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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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"Cycle detected" error #1326

Open rishipurohit opened 3 months ago

rishipurohit commented 3 months ago

I'm trying to run cactus-pangenome to construct a pangenome of 6 different samples of the same species (including a reference). My invocation is below: cactus-pangenome ./js seqFile.txt --outDir ./out --outName pigtail --reference Ma2 --batchSystem slurm --batchLogsDir batch-logs --consMemory 350G --maxMemory 350G --refContigs $(for i in $(seq 20); do printf "chr$i "; done ; echo "chrX chrY") --consCores 64 --indexCores 64 --mgCores 64 --vcf --gbz --gfa --odgi --chrom-og --viz --draw --xg --restart

However, I'm receiving the following error:

pangenome-error Any ideas on what the issue might be? Thanks!

glennhickey commented 3 months ago

Looking at this error, I would suspect maybe a bug in gfaffix which is introducing a cycle along the reference path during normalization. You can turn off normalization by 

cat src/cactus/cactus_progressive_config.xml | sed -e `'s/gfaffix="1"/gfaffix="0"/g'` > config-nofix.xml

then add --configFile config-nofix.xml to your cactus command(s).

If you can share your input data, I'd be very interested in reproducing this issue and getting whatever's causing it fixed asap.