traviswheelerlab / bath Goto Github PK

Hello,

I installed FraHMMER on our cluster and at the last step I got a permission error:

$ make install
     SUBDIR easel
     SUBDIR miniapps
     SUBDIR libdivsufsort
     SUBDIR src
     SUBDIR impl_sse
     SUBDIR profmark
if [ ! -d /usr/local/bin ]; then /usr/bin/install -c -d /usr/local/bin; fi
if [ ! -d /usr/local/share/man/man1 ]; then /usr/bin/install -c -d /usr/local/share/man/man1; fi
make -C src install
make[1]: Entering directory '/newwing/wing2/users/dcopetti/bin/FraHMMER/src'
for file in frahmmer frahmmbuild frahmmconvert frahmmfetch frahmmstat; do \
   /usr/bin/install -c -m 0755 $file /usr/local/bin/ ;\
done
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmer': Permission denied
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmbuild': Permission denied
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmconvert': Permission denied
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmfetch': Permission denied
/usr/bin/install: cannot create regular file '/usr/local/bin/frahmmstat': Permission denied
make[1]: *** [Makefile:321: install] Error 1
make[1]: Leaving directory '/newwing/wing2/users/dcopetti/bin/FraHMMER/src'
make: *** [Makefile:135: install] Error 2

I am working with my sys admin to resolve it.

I am still able to run frahmmer, with -h I see the parameters.
I can't find the executable for frahmmsearch though: is it because of the error at the make install command above?

I tried running frahmmer as
frahmmer --cpu 48 -o output --tblout output.tab query.fa genome.fa
with the query being a unaligned multifasta of 5 protein sequences.
Can I do the alignment with frahmmer or fo I need frahmmsearch? If so, where do I find it?
Thanks!

Hello,
can you please describe or point me to a resource for understanding the tabular output of frahmmer?
Especially for the less intuitive columns like env, bias, shifts, stops, pipe.
Thanks,
Dario

I see from a recent commit that you commented profmark out of the Makefile.in, but the configure.ac file is still looking for it, so the configure step fails:

configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating testsuite/Makefile
config.status: error: cannot find input file: `profmark/Makefile.in'

"protein" is mis-spelled in the README.md file. ;-)

Dear BATH developers,

I sincerely thank you for developing such an excellent tool.

I have a question about the BATH output format.
As bash follows a kind of hmmer, I think the result file is hmm format.
However, I would like to see the results in gff format in order to utilise it for gene prediction based on robust features such as frameshift.

Do you plan to increase the number of output formats or do you know anything about how to convert them?

Best regards,

Keigo