Problems in running test.py

Question

Problems in running test.py

Closed this issue 6 years ago · 14 comments

Hi! When trying to run: python3 test.py in terminal I got:

...
Test 2: Correlation analysis... PASSED
Traceback (most recent call last):
File "../../conan.py", line 2087, in
call_hierarchical('cluster_trj', vectors, trunc, trunc_inter, rmsd_interframe_cond, nframes, ks_traj, 'Trajectory', time_vec, 'trj', xterm, xres, yterm, yres, asymm, matrices)
File "../../conan.py", line 1365, in call_hierarchical
Z = linkage(condensed_dist, 'ward')
File "/usr/lib/python3/dist-packages/scipy/cluster/hierarchy.py", line 633, in linkage
raise ValueError("Valid methods when the raw observations are "
ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average'.
This file doesn't exist at all: cluster_trj/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/assignment.dat, file_b: cluster_trj/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster0/average_map.dat, file_b: cluster_trj/2/cluster0/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster0/lifetime.dat, file_b: cluster_trj/2/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster1/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster1/average_map.dat, file_b: cluster_trj/2/cluster1/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster1/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster1/lifetime.dat, file_b: cluster_trj/2/cluster1/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/assignment.dat, file_b: cluster_trj/1/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/cluster0/average_map.dat, file_b: cluster_trj/1/cluster0/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/cluster0/lifetime.dat, file_b: cluster_trj/1/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/assignment.dat, file_b: cluster_trj/3/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster0/average_map.dat, file_b: cluster_trj/3/cluster0/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster0/lifetime.dat, file_b: cluster_trj/3/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster2/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster2/average_map.dat, file_b: cluster_trj/3/cluster2/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster2/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster2/lifetime.dat, file_b: cluster_trj/3/cluster2/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster1/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster1/average_map.dat, file_b: cluster_trj/3/cluster1/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster1/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster1/lifetime.dat, file_b: cluster_trj/3/cluster1/lifetime.dat, errors:-1
Test 3: Framewise cluster analysis.... FAILED
Traceback (most recent call last):
File "../../conan.py", line 2020, in
call_hierarchical("cluster_res/lifetime", vectors, trunc, trunc_inter, life_cond, xres, ks_res, "lifetime", None, 'res', xterm, xres, yterm, yres, asymm, matrices)
File "../../conan.py", line 1365, in call_hierarchical
Z = linkage(condensed_dist, 'ward')
File "/usr/lib/python3/dist-packages/scipy/cluster/hierarchy.py", line 633, in linkage
raise ValueError("Valid methods when the raw observations are "
ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average'.
This file doesn't exist at all: cluster_res/distance/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/2/assignment.dat, file_b: cluster_res/distance/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/distance/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/1/assignment.dat, file_b: cluster_res/distance/1/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/distance/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/3/assignment.dat, file_b: cluster_res/distance/3/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/lifetime/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/2/assignment.dat, file_b: cluster_res/lifetime/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/lifetime/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/1/assignment.dat, file_b: cluster_res/lifetime/1/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/lifetime/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/3/assignment.dat, file_b: cluster_res/lifetime/3/assignment.dat, errors:-1
Test 4: Residue-wise cluster analysis.... FAILED
Test 5: Blocking analysis.... PASSED
Test 6: Principal component analysis.... PASSED
Test 7: Rereading of sparse files.... PASSED
Test 8: Asymmetric mode.... PASSED
2 test(s) failed. The output of the failed tests has been preserved.
It is possible that the deviations are minor.
The failures are in the following folders:
3_ClusterTraj
4_ClusterRes

Seraching for "ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average' ", I found out that there might be a compatibility problem related to scipy 0.17, as you can see here: scipy/scipy#6180

Can anyone help me to solve this? Thank you

Answer 1 · 2018-11-28T17:54:47.000Z

Hey there, This error occurs when the scipy distribution is not the newest version. Could you install the newest Anaconda version and try again? Thanks! Csaba Dr. Csaba Daday Postdoc Molecular Biomechanics HITS gGmbH Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone +49 6221 533 311 fax +49 6221 533 298 email: csaba.daday@h-its.org http://www.h-its.org

…

_________________________________________________ Amtsgericht Mannheim / HRB 337446 Managing Director: Dr. Gesa Schönberger Scientific Director: Prof. Dr. Michael Strube

