Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error running Propanet with example data #1

Open
archanabhardwaj opened this issue Nov 20, 2020 · 1 comment
Open

Error running Propanet with example data #1

archanabhardwaj opened this issue Nov 20, 2020 · 1 comment

Comments

@archanabhardwaj
Copy link

Hello
I would like to use PropaNet in my project. I am working on gene expression based time series data. Based on the instruction, installed python2.7 with all required libraries such as networkx,multiprocessing and scipy.stats. As a test run, preferred to work with example data. But during test run, I am getting only PropaNet.nwk.t* and PropaNet.DEGli.t* files but ranked files are missing and not able to get the final network. Detail error information is given below:
network done
('TF length', 1717)
Traceback (most recent call last):
File "Target_genes.py", line 83, in
with open(args.DEGfile) as f, open(args.TFfile) as f2:
IOError: [Errno 2] No such file or directory: 'result/intermediate_results/PropaNet.TF_rank.t1.trim'
Traceback (most recent call last):
File "Target_genes.py", line 83, in
with open(args.DEGfile) as f, open(args.TFfile) as f2:
IOError: [Errno 2] No such file or directory: 'result/intermediate_results/PropaNet.TF_rank.t2.trim'
Traceback (most recent call last):
File "Target_genes.py", line 83, in
with open(args.DEGfile) as f, open(args.TFfile) as f2:
IOError: [Errno 2] No such file or directory: 'result/intermediate_results/PropaNet.TF_rank.t3.trim'
Traceback (most recent call last):
File "Target_genes.py", line 83, in
with open(args.DEGfile) as f, open(args.TFfile) as f2:
IOError: [Errno 2] No such file or directory: 'result/intermediate_results/PropaNet.TF_rank.t4.trim'
Please help me to sort this issue.

@edugenetico
Copy link

Hello,
I have had the same problem running PropaNet with the example. It is similar to what happened to archanabhardwa
I put my error:

bash run.sh [10:35]

network done
('TF length', 1717)
Traceback (most recent call last):
File "Target_genes.py", line 83, in
with open(args.DEGfile) as f, open(args.TFfile) as f2:
IOError: [Errno 2] No such file or directory: 'result/intermediate_results/PropaNet.TF_rank.t2.trim'
Traceback (most recent call last):
File "Target_genes.py", line 83, in
with open(args.DEGfile) as f, open(args.TFfile) as f2:
IOError: [Errno 2] No such file or directory: 'result/intermediate_results/PropaNet.TF_rank.t1.trim'
Traceback (most recent call last):
File "Target_genes.py", line 83, in
with open(args.DEGfile) as f, open(args.TFfile) as f2:
IOError: [Errno 2] No such file or directory: 'result/intermediate_results/PropaNet.TF_rank.t3.trim'
Traceback (most recent call last):
File "Target_genes.py", line 83, in
with open(args.DEGfile) as f, open(args.TFfile) as f2:
IOError: [Errno 2] No such file or directory: 'result/intermediate_results/PropaNet.TF_rank.t4.trim'

Could you tell me how to solve it?
I work with Ubuntu 14. thanks

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants