Does PGGB miss odgi sort -O? about pggb HOT 5 CLOSED

@brettChapman
Where there errors while you ran PGGB with a certain combination of parameters? Or was this independent of a PGGB run?
Could you please write the commands you used? Or give an example with a minimal data set?
Thanks!

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Hi @subwaystation

These were errors I received after I had completed the PGGB run. It happened with some graphs but not all.

After I generated the smoothed GFA, they contained consensus paths (an earlier build of PGGB before consensus paths were dropped by default). I proceeded to remove the consensus paths and was left with VG graphs without the consensus. I then converted these to GFA so I could then build OG graphs with ODGI and visualise the 2D graphs without the consensus paths. Some ODGI runs complained that the graph was unsorted and suggested I run odgi sort with -O. See an error below for my 3H graph.

odgi viz -i barley_pangenome_graph_3H.gfa.og -o barley_pangenome_graph_3H.gfa.og.viz_mqc.png -x 1500 -y 500 -P 10 -b
[odgi::viz] error: the graph is not optimized. Please run 'odgi sort' using -O, --optimize

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How did you remove the consensus graphs?
Note that odgi viz has the -I, --ignore-prefix option, which would allow you to ignore paths with a certain prefix.

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Hi @subwaystation

I needed to remove the consensus paths because they were getting in the way when using sequenceTubeMap. The plan was to visualise interactively in sequenceTubeMap for our end users (barley breeders and geneticists). Lots of consensus paths would just confuse the visualisation. I ended up running vg chunk on the entire graph to get gene chunks into sequenceTubeMap because it currently can not visualise the whole pangenome graph at once.

I ran this code to remove the consensus paths:

vg convert -g test_graph.gfa -p > test_graph.pg
vg index test_graph.pg -x test_graph.xg
vg paths -x test_graph.xg -L | grep Consensus > consensus_paths.txt
vg paths -v test_graph.pg -p consensus_paths.txt -d > test_graph.noConsensus.vg
vg index test_graph.noConsensus.vg -x test_graph.noConsensus.xg

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Seems like this is solved as mentioned in pangenome/odgi#282.

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