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CshlSiepelLab / phast

PHAST
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warning: maf_read: MAF file must be sorted with respect to reference sequence if store_order=TRUE. Ignoring out-of-order blocks #57

Open aaannaw opened 2 years ago

aaannaw commented 2 years ago

Hello,Professor I have sorted the maf file produced by lastz using multiz tool maf_sort multiz-20190527/maf_sort 00.Ma.ref.maf Ma > multiz.00.Ma.ref.maf. Then I split sorted maf file by Chromosome USCS_tools/mafSplit _.bed . multiz.00.Ma.ref.maf -byTarget -useFullSequenceName. But I still got the warning warning: maf_read: MAF file must be sorted with respect to reference sequence if store_order=TRUE. Ignoring out-of-order blocks when I run the command phastCons --estimate-rho Chr10 --no-post-probs Chr10.maf 4d.nonconserved.mod Could you give me any suggestion? Thanks!

diekhans commented 6 months ago

We are getting this warning, which is not obvious what the error message actually means. The MAF is not out-of-order with respect to blocks within a chromosome.

Without looking at the code, this message makes little sense. One doesn't know how to change store_order=TRUE.

If this is actually ignoring data, it seems it should be an error, not a warning.

austinchipps commented 4 months ago

I've run into the same issue - has anyone found a solution?