original sequence not found
hhy18 opened this issue · comments
I add a my species to the reference databases use add addTaxon1s command, but it always show the "original sequence not found" when i choose the new species as ref-species with common "h1s --seqFile infile.fa --seqName test3 --refspec ARIFI@158543@1 --force", can you help me solved it ?
i add a new species use the command "addTaxon1s -f genome/2019_043_Pni.pep.filter.fa -i 13216 -o /data/01/user102/orthology/hamstr -c --force", there is no error on runing;
Hi @hhy18
first of all, as stated in the README of this repo, HaMStR (or hamstr1s) is dead and has been replaced by fDOG.
Secondly, for your issue, my best guess is that you are using a human seed protein with a non-human reference species (158543 is the ID for a plant, if I am correct). So, it can cause the problem for the (re-)blast search, that the seed sequence could not be found. If you want to test it, you can take any sequence from your ARIFI@158543@1 species as the seed protein and run HaMStR again with that sequence. The reference species for HaMStR should always be the species where you get the seed sequence from.
However, I really recommend you change this tool to fDOG, because we are not supporting HaMStR any longer :-)
Regards,
Vinh