________________________________________ From: eduardodinizRO [notifications@github.com] Sent: Wednesday, November 28, 2018 5:15 PM To: HITS-MBM/conan Cc: Subscribed Subject: [HITS-MBM/conan] Problems in running test.py (#2) Hi! When trying to run: python3 test.py in terminal I got: ... Test 2: Correlation analysis... PASSED Traceback (most recent call last): File "../../conan.py", line 2087, in call_hierarchical('cluster_trj', vectors, trunc, trunc_inter, rmsd_interframe_cond, nframes, ks_traj, 'Trajectory', time_vec, 'trj', xterm, xres, yterm, yres, asymm, matrices) File "../../conan.py", line 1365, in call_hierarchical Z = linkage(condensed_dist, 'ward') File "/usr/lib/python3/dist-packages/scipy/cluster/hierarchy.py", line 633, in linkage raise ValueError("Valid methods when the raw observations are " ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average'. This file doesn't exist at all: cluster_trj/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/assignment.dat, file_b: cluster_trj/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster0/average_map.dat, file_b: cluster_trj/2/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster0/lifetime.dat, file_b: cluster_trj/2/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster1/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster1/average_map.dat, file_b: cluster_trj/2/cluster1/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster1/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster1/lifetime.dat, file_b: cluster_trj/2/cluster1/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/assignment.dat, file_b: cluster_trj/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/cluster0/average_map.dat, file_b: cluster_trj/1/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/cluster0/lifetime.dat, file_b: cluster_trj/1/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/assignment.dat, file_b: cluster_trj/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster0/average_map.dat, file_b: cluster_trj/3/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster0/lifetime.dat, file_b: cluster_trj/3/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster2/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster2/average_map.dat, file_b: cluster_trj/3/cluster2/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster2/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster2/lifetime.dat, file_b: cluster_trj/3/cluster2/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster1/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster1/average_map.dat, file_b: cluster_trj/3/cluster1/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster1/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster1/lifetime.dat, file_b: cluster_trj/3/cluster1/lifetime.dat, errors:-1 Test 3: Framewise cluster analysis.... FAILED Traceback (most recent call last): File "../../conan.py", line 2020, in call_hierarchical("cluster_res/lifetime", vectors, trunc, trunc_inter, life_cond, xres, ks_res, "lifetime", None, 'res', xterm, xres, yterm, yres, asymm, matrices) File "../../conan.py", line 1365, in call_hierarchical Z = linkage(condensed_dist, 'ward') File "/usr/lib/python3/dist-packages/scipy/cluster/hierarchy.py", line 633, in linkage raise ValueError("Valid methods when the raw observations are " ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average'. This file doesn't exist at all: cluster_res/distance/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/2/assignment.dat, file_b: cluster_res/distance/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/1/assignment.dat, file_b: cluster_res/distance/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/3/assignment.dat, file_b: cluster_res/distance/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/2/assignment.dat, file_b: cluster_res/lifetime/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/1/assignment.dat, file_b: cluster_res/lifetime/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/3/assignment.dat, file_b: cluster_res/lifetime/3/assignment.dat, errors:-1 Test 4: Residue-wise cluster analysis.... FAILED Test 5: Blocking analysis.... PASSED Test 6: Principal component analysis.... PASSED Test 7: Rereading of sparse files.... PASSED Test 8: Asymmetric mode.... PASSED 2 test(s) failed. The output of the failed tests has been preserved. It is possible that the deviations are minor. The failures are in the following folders: 3_ClusterTraj 4_ClusterRes Seraching for "ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average' ", I found out that there might be a compatibility problem related to scipy 0.17, as you can see here: scipy/scipy#6180<scipy/scipy#6180> Can anyone help me to solve this? Thank you — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#2>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AclzujKPY-OlYBzF6oIJtIW1s5UaI1fOks5uzraSgaJpZM4Y38WU>.

Answer 2 · 2018-11-29T15:29:03.000Z

Hey, I changed the README file to reflect this. Let me know if updating SciPy helped. On the other hand, if you are not interested in cluster analysis, feel free to use older version as well!

Answer 3 · 2018-11-30T13:58:31.000Z

Hi, thank you for your reply. I've installed anaconda3 and tried again. I got a similar error:

