Pfam Error about gtdbtk HOT 9 CLOSED

Hello,

Thanks for your message!
" /PATH/To/GtdbTK/data/ " is actually a generic path that people need to modify to fit their server configuration.

in your example it has to be replaced with "/projects/b1052/pythonenvs/python2.7/GTDB/gtdb_database/release83/" but that does not mean that another user will have the data at the exact same location on their server.

Thanks,
Pierre

from gtdbtk.

Thanks, Pierre! i have changed " /PATH/To/GtdbTK/data/ " to "/projects/b1052/pythonenvs/python2.7/GTDB/gtdb_database/release83/", i came across with the pfam error, is it because the database could not be identified?
The error message is as below:
1)
Can't locate IPC/Run.pm in @inc (@inc contains: /projects/b1052/pythonenvs/python2.7/GTDB/lib/python2.7/site-packages/gtdbtk/external /software/activeperl/5.16/site/lib /software/activeperl/5.16/lib .) at /projects/b1052/pythonenvs/python2.7/GTDB/lib/python2.7/site-packages/gtdbtk/external/Bio/Pfam/Scan/PfamScan.pm line 39.
BEGIN failed--compilation aborted at /projects/b1052/pythonenvs/python2.7/GTDB/lib/python2.7/site-packages/gtdbtk/external/Bio/Pfam/Scan/PfamScan.pm line 39.
2)
[2018-08-22 17:49:51] INFO: Identifying Pfam protein families.
[2018-08-22 17:49:53] ERROR: Pfam Error
('Unexpected error:', <type 'exceptions.ValueError'>)
3)
File "/projects/b1052/pythonenvs/python2.7/GTDB/lib/python2.7/site-packages/gtdbtk/markers.py", line 238, in identify
pfam_search.run(gene_files)
File "/projects/b1052/pythonenvs/python2.7/GTDB/lib/python2.7/site-packages/gtdbtk/external/pfam_search.py", line 188, in run
raise ValueError("Pfam Error")
ValueError: Pfam Error
File "/projects/b1052/pythonenvs/python2.7/GTDB/lib/python2.7/site-packages/gtdbtk/external/pfam_search.py", line 136, in _workerThread
raise error
raise error

from gtdbtk.

It looks like the IPC::Run Perl module is not installed or not included in the @inc variable .

You first need to install the perl module using ' perl -MCPAN -e"install IPC::Run" '
Make sure that the IPC::Run module (.pm) paths is part of the @inc variable.

If not , Please modify the PERL5LIB ( or PERLIB) environment variable to include the module :
export PERL5LIB="$PERL5LIB:/path/to/directory/where/ipc/module/.pm/is/installed"

from gtdbtk.

Hi pchaumeil,

Thanks for the information, the above error was solved after installing the modules needed. While i came across with another error in the FastANI step, the detailed information is as below:

1. outlog:
   [2018-08-31 15:58:14] INFO: Calculating Average Nucleotide Identity using FastANI.
   list index out of range;

2. errorlog
   File "/projects/b1052/pythonenvs/python2.7/GTDB/lib/python2.7/site-packages/gtdbtk/classify.py", line 648, in _parse_fastani_results
   ref_genome = os.path.basename(info[1]).replace(Config.FASTANI_GENOMES_EXT,"")
   IndexError: list index out of range

"list index out of range" is a python error, which most likely indicates the data being input is not the right size for the program to process.

Thanks!

from gtdbtk.

Hi,
Which version of GTDB-Tk are you running?

Cheers,
Pierre

from gtdbtk.

Hi Pierre,

I am using GTDB-Tk v0.0.7

Thanks,
Yubo

from gtdbtk.

Hi Yubo,
Can you try to update GTDB-Tk to the latest version ( v0.1.2 ) and see if the problem still occurs?
You will also have to download the latest data ( release 86 ).

Thanks,
Pierre

from gtdbtk.

Hi Pierre,

Thanks!

I have downloaded the new data (release 86), and successfully updated the GTDB-Tk to the latest version (gtdbtk-0.1.3);

while i encountered errors in the test by running the command "gtdbtk -h"

the error message is as below:

"Successfully installed gtdbtk-0.1.3
(/projects/b1052/pythonenvs/python2.7/GTDB) [ywx1845@quser13 genes]$ gtdbtk -h
Traceback (most recent call last):
File "/projects/b1052/pythonenvs/python2.7/GTDB/bin/gtdbtk", line 37, in
from gtdbtk.main import OptionsParser
File "/home/ywx1845/.local/lib/python2.7/site-packages/gtdbtk/main.py", line 22, in
from markers import Markers
File "/home/ywx1845/.local/lib/python2.7/site-packages/gtdbtk/markers.py", line 35, in
import config.config as Config
ImportError: No module named config"

i did not came up with this type of error with the previous version

Thanks,
Yubo

from gtdbtk.

Hi Yubo,
Could you please confirm that you have created the config (config.py) file under /home/ywx1845/.local/lib/python2.7/site-packages/gtdbtk/config/ and it is readable?

Thanks,
Pierre

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