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License: GNU General Public License v3.0
Hello developers,
I am trying to run PredicTF and am running into some issues. The installation (on Ubuntu 16.04.6 LTS, 40 cores, 1.5TB RAM, local installation, no GPUs on this system(and hence i dont want to do any model training)) ran without any problems according your instructions but when trying to use your script predictf_in_genome.sh to use your model on my genomes, i ran into the following issues:
The command i ran was:
sh predictf_in_genome.sh ~/03bioinformaticstools/102predictTF/PredicTF ../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11.genes.faa ../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11_out
and the console output i got was(i had run the same command previously, hence the mkdir warning; there seem to be additional calls to diamond also using the wrong PATH that i havent modified yet to the relative PATH; hence only the first db call of diamond works and the later one complains about the /deeparg//bin/diamond PATH):
mkdir: cannot create directory '../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11_out': File exists
path
/home/till/anaconda3/envs/deeparg_env/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
"downsample module has been moved to the theano.tensor.signal.pool module.")
DIAMOND blastp alignment
diamond blastp -q ../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11.genes.faa -d /home/till/03bioinformaticstools/102predictTF/PredicTF/BacTFDB//database/v2/features -k 1000 --id 30 --sensitive -e 1e-10 -a ../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11_out/file.out.align
diamond v0.9.24.125 | by Benjamin Buchfink <[email protected]>
Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>
Check http://github.com/bbuchfink/diamond for updates.
#CPU threads: 40
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: ../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11_out
Opening the database... [8.3e-05s]
Error: Database was built with a different version of Diamond and is incompatible.
parsing output file
sh: 1: /deeparg//bin/diamond: not found
Loading deep learning model ...
Traceback (most recent call last):
File "/home/till/03bioinformaticstools/102predictTF/PredicTF/deeparg-largerepo/deepARG.py", line 157, in <module>
'.mapping', iden, mdl, evalue, prob, minCoverage, pipeline, version)
File "/home/till/03bioinformaticstools/102predictTF/PredicTF/deeparg-largerepo/predict/bin/deepARG.py", line 149, in process
open(path+"BacTFDB/model/"+version_m+"/metadata"+version+".pkl"))
IOError: [Errno 2] No such file or directory: '/home/till/03bioinformaticstools/102predictTF/PredicTF/BacTFDB/BacTFDB/model/v2/metadata_LS.pkl'
If i remove the duplicated BacTFDB, i now get a cPickle error (using the same command; this one indicates to me that you may be using a different pickle version though cPickle was installed into the conda env and you thus at least indirectly install it with the installation commands):
mkdir: cannot create directory '../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11_out': File exists
path
/home/till/anaconda3/envs/deeparg_env/lib/python2.7/site-packages/theano/tensor/signal/downsample.py:6: UserWarning: downsample module has been moved to the theano.tensor.signal.pool module.
"downsample module has been moved to the theano.tensor.signal.pool module.")
DIAMOND blastp alignment
diamond blastp -q ../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11.genes.faa -d /home/till/03bioinformaticstools/102predictTF/PredicTF/BacTFDB//database/v2/features -k 1000 --id 30 --sensitive -e 1e-10 -a ../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11_out/file.out.align
diamond v0.9.24.125 | by Benjamin Buchfink <[email protected]>
Licensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>
Check http://github.com/bbuchfink/diamond for updates.
#CPU threads: 40
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: ../../genome/WB01no11_MG_WBTS_GAME_concat_Anaerolineae_51_11_out
Opening the database... [0.00017s]
Error: Database was built with a different version of Diamond and is incompatible.
parsing output file
sh: 1: /deeparg//bin/diamond: not found
Loading deep learning model ...
Traceback (most recent call last):
File "/home/till/03bioinformaticstools/102predictTF/PredicTF/deeparg-largerepo/deepARG.py", line 157, in <module>
'.mapping', iden, mdl, evalue, prob, minCoverage, pipeline, version)
File "/home/till/03bioinformaticstools/102predictTF/PredicTF/deeparg-largerepo/predict/bin/deepARG.py", line 149, in process
open(path+"/model/"+version_m+"/metadata"+version+".pkl"))
cPickle.UnpicklingError: invalid load key, 'v'.
Is there anything you can suggest to fix these errors?
Best regards,
Till
PS: Maybe adding a little note on how to limit core/thread usage to the README would be nice as users might not want to allocate all the 40 threads for this (i can modify the deeparg.py to that effect but it might be a nice info to share).
Hi,
tried to install but found these files are no longer available... will they be back?
thanks!
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