Test 1: I/O, Result: PASSED
Test 2: Correlation analysis... PASSED
ln: failed to create symbolic link './dmf.xpm': File exists
Traceback (most recent call last):
File "../../conan.py", line 2087, in
call_hierarchical('cluster_trj', vectors, trunc, trunc_inter, rmsd_interframe_cond, nframes, ks_traj, 'Trajectory', time_vec, 'trj', xterm, xres, yterm, yres, asymm, matrices)
File "../../conan.py", line 1365, in call_hierarchical
Z = linkage(condensed_dist, 'ward')
File "/usr/lib/python3/dist-packages/scipy/cluster/hierarchy.py", line 633, in linkage
raise ValueError("Valid methods when the raw observations are "
ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average'.
This file doesn't exist at all: cluster_trj/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/assignment.dat, file_b: cluster_trj/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster0/average_map.dat, file_b: cluster_trj/2/cluster0/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster0/lifetime.dat, file_b: cluster_trj/2/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster1/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster1/average_map.dat, file_b: cluster_trj/2/cluster1/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster1/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster1/lifetime.dat, file_b: cluster_trj/2/cluster1/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/assignment.dat, file_b: cluster_trj/1/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/cluster0/average_map.dat, file_b: cluster_trj/1/cluster0/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/cluster0/lifetime.dat, file_b: cluster_trj/1/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/assignment.dat, file_b: cluster_trj/3/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster0/average_map.dat, file_b: cluster_trj/3/cluster0/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster0/lifetime.dat, file_b: cluster_trj/3/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster2/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster2/average_map.dat, file_b: cluster_trj/3/cluster2/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster2/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster2/lifetime.dat, file_b: cluster_trj/3/cluster2/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster1/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster1/average_map.dat, file_b: cluster_trj/3/cluster1/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster1/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster1/lifetime.dat, file_b: cluster_trj/3/cluster1/lifetime.dat, errors:-1
Test 3: Framewise cluster analysis.... FAILED
ln: failed to create symbolic link './dmf.xpm': File exists
Traceback (most recent call last):
File "../../conan.py", line 2020, in
call_hierarchical("cluster_res/lifetime", vectors, trunc, trunc_inter, life_cond, xres, ks_res, "lifetime", None, 'res', xterm, xres, yterm, yres, asymm, matrices)
File "../../conan.py", line 1365, in call_hierarchical
Z = linkage(condensed_dist, 'ward')
File "/usr/lib/python3/dist-packages/scipy/cluster/hierarchy.py", line 633, in linkage
raise ValueError("Valid methods when the raw observations are "
ValueError: Valid methods when the raw observations are omitted are 'single', 'complete', 'weighted', and 'average'.
This file doesn't exist at all: cluster_res/distance/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/2/assignment.dat, file_b: cluster_res/distance/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/distance/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/1/assignment.dat, file_b: cluster_res/distance/1/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/distance/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/3/assignment.dat, file_b: cluster_res/distance/3/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/lifetime/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/2/assignment.dat, file_b: cluster_res/lifetime/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/lifetime/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/1/assignment.dat, file_b: cluster_res/lifetime/1/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/lifetime/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/3/assignment.dat, file_b: cluster_res/lifetime/3/assignment.dat, errors:-1
Test 4: Residue-wise cluster analysis.... FAILED
Test 5: Blocking analysis.... PASSED
Test 6: Principal component analysis.... PASSED
Test 7: Rereading of sparse files.... PASSED
Test 8: Asymmetric mode.... PASSED
2 test(s) failed. The output of the failed tests has been preserved.
It is possible that the deviations are minor.
The failures are in the following folders:
3_ClusterTraj
4_ClusterRes

Anyway, I think I won't need this cluster analysis.

Answer 4 · 2018-11-30T14:51:11.000Z

OK this is quite strange. Are you sure the Anaconda version Python is executing conan? Either way, if no cluster analysis is needed then we can forget about it for now.

Sorry and please tell me if I can do something else.

Answer 5 · 2018-11-30T15:43:22.000Z

I've installed anaconda3 with the following commands:
wget https://repo.anaconda.com/archive/Anaconda3-5.3.1-Linux-x86_64.sh
bash Anaconda3-5.3.1-Linux-x86_64.sh

which installed anaconda in /home/../anaconda3
Then I cd to ../conan-master/test/ and entered the command:
/home/.../anaconda3/bin/python test.py

which produced the error I showed above. I don't know if I did something wrong. Thank you.

Answer 6 · 2018-11-30T16:07:22.000Z

Yes I think I know what's going on. test.py is a wrapper so it calls python3 again. That means that if "which python3" does not call the Anaconda installation, the wrong version is called. Ironically, everything is working fine in your case except the test script :)

Answer 7 · 2018-11-30T16:46:58.000Z

That's probably what happened. I tried to change line 66 of test.py script from:
e = os.system("python ../compare_all.py")
to:
e = os.system("/home/eduardo/anaconda3/bin/python3 ../compare_all.py")

but it didn't work.

Answer 8 · 2018-11-30T16:52:57.000Z

The line before runs conan, and that line is what generates the issues. Could you rewrite that as well (instead of running conan.py, name the python version that should read it)?

