search

CshlSiepelLab / phast

PHAST
Other
67 stars 24 forks source link

Segmentation fault (core dumped) #64

Open songxh1996 opened 1 year ago

songxh1996 commented 1 year ago

hello,I took the first chromosomes of the three bovine genomes and compared them, and it is worth noting that the chromosomes are not named differently. I got the .hal file with cactus and replaced it with a maf file, but when I used phastCons I got an error and I didn't know how to fix it. and I guess is doing something wrong.

niu.tar.gz

# cactus jobStore chr1.dnd niu_align_chr1.hal --maxCores 16 # cactus-hal2maf jobStore niu_align_chr1.hal \ niu_align_chr1.maf \ --chunkSize 1000000 \ --refGenome ARS-UCD_CHR1

phyloFit -i MAF niu_align_chr1.maf --tree chr1.dnd

phastCons niu_align_chr1.maf phyloFit.mod --target-coverage 0.25 --expected-length 12 --rho 0.4 --msa-format MAF > niu_align_chr1.wig

Reading tree model from phyloFit.mod... Reading alignment from niu_align_chr1.maf... Creating 'conserved' and 'nonconserved' states in HMM... Computing emission probs (state 0, cat 0, mod 0)... Computing emission probs (state 1, cat 1, mod 1)... Computing posterior probabilities... Segmentation fault (core dumped)

chenzhao12 commented 1 year ago

i have same issue and you slove it?

sgyproject commented 3 months ago

Based on my tests, if the input MAF file contains paralogous alignments, PhyloP seems unable to score accurately. You might want to check your MAF file to see if this issue is present. As a solution, you can specify --dupeMode single when converting to MAF. #68