When I run multiple fast files, it

Screen Shot 2021-01-26 at 5 08 32 PM

says segmentation fault.

lh3 commented 3 years ago

BED shows the reference coordinate. Minigraph doesn't generate translocations. I may need your input files to understand the segfault.

rthapa1 commented 3 years ago

Thank you. I have sent you the files at lh3@me.com.

lh3 commented 3 years ago

Thanks for the email. Which minigraph version are you using? I tried the minigraph but didn't see an error in the asan debugging mode.

rthapa1 commented 3 years ago

It is minigraph 0.14-r415. There is no error but the output gfa file is empty.