search

wandreopoulos / deeplasmid

12 stars 2 forks source link

Failed run due to missing package "multiprocessing" #4

Open cchauve opened 1 year ago

cchauve commented 1 year ago

Hello

I tried to run deeplasmid using the GPU version. I built a singularity contained from the docker container billandreo/deeplasmid-gpu. When I ran it, I got the output

Deeplasmid - Plasmid finder for microbial genome assemblies.
Running feature_DL_plasmid_predict.sh .
This .sh script is meant for running Deeplasmid from the Docker image.
Usage: please specify 2 arguments - the input fasta file and output directory - as follows:
 docker run -it  -v /path/to/input/fasta:/srv/jgi-ml/classifier/dl/in.fasta  -v  /path/to/output/directory:/srv/jgi-ml/classifier/dl/outdir   billandreo/deeplasmid     feature_DL
_plasmid_predict.sh  in.fasta outdir
Contact person: Bill Andreopoulos, wandreopoulos@lbl.gov
Last maintained: January 12, 2020
Using 20220726_203935 for outdir suffix
Traceback (most recent call last):
  File "/srv/jgi-ml/classifier/dl/read_fasta2_plasmids.py", line 44, in <module>
    from multiprocessing import Process, Queue
ImportError: No module named multiprocessing

cedric chauve

wandreopoulos commented 1 year ago

Hello Cedric @cchauve :

Apologies for the delay. I got absorbed into my teaching duties at SJSU and I just saw a few messages I've missed.

I have not tested it with Singularity, only with Docker. I am guessing there is a conflict as read_fasta2_plasmids.py is old and I need to re-engineer it from Py2 to Py3 (haven't found the time yet, but one of these days will get to it). I believe your issue will be solved if you change the shebang line in read_fasta2_plasmids.py to #!/usr/bin/python2.7 , such that it doesn't conflict with the rest of the code that is py3.

I just released a new Docker image for GPUs, that is built on tensorflow/tensorflow:latest-gpu. I left the CNTK stuff behind and moved to TensorFlow.

As described in the README, the usage is much simpler. For example: docker pull billandreo/deeplasmid.tf.gpu2 sudo /usr/bin/docker run -it -v /path/to/fasta:/srv/jgi-ml/classifier/dl/in.fasta -v /path/to/OUT/dir:/srv/jgi-ml/classifier/dl/outdir billandreo/deeplasmid.tf.gpu2 deeplasmid.sh in.fasta outdir

You may want to try that out. Thanks