Hello everyone: I am somewhat familiar with Hamstr,now, I use this software to get the ortholog betwwen some species.The first i need is to generate of new core-ortholog sets ,and i construct my own core-orthologs da protocal.And i run command like this:
hamstr -sequence_file=test.fa -taxon=test -hmmset=custom1 -refspec=DANIO -central -cpu=20 -representative
But i get some error message :
setting dboutpath to .nentferner.pl succeeded. Checking for sequence type Guessing sequence type: Protein Checking for the blast program succeeded Checking for hmmsearch succeeded Checking for genewise succeeded checking for presence of the hmm files: failed checking for presence of the core-ortholog file: failed testing whether the taxon has been determined: succeeded Checking for reference species and blast-dbs succeeded checking for blast-dbs: failed checking for low complexity filter setting: succeeded
Any links to good reviews would also be appreciated.