Answer 9 · 2018-12-03T14:21:17.000Z

Hi! I've changed also line 65 (as you said) and line 42. This is the result:

Test 1: I/O, Result: FAILED
Test 2: Correlation analysis... PASSED
ln: failed to create symbolic link './dmf.xpm': File exists
QApplication: invalid style override passed, ignoring it.
Test 3: Framewise cluster analysis.... PASSED
ln: failed to create symbolic link './dmf.xpm': File exists
QApplication: invalid style override passed, ignoring it.
Test 4: Residue-wise cluster analysis.... PASSED
Test 5: Blocking analysis.... PASSED
Test 6: Principal component analysis.... PASSED
Test 7: Rereading of sparse files.... PASSED
Test 8: Asymmetric mode.... PASSED
All tests passed! Everything looks good.

Despite some notes, it says that it's alright. Thank you!

Answer 10 · 2018-12-03T14:33:59.000Z

You're welcome! Yes the linking errors are just there because testing script doesn't clean up folders with errors. Good luck with your contact maps!!

Answer 11 · 2019-05-18T17:31:22.000Z

I am also having problems withe the test.py can you help? The error message I get is below.
Thanks

sh: 1: Syntax error: Bad fd number
This file doesn't exist at all: aggregate/timeline.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/timeline.dat, file_b: aggregate/timeline.dat, errors:-1
This file doesn't exist at all: aggregate/native_contacts.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/native_contacts.dat, file_b: aggregate/native_contacts.dat, errors:-1
This file doesn't exist at all: aggregate/time_mdmat_rmsd.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/time_mdmat_rmsd.dat, file_b: aggregate/time_mdmat_rmsd.dat, errors:-1
This file doesn't exist at all: aggregate/local_interactions.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/local_interactions.dat, file_b: aggregate/local_interactions.dat, errors:-1
This file doesn't exist at all: aggregate/mdmat_average_rmsf.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/mdmat_average_rmsf.dat, file_b: aggregate/mdmat_average_rmsf.dat, errors:-1
This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1
This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1
This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1
This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1
This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1
This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1
This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1
This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1
This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1
This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1
This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1
Test 1: I/O, Result: FAILED
Removing files from old tests...
sh: 1: Syntax error: Bad fd number
This file doesn't exist at all: aggregate/pearson_map_density.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/pearson_map_density.dat, file_b: aggregate/pearson_map_density.dat, errors:-1
This file doesn't exist at all: aggregate/pearson_data_obs_1.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/pearson_data_obs_1.dat, file_b: aggregate/pearson_data_obs_1.dat, errors:-1
This file doesn't exist at all: aggregate/pearson_data.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/pearson_data.dat, file_b: aggregate/pearson_data.dat, errors:-1
Test 2: Correlation analysis... FAILED
sh: 1: Syntax error: Bad fd number
This file doesn't exist at all: cluster_trj/rmsd_interframe.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/rmsd_interframe.dat, file_b: cluster_trj/rmsd_interframe.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/assignment.dat, file_b: cluster_trj/3/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster0/lifetime.dat, file_b: cluster_trj/3/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster0/average_map.dat, file_b: cluster_trj/3/cluster0/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster2/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster2/lifetime.dat, file_b: cluster_trj/3/cluster2/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster2/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster2/average_map.dat, file_b: cluster_trj/3/cluster2/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster1/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster1/lifetime.dat, file_b: cluster_trj/3/cluster1/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/3/cluster1/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/3/cluster1/average_map.dat, file_b: cluster_trj/3/cluster1/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/assignment.dat, file_b: cluster_trj/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster0/lifetime.dat, file_b: cluster_trj/2/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster0/average_map.dat, file_b: cluster_trj/2/cluster0/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster1/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster1/lifetime.dat, file_b: cluster_trj/2/cluster1/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/2/cluster1/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/2/cluster1/average_map.dat, file_b: cluster_trj/2/cluster1/average_map.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/assignment.dat, file_b: cluster_trj/1/assignment.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/cluster0/lifetime.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/cluster0/lifetime.dat, file_b: cluster_trj/1/cluster0/lifetime.dat, errors:-1
This file doesn't exist at all: cluster_trj/1/cluster0/average_map.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_trj/1/cluster0/average_map.dat, file_b: cluster_trj/1/cluster0/average_map.dat, errors:-1
Test 3: Framewise cluster analysis.... FAILED
sh: 1: Syntax error: Bad fd number
This file doesn't exist at all: cluster_res/lifetime/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/3/assignment.dat, file_b: cluster_res/lifetime/3/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/lifetime/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/2/assignment.dat, file_b: cluster_res/lifetime/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/lifetime/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/lifetime/1/assignment.dat, file_b: cluster_res/lifetime/1/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/distance/3/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/3/assignment.dat, file_b: cluster_res/distance/3/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/distance/2/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/2/assignment.dat, file_b: cluster_res/distance/2/assignment.dat, errors:-1
This file doesn't exist at all: cluster_res/distance/1/assignment.dat. This probably means that CONAN could not run at all.
file_a: correct_output/cluster_res/distance/1/assignment.dat, file_b: cluster_res/distance/1/assignment.dat, errors:-1
Test 4: Residue-wise cluster analysis.... FAILED
sh: 1: Syntax error: Bad fd number
This file doesn't exist at all: blocking/block_out.txt. This probably means that CONAN could not run at all.
file_a: correct_output/blocking/block_out.txt, file_b: blocking/block_out.txt, errors:-1
Test 5: Blocking analysis.... FAILED
sh: 1: Syntax error: Bad fd number
This file doesn't exist at all: pca/pc.10.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.10.dat, file_b: pca/pc.10.dat, errors:-1
