not pass tests

[pnatsi]

Hi,

I download SwiftOrtho and ran the tests, but they failed to complete. Here is the error message:

('chk size', 50000)
Traceback (most recent call last):
File "../bin/find_cluster.py", line 22, in
import networkx as nx
ImportError: No module named networkx
Traceback (most recent call last):
File "../bin/find_cluster.py", line 22, in
import networkx as nx
ImportError: No module named networkx
not pass test 1
nohup: ignoring input and redirecting stderr to stdout
('all to all homologous searching time:', 61.62682485580444)
('orthomcl algorithm time:', 1.9388201236724854)
nohup: ignoring input and redirecting stderr to stdout
Traceback (most recent call last):
File "../scripts/run_all.py", line 177, in
out = '\t'.join(k)
TypeError: sequence item 0: expected string, NoneType found
not pass test 2

[Rinoahu]

Hi,

I download SwiftOrtho and ran the tests, but they failed to complete. Here is the error message:

('chk size', 50000)
Traceback (most recent call last):
File "../bin/find_cluster.py", line 22, in
import networkx as nx
ImportError: No module named networkx
Traceback (most recent call last):
File "../bin/find_cluster.py", line 22, in
import networkx as nx
ImportError: No module named networkx
not pass test 1
nohup: ignoring input and redirecting stderr to stdout
('all to all homologous searching time:', 61.62682485580444)
('orthomcl algorithm time:', 1.9388201236724854)
nohup: ignoring input and redirecting stderr to stdout
Traceback (most recent call last):
File "../scripts/run_all.py", line 177, in
out = '\t'.join(k)
TypeError: sequence item 0: expected string, NoneType found
not pass test 2

The error shows that the networkx package of python is not installed. If you use conda, you install it by running the command: conda install -c anaconda networkx.. If you are familiar with pip, you can also install it by running the command: pip install networkx. Or you can download the source code at https://networkx.github.io/ and install it manually.

[weifei888]

i didn't pass the test 2, and i found i got all the result except the "ref.fas.pan" which is 0 byte, where or which file should i check?

[Rinoahu]

Hi, could you please upload the log file?