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pangenome / odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
https://doi.org/10.1093/bioinformatics/btac308
MIT License
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Error with ODGI Extract #464

Open brettChapman opened 1 year ago

brettChapman commented 1 year ago

Hi

I'm getting an error with ODGI Extract.

I get the following error:

srun -n 1 singularity exec --bind /data/pangenome_snp_calling_latest/morex_v3_run:/data/pangenome_snp_calling_latest/morex_v3_run /data/bedtools_builds/bedtools.sif bedtools merge -i barley_pangenome_1H.r1-129126483.sorted.bed -d 1000000000
+ srun -n 1 singularity exec --bind /data/pangenome_snp_calling_latest/morex_v3_run:/data/pangenome_snp_calling_latest/morex_v3_run /data/pggb_builds/pggb_v0.4.1.sif odgi extract -t 32 -i barley_pangenome_1H.og -b barley_pangenome_1H.r1-129126483.sorted.merged.bed -r Morex_v3_chr1H:1-129126483 -d 1000000 -e 20 -L 1000000 -o barley_pangenome_1H.r1-129126483.og
odgi: /smoothxg/deps/odgi/src/odgi.cpp:201: odgi::graph_t::path_metadata_t& odgi::graph_t::get_path_metadata(const handlegraph::path_handle_t&) const: Assertion `false' failed.

I've been trying to segment the pangenome graph into 4 different regions for further investigation to show zoomed in regions, slicing at specific genome coordinates, sorting the graph, getting the merged BED file, and finally extracting the final OG graph, however it seems to fail. It worked with a different graph I had generated previously. I created a new graph with the latest PGGB build and used a different and shorter segment length (100kbp instead of 1Mbp). Perhaps I should use different parameters to extract the graph? Increase the -d, -e and -L parameters?

My merged BED file looks ok:

Morex_v3_chr1H  1       129126483
Akashinriki_v1_chr1H    17862   483871863
B1K-04-12_v1_chr1H      32779   467459407
Barke_v1_chr1H  23242   458703893
Golden_Promise_v1_chr1H 89687   427408919
HOR10350_v1_chr1H       283627  458933786
HOR13821_v1_chr1H       125855  477577411
HOR13942_v1_chr1H       0       467808327
HOR21599_v1_chr1H       333079  478360648
HOR3081_v1_chr1H        60214   466285117
HOR3365_v1_chr1H        1472    498852392
HOR7552_v1_chr1H        5131    467959145
HOR8148_v1_chr1H        93103   470082024
HOR9043_v1.1_chr1H      63702   469709242
Hockett_v1_chr1H        11484   445112985
Igri_v1_chr1H   59513   464617969
OUN333_v1_chr1H 6236    483994898
RGT_Planet_v1_chr1H     8847    465824729
ZDM01467_v1_chr1H       124917  491987155
ZDM02064_v1_chr1H       706     448136685

Thanks.

subwaystation commented 1 year ago

Are you still seeing this @brettChapman? If so, is there a way to share the data?