This file doesn't exist at all: pca/pc.5.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.5.dat, file_b: pca/pc.5.dat, errors:-1
This file doesn't exist at all: pca/pc.2.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.2.dat, file_b: pca/pc.2.dat, errors:-1
This file doesn't exist at all: pca/pc.6.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.6.dat, file_b: pca/pc.6.dat, errors:-1
This file doesn't exist at all: pca/pc.9.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.9.dat, file_b: pca/pc.9.dat, errors:-1
This file doesn't exist at all: pca/pc.4.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.4.dat, file_b: pca/pc.4.dat, errors:-1
This file doesn't exist at all: pca/pc.8.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.8.dat, file_b: pca/pc.8.dat, errors:-1
This file doesn't exist at all: pca/pc.3.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.3.dat, file_b: pca/pc.3.dat, errors:-1
This file doesn't exist at all: pca/pca_projections.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pca_projections.dat, file_b: pca/pca_projections.dat, errors:-1
This file doesn't exist at all: pca/pca_output.txt. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pca_output.txt, file_b: pca/pca_output.txt, errors:-1
This file doesn't exist at all: pca/pc.1.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.1.dat, file_b: pca/pc.1.dat, errors:-1
This file doesn't exist at all: pca/pc.7.dat. This probably means that CONAN could not run at all.
file_a: correct_output/pca/pc.7.dat, file_b: pca/pc.7.dat, errors:-1
Test 6: Principal component analysis.... FAILED
sh: 1: Syntax error: Bad fd number
This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1
This file doesn't exist at all: matrices/00007_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00007_dr.init.dat, file_b: matrices/00007_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1
This file doesn't exist at all: matrices/00009_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00009_dr.init.dat, file_b: matrices/00009_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00003_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00003_dr.init.dat, file_b: matrices/00003_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1
This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1
This file doesn't exist at all: matrices/00009_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00009_dr.prev.dat, file_b: matrices/00009_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00004_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00004_dr.prev.dat, file_b: matrices/00004_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1
This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1
This file doesn't exist at all: matrices/00006_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00006_dr.prev.dat, file_b: matrices/00006_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00008_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00008_dr.init.dat, file_b: matrices/00008_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00001_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00001_dr.prev.dat, file_b: matrices/00001_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1
This file doesn't exist at all: matrices/00005_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00005_dr.prev.dat, file_b: matrices/00005_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00001_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00001_dr.init.dat, file_b: matrices/00001_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00005_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00005_dr.init.dat, file_b: matrices/00005_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00008_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00008_dr.prev.dat, file_b: matrices/00008_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1
This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1
This file doesn't exist at all: matrices/00002_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00002_dr.prev.dat, file_b: matrices/00002_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00004_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00004_dr.init.dat, file_b: matrices/00004_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00002_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00002_dr.init.dat, file_b: matrices/00002_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1
This file doesn't exist at all: matrices/00010_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00010_dr.prev.dat, file_b: matrices/00010_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00003_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00003_dr.prev.dat, file_b: matrices/00003_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00006_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00006_dr.init.dat, file_b: matrices/00006_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00007_dr.prev.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00007_dr.prev.dat, file_b: matrices/00007_dr.prev.dat, errors:-1
This file doesn't exist at all: matrices/00010_dr.init.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00010_dr.init.dat, file_b: matrices/00010_dr.init.dat, errors:-1
This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1
Test 7: Rereading of sparse files.... FAILED
sh: 1: Syntax error: Bad fd number
This file doesn't exist at all: aggregate/timeline.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/timeline.dat, file_b: aggregate/timeline.dat, errors:-1
This file doesn't exist at all: aggregate/native_contacts.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/native_contacts.dat, file_b: aggregate/native_contacts.dat, errors:-1
This file doesn't exist at all: aggregate/total_interactions.y.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/total_interactions.y.dat, file_b: aggregate/total_interactions.y.dat, errors:-1
This file doesn't exist at all: aggregate/total_interactions.x.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/total_interactions.x.dat, file_b: aggregate/total_interactions.x.dat, errors:-1
This file doesn't exist at all: aggregate/time_mdmat_rmsd.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/time_mdmat_rmsd.dat, file_b: aggregate/time_mdmat_rmsd.dat, errors:-1
This file doesn't exist at all: aggregate/mdmat_average_rmsf.dat. This probably means that CONAN could not run at all.
file_a: correct_output/aggregate/mdmat_average_rmsf.dat, file_b: aggregate/mdmat_average_rmsf.dat, errors:-1
This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1
This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1
This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1
This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1
This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1
This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1
This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1
This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1
This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1
This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1
This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all.
file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1
Test 8: Asymmetric mode.... FAILED
7 test(s) failed. The output of the failed tests has been preserved.
It is possible that the deviations are minor.
The failures are in the following folders:
2_Pearson
3_ClusterTraj
4_ClusterRes
5_Blocking
6_PCA
7_Reread
8_Asymmetric

