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tvkent / GERPplusplus

GERP++ code from Sidow Lab modified by Kevin Thornton to compile properly.
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a error about species is not present #3

Open gruit01 opened 2 years ago

gruit01 commented 2 years ago

When i ran GERP like " ./gerpcol -t ./test/align/NeuTree.txt -f ./test/align/29Mamms_Alignment.mfa -e human" , it reported like " Tree species ajbat not present in alignment and therefore ignored. Tree species armadillo not present in alignment and therefore ignored. Tree species baboon not present in alignment and therefore ignored. Tree species cat not present in alignment and therefore ignored. Tree species chimp not present in alignment and therefore ignored. Tree species cow not present in alignment and therefore ignored. Tree species dog not present in alignment and therefore ignored. Tree species dusky_titi not present in alignment and therefore ignored. Tree species galago not present in alignment and therefore ignored. Tree species gorilla not present in alignment and therefore ignored. Tree species hedgehog not present in alignment and therefore ignored. Tree species horse not present in alignment and therefore ignored. Tree species human not present in alignment and therefore ignored. Tree species lemur not present in alignment and therefore ignored. Tree species macaque not present in alignment and therefore ignored. Tree species marmoset not present in alignment and therefore ignored. Tree species mouse not present in alignment and therefore ignored. Tree species mouse_lemur not present in alignment and therefore ignored. Tree species muntjak_indian not present in alignment and therefore ignored. Tree species nrooted (((opossum:0.034160,monodelphis:0.022496):0.032669,wallaby:0.049042) not present in alignment and therefore ignored."

but my Alignment.mfa had these species,. Can you give me a solution, thank you in advance.

gubrins commented 2 years ago

could you share your alignment file?

YanCheer commented 1 year ago

could you share your alignment file?

https://asia.ensembl.org/info/genome/compara/multiple_genome_alignments.html

gruit01 commented 1 year ago

Time is too long, my memory is a little fuzzy, you can refer to the following instruction. https://alphagenes.roslin.ed.ac.uk/wp/wp-content/uploads/2019/05/Deleterious_variants_2.pdf