traviswheelerlab / bath Goto Github PK

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

Hello,

I am having issues during the build process (linker errors), indicating that the linker (ld) cannot find the implementations of certain functions referenced in the code.
I tried with new conda environment but still getting the same error. can you please let me know how to solve this issue?

Here is the error message:
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.o: in function pipeline_thread':
bathsearch.c:(.text.pipeline_thread+0x129): undefined reference to p7_Pipeline_BATH' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.pipeline_thread+0x137): undefined reference to p7_pipeline_fs_Reuse'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.pipeline_thread+0x209): undefined reference to p7_Pipeline_BATH' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.pipeline_thread+0x217): undefined reference to p7_pipeline_fs_Reuse'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.o: in function serial_master': bathsearch.c:(.text.serial_master+0x945): undefined reference to p7_profile_fs_Create'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x9e5): undefined reference to p7_ProfileConfig_fs' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0xa05): undefined reference to p7_pipeline_fs_Create'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0xb4b): undefined reference to p7_profile_fs_Clone' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0xb7f): undefined reference to p7_pipeline_fs_Create'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x1086): undefined reference to p7_tophits_ComputeBATHEvalues' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x10c8): undefined reference to p7_pipeline_fs_Destroy'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x10f0): undefined reference to p7_profile_fs_Destroy' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x13c3): undefined reference to p7_tophits_TabularFrameshifts'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x1414): undefined reference to p7_pipeline_fs_Destroy' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x143e): undefined reference to p7_profile_fs_Destroy'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x19ec): undefined reference to p7_Pipeline_BATH' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x19fa): undefined reference to p7_pipeline_fs_Reuse'
/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:/home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x1b79): undefined reference to p7_pipeline_fs_Reuse' /home/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/12.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: bathsearch.c:(.text.serial_master+0x2dd8): undefined reference to p7_bg_fs_Create'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:251: bathsearch] Error 1
make: *** [Makefile:115: check] Error 2`

Thanks,
Qussai

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'

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

Hello,

I have encountered an issue while attempting to run BATH with some protein files.

I used this command:
bathsearch -M --cpu 64 --tblout perseable_hits.out --fstblout frameshift_locations.out --hmmout produced_hmms.bhmm -o output.out ~/proteins.faa ~/genome.fa

and I got this error:
/var/spool/slurm/d/job71513/slurm_script: line 12: 1992990 Segmentation fault (core dumped) ~/BATH/BATH/src/bathsearch -M --cpu 64 --tblout perseable_hits.out --fstblout frameshift_locations.out --hmmout produced_hmms.bhmm -o output.out ~/proteins.faa ~/genome.fa
However BATH works with no errors using a different protein file.

Could you provide insight into what might be causing this issue? I attached the genome and protein files for you review.
Files.zip

Thank you,
Qussai

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!

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