Answer 12 · 2019-05-18T18:29:28.000Z

Hello, This looks like you may be working in a shell different from bash? What does the output of: ls -l /bin/sh Looks like? If that links to “/bin/dash” that’s where the problem may be. D.

…

On 18 May 2019, at 19:31, maryam-yemz ***@***.***> wrote: I am also having problems withe the test.py can you help? The error message I get is below. Thanks sh: 1: Syntax error: Bad fd number This file doesn't exist at all: aggregate/timeline.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/timeline.dat, file_b: aggregate/timeline.dat, errors:-1 This file doesn't exist at all: aggregate/native_contacts.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/native_contacts.dat, file_b: aggregate/native_contacts.dat, errors:-1 This file doesn't exist at all: aggregate/time_mdmat_rmsd.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/time_mdmat_rmsd.dat, file_b: aggregate/time_mdmat_rmsd.dat, errors:-1 This file doesn't exist at all: aggregate/local_interactions.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/local_interactions.dat, file_b: aggregate/local_interactions.dat, errors:-1 This file doesn't exist at all: aggregate/mdmat_average_rmsf.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/mdmat_average_rmsf.dat, file_b: aggregate/mdmat_average_rmsf.dat, errors:-1 This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 Test 1: I/O, Result: FAILED Removing files from old tests... sh: 1: Syntax error: Bad fd number This file doesn't exist at all: aggregate/pearson_map_density.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_map_density.dat, file_b: aggregate/pearson_map_density.dat, errors:-1 This file doesn't exist at all: aggregate/pearson_data_obs_1.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_data_obs_1.dat, file_b: aggregate/pearson_data_obs_1.dat, errors:-1 This file doesn't exist at all: aggregate/pearson_data.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_data.dat, file_b: aggregate/pearson_data.dat, errors:-1 Test 2: Correlation analysis... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: cluster_trj/rmsd_interframe.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/rmsd_interframe.dat, file_b: cluster_trj/rmsd_interframe.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/assignment.dat, file_b: cluster_trj/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster0/lifetime.dat, file_b: cluster_trj/3/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster0/average_map.dat, file_b: cluster_trj/3/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster2/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster2/lifetime.dat, file_b: cluster_trj/3/cluster2/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster2/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster2/average_map.dat, file_b: cluster_trj/3/cluster2/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster1/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster1/lifetime.dat, file_b: cluster_trj/3/cluster1/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster1/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster1/average_map.dat, file_b: cluster_trj/3/cluster1/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/assignment.dat, file_b: cluster_trj/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster0/lifetime.dat, file_b: cluster_trj/2/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster0/average_map.dat, file_b: cluster_trj/2/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster1/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster1/lifetime.dat, file_b: cluster_trj/2/cluster1/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster1/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster1/average_map.dat, file_b: cluster_trj/2/cluster1/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/assignment.dat, file_b: cluster_trj/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/cluster0/lifetime.dat, file_b: cluster_trj/1/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/cluster0/average_map.dat, file_b: cluster_trj/1/cluster0/average_map.dat, errors:-1 Test 3: Framewise cluster analysis.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: cluster_res/lifetime/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/3/assignment.dat, file_b: cluster_res/lifetime/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/2/assignment.dat, file_b: cluster_res/lifetime/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/1/assignment.dat, file_b: cluster_res/lifetime/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/3/assignment.dat, file_b: cluster_res/distance/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/2/assignment.dat, file_b: cluster_res/distance/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/1/assignment.dat, file_b: cluster_res/distance/1/assignment.dat, errors:-1 Test 4: Residue-wise cluster analysis.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: blocking/block_out.txt. This probably means that CONAN could not run at all. file_a: correct_output/blocking/block_out.txt, file_b: blocking/block_out.txt, errors:-1 Test 5: Blocking analysis.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: pca/pc.10.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.10.dat, file_b: pca/pc.10.dat, errors:-1 This file doesn't exist at all: pca/pc.5.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.5.dat, file_b: pca/pc.5.dat, errors:-1 This file doesn't exist at all: pca/pc.2.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.2.dat, file_b: pca/pc.2.dat, errors:-1 This file doesn't exist at all: pca/pc.6.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.6.dat, file_b: pca/pc.6.dat, errors:-1 This file doesn't exist at all: pca/pc.9.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.9.dat, file_b: pca/pc.9.dat, errors:-1 This file doesn't exist at all: pca/pc.4.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.4.dat, file_b: pca/pc.4.dat, errors:-1 This file doesn't exist at all: pca/pc.8.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.8.dat, file_b: pca/pc.8.dat, errors:-1 This file doesn't exist at all: pca/pc.3.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.3.dat, file_b: pca/pc.3.dat, errors:-1 This file doesn't exist at all: pca/pca_projections.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pca_projections.dat, file_b: pca/pca_projections.dat, errors:-1 This file doesn't exist at all: pca/pca_output.txt. This probably means that CONAN could not run at all. file_a: correct_output/pca/pca_output.txt, file_b: pca/pca_output.txt, errors:-1 This file doesn't exist at all: pca/pc.1.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.1.dat, file_b: pca/pc.1.dat, errors:-1 This file doesn't exist at all: pca/pc.7.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.7.dat, file_b: pca/pc.7.dat, errors:-1 Test 6: Principal component analysis.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00007_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007_dr.init.dat, file_b: matrices/00007_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00009_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009_dr.init.dat, file_b: matrices/00009_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00003_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003_dr.init.dat, file_b: matrices/00003_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00009_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009_dr.prev.dat, file_b: matrices/00009_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00004_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004_dr.prev.dat, file_b: matrices/00004_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 This file doesn't exist at all: matrices/00006_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006_dr.prev.dat, file_b: matrices/00006_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00008_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008_dr.init.dat, file_b: matrices/00008_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00001_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001_dr.prev.dat, file_b: matrices/00001_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00005_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005_dr.prev.dat, file_b: matrices/00005_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00001_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001_dr.init.dat, file_b: matrices/00001_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00005_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005_dr.init.dat, file_b: matrices/00005_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00008_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008_dr.prev.dat, file_b: matrices/00008_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00002_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002_dr.prev.dat, file_b: matrices/00002_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00004_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004_dr.init.dat, file_b: matrices/00004_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00002_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002_dr.init.dat, file_b: matrices/00002_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00010_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010_dr.prev.dat, file_b: matrices/00010_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00003_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003_dr.prev.dat, file_b: matrices/00003_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00006_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006_dr.init.dat, file_b: matrices/00006_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00007_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007_dr.prev.dat, file_b: matrices/00007_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00010_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010_dr.init.dat, file_b: matrices/00010_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 Test 7: Rereading of sparse files.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: aggregate/timeline.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/timeline.dat, file_b: aggregate/timeline.dat, errors:-1 This file doesn't exist at all: aggregate/native_contacts.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/native_contacts.dat, file_b: aggregate/native_contacts.dat, errors:-1 This file doesn't exist at all: aggregate/total_interactions.y.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/total_interactions.y.dat, file_b: aggregate/total_interactions.y.dat, errors:-1 This file doesn't exist at all: aggregate/total_interactions.x.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/total_interactions.x.dat, file_b: aggregate/total_interactions.x.dat, errors:-1 This file doesn't exist at all: aggregate/time_mdmat_rmsd.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/time_mdmat_rmsd.dat, file_b: aggregate/time_mdmat_rmsd.dat, errors:-1 This file doesn't exist at all: aggregate/mdmat_average_rmsf.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/mdmat_average_rmsf.dat, file_b: aggregate/mdmat_average_rmsf.dat, errors:-1 This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 Test 8: Asymmetric mode.... FAILED 7 test(s) failed. The output of the failed tests has been preserved. It is possible that the deviations are minor. The failures are in the following folders: 2_Pearson 3_ClusterTraj 4_ClusterRes 5_Blocking 6_PCA 7_Reread 8_Asymmetric — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2?email_source=notifications&email_token=AD4RK3Z7MRKD5GHJZJKXEJ3PWA4OXA5CNFSM4GG7YWKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVWSVZI#issuecomment-493693669>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD4RK3YNMUNFSTVFAIJNQDDPWA4OXANCNFSM4GG7YWKA>.

