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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Division by zero error when MAPQ is set to 1 #1363

Closed MarionPerrier closed 2 months ago

MarionPerrier commented 2 months ago

Dear developers,

I am using Minigraph-Cactus v2.8.1 to create a pangenome graph of 15 haploid fungal isolates. I have fragmented assemblies, so I am trying to be as loose as possible in the parameters to retain as many contigs as possible. As advised in this issue: https://github.com/ComparativeGenomicsToolkit/cactus/issues/1212, when I set the MAPQ to 1 in the cactus_progressive_config.xml, I get a div/0 error.

Here is my command line: singularity run --cleanenv docker://quay.io/comparative-genomics-toolkit/cactus:v2.8.1 cactus-pangenome ./js input_corrected.txt --outDir 20240419_pg2_Af293_corrected --outName 20240419_pg2_Af293 --reference Af293 --vcf --giraffe --gfa --gbz --odgi --draw --viz --permissiveContigFilter --refContigs Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 mito --configFile cactus_progressive_config.xml

Here is the log file: log_div_0.txt

And my config file: cactus_progressive_config.xml.txt

Am-I doing something wrong, or is it a bug?

I wish you a nice day, Regards, Marion

MarionPerrier commented 2 months ago

Whoops, my bad. The error was not linked to the changes in the config file, but to the "--refContigs" commands. I misspelled the chromosome names.