find orthology genes

Question

[chenjuanihb80119]

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.

Best,

CJ

[lieven.sterck]

Hi chenjuanihb80119 ,

I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[GenoMax]

checking for blast-dbs: failed

Have you downloaded and configured blast databases you need for this tool?

checking for presence of the core-ortholog file: failed

This file also seems to be missing. If

i construct my own core-orthologs da protocal.

refers to that file then you may need to make sure that it is in the current directory (or configured in software correctly).

[chenjuanihb80119]

thank you for your reply, but ,i try examples which belongs to the software,everthing goes well.i really don't know what happed .

Answer 1

[Philipp Bayer]

Looking at the hamstr code at https://github.com/BIONF/HaMStR/blob/master/bin/hamstr.pl, this error you're seeing: "checking for presence of the hmm files:, prints a few more lines to the log-file, NOT to the standard out:

in case the hmmset is broken it writes this to the log file:
push @log, "${bold}FATAL:${norm} You need to specify a valid core ortholog set. Make also sure that you provide the path to this set if it is not in the default location $hmmpath. You can check available core ortholog sets using the option -show_hmmsets.";

in case the hmm-dir does not exist:
push @log, "${bold}FATAL:${norm} Could not find $hmm_dir";

in case the hmm-dir does exist, but the hmm file is not existing:
push @log, "${bold}FATAL:${norm} $hmms[$k] has been defined but could not be found in $hmm_dir/$hmms[$k]";

and so on, so check your log file :)