Answer 13 · 2019-05-18T19:37:23.000Z

Hi, Davide is right, this is a sh version. I will fix it soon, but at the moment I am in the middle of adding some features in the main script and am not ready to commit them. In the meantime, could you replace line 46 in test.py: os.system("echo 2 | ../../conan.py test.inp > /dev/null >& /dev/null") with os.system("echo 2 | ../../conan.py test.inp > /dev/null 2>&1 and the same for line 72? Sorry! Best, Csaba Dr. Csaba Daday Postdoc Molecular Biomechanics HITS gGmbH Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone +49 6221 533 311 fax +49 6221 533 298 email: csaba.daday@h-its.org http://www.h-its.org<http://www.h-its.org/>

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_________________________________________________ Amtsgericht Mannheim / HRB 337446 Managing Director: Dr. Gesa Schönberger Scientific Director: PD Dr. Wolfgang Müller

________________________________ From: maryam-yemz <notifications@github.com> Sent: Saturday, May 18, 2019 7:31 PM To: HITS-MBM/conan Cc: Daday, Csaba; State change Subject: Re: [HITS-MBM/conan] Problems in running test.py (#2) I am also having problems withe the test.py can you help? The error message I get is below. Thanks sh: 1: Syntax error: Bad fd number This file doesn't exist at all: aggregate/timeline.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/timeline.dat, file_b: aggregate/timeline.dat, errors:-1 This file doesn't exist at all: aggregate/native_contacts.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/native_contacts.dat, file_b: aggregate/native_contacts.dat, errors:-1 This file doesn't exist at all: aggregate/time_mdmat_rmsd.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/time_mdmat_rmsd.dat, file_b: aggregate/time_mdmat_rmsd.dat, errors:-1 This file doesn't exist at all: aggregate/local_interactions.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/local_interactions.dat, file_b: aggregate/local_interactions.dat, errors:-1 This file doesn't exist at all: aggregate/mdmat_average_rmsf.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/mdmat_average_rmsf.dat, file_b: aggregate/mdmat_average_rmsf.dat, errors:-1 This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 Test 1: I/O, Result: FAILED Removing files from old tests... sh: 1: Syntax error: Bad fd number This file doesn't exist at all: aggregate/pearson_map_density.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_map_density.dat, file_b: aggregate/pearson_map_density.dat, errors:-1 This file doesn't exist at all: aggregate/pearson_data_obs_1.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_data_obs_1.dat, file_b: aggregate/pearson_data_obs_1.dat, errors:-1 This file doesn't exist at all: aggregate/pearson_data.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/pearson_data.dat, file_b: aggregate/pearson_data.dat, errors:-1 Test 2: Correlation analysis... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: cluster_trj/rmsd_interframe.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/rmsd_interframe.dat, file_b: cluster_trj/rmsd_interframe.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/assignment.dat, file_b: cluster_trj/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster0/lifetime.dat, file_b: cluster_trj/3/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster0/average_map.dat, file_b: cluster_trj/3/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster2/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster2/lifetime.dat, file_b: cluster_trj/3/cluster2/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster2/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster2/average_map.dat, file_b: cluster_trj/3/cluster2/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster1/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster1/lifetime.dat, file_b: cluster_trj/3/cluster1/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/3/cluster1/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/3/cluster1/average_map.dat, file_b: cluster_trj/3/cluster1/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/assignment.dat, file_b: cluster_trj/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster0/lifetime.dat, file_b: cluster_trj/2/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster0/average_map.dat, file_b: cluster_trj/2/cluster0/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster1/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster1/lifetime.dat, file_b: cluster_trj/2/cluster1/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/2/cluster1/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/2/cluster1/average_map.dat, file_b: cluster_trj/2/cluster1/average_map.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/assignment.dat, file_b: cluster_trj/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/cluster0/lifetime.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/cluster0/lifetime.dat, file_b: cluster_trj/1/cluster0/lifetime.dat, errors:-1 This file doesn't exist at all: cluster_trj/1/cluster0/average_map.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_trj/1/cluster0/average_map.dat, file_b: cluster_trj/1/cluster0/average_map.dat, errors:-1 Test 3: Framewise cluster analysis.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: cluster_res/lifetime/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/3/assignment.dat, file_b: cluster_res/lifetime/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/2/assignment.dat, file_b: cluster_res/lifetime/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/lifetime/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/lifetime/1/assignment.dat, file