Database was built with a different version of Diamond

[lcottret]

Hi,

Thanks for this work which looks very promising ! I tried carve but it returns : Database was built with a different version of Diamond as is incompatible.

How to solve this issue without installing a different version of Diamond (I tried it on a server) ?

Regards, Ludo

[cdanielmachado]

Just run carveme_init to rebuild the database.

Regards, Daniel

[lcottret]

Dear Daniel,

Thanks. Indeed, I did not see that an error arised when launching carveme_init: Building diamond database... Traceback (most recent call last):   File "/usr/local/bin/carveme_init", line 49, in     subprocess.call(cmd)   File "/usr/lib/python2.7/subprocess.py", line 172, in call     return Popen(*popenargs, **kwargs).wait()   File "/usr/lib/python2.7/subprocess.py", line 394, in init     errread, errwrite)   File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child     raise child_exception OSError: [Errno 2] No such file or directory

My version of diamond : v0.9.18.119. Note that diamond is in the path.

Regards, Ludo

Le 26/06/2018 à 16:32, Daniel Machado a écrit :

Just run |carveme_init| to rebuild the database.

Regards, Daniel

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Be careful, my email has changed and is now ludovic.cottret@inra.fr

Ludovic COTTRET INRA, 24 Chemin de Borde Rouge - Auzeville CS 52627 31326 Castanet Tolosan cedex, France Tel: +33 5.61.28.57.06 Fax : +33 5.61.28.50.61 Lab website: http://www.toulouse.inra.fr/lipm Personal website: http://sites.google.com/site/lcottret/

[cdanielmachado]

What happens when you run this?

python -c 'import subprocess; subprocess.call("diamond", shell=True)'

[thh32]

@lcottret what was your solution for this issue in the end as I currently have the same error

EDIT: Changing 'carveme_init' to include the 'shell=True' flag seemed to sort out that issue, however now the following occurs;

Building diamond database...
makedb: 1: makedb: diamond: not found
makedb: 1: makedb: diamond: not found
Failed to run diamond. Please make sure diamond is installed and add it to your PATH.

I have tested calling diamond in python and it seems to work as such;

python -c 'import subprocess; subprocess.call("diamond makedb --in Acutalibacter_muris.faa --db temp", shell=True)'
diamond v0.9.22.123 | by Benjamin Buchfink <buchfink@gmail.com>
Licensed under the GNU AGPL <https://www.gnu.org/licenses/agpl.txt>
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 12
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database file: Acutalibacter_muris.faa
Opening the database file...  [0.001095s]
Loading sequences...  [0.009427s]
Masking sequences...  [0.069242s]
Writing sequences...  [0.002912s]
Hashing sequences...  [0.000913s]
Loading sequences...  [2.2e-05s]
Writing trailer...  [0.00011s]
Closing the input file...  [1.1e-05s]
Closing the database file...  [0.00041s]
Database hash = 35c4395cfe7ed65a183f7fb84bed40bb
Processed 3849 sequences, 1122871 letters.
Total time = 0.0844s

@cdanielmachado any idea whats causing this error?

I have managed to get around it by running diamond manually, however of interest I was unable to run diamond with sudo so had to move the file to another directory, make the database, then transfer the database back. Now Carveme seems to work fine.

[cdanielmachado]

@thh32 What is your output for the command above?

[thh32]

The output was; Error: Syntax: diamond COMMAND [OPTIONS]. To print help message: diamond help

[fairquestion]

Hi all,

I am having the exactly same isue than thh32. Any idea about it?

[cdanielmachado]

@fairquestion can you run the following command and see if it works?

python -c 'import subprocess; subprocess.call(["diamond", "help"])'

[willnotburn]

Hi all

Did this get resolved? I am having the same issue now.

I: python -c 'import subprocess; subprocess.call("diamond", shell=True)' O: Error: Syntax: diamond COMMAND [OPTIONS]. To print help message: diamond help

I: python -c 'import subprocess; subprocess.call(["diamond", "help"])' O: a long diamond help file; no errors.

[bilehtin]

Hi all,

I'm experiencing this as well. I was successfully carving about a year ago with the same setup (I saved the virtual environment) Now I wanted to make a few more models to test them with Smetana afterwards

carve genome.faa Error: Database was built with a different version of Diamond and is incompatible. Failed to run diamond. carveme_init urllib.error.HTTPError: HTTP Error 404: Not Found python -c 'import subprocess; subprocess.call("diamond", shell=True)' Error: Syntax: diamond COMMAND [OPTIONS]. To print help message: diamond help python -c 'import subprocess; subprocess.call(["diamond", "help"])' Prints the helpfile

Would be nice to have it up and running again

Hi all

Did this get resolved? I am having the same issue now.

I: python -c 'import subprocess; subprocess.call("diamond", shell=True)' O: Error: Syntax: diamond COMMAND [OPTIONS]. To print help message: diamond help

I: python -c 'import subprocess; subprocess.call(["diamond", "help"])' O: a long diamond help file; no errors.

[cdanielmachado]

Which version of CarveMe are you using? Can you uninstall and do a fresh install of the latest version?

[bilehtin]

Which version of CarveMe are you using? Can you uninstall and do a fresh install of the latest version?

Thanks a lot! Should have tried that before asking, of course. My apologies for not having done the basic measures before posting. It seems to be working now.

[cdanielmachado]

No problem, I'm glad it is working :)