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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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ERROR: bad integers or strand in MAF (strand must be + for reference sequence) -- #89

Open chun-he-316 opened 5 months ago

chun-he-316 commented 5 months ago

Hi,

I ran multiple whole genome alignments using cactus to generate the hal file, and ran the "cactus-hal2maf js_hal2maf evolver27species.hal evolver27species.maf.gz --refGenome xxxx --chunkSize 500000" to transform the hal file. Then when I ran "phyloFit -i MAF evolver27species.maf", I met the the issue" ERROR: bad integers or strand in MAF (strand must be + for reference sequence) --". I do not know the reason.

Can you tell me how to resolve this problem? Thank you.

The best,

Chun

mikolmogorov commented 5 months ago

Hi Chun - this seems to be an issue with either Cactus or phyloFit, rather than Ragout? If so, it is better to contact the developers of the corresponding tools.

bkffadia commented 1 month ago

@chun-he-316 any updates regarding this ? did you manage to solve it because I'm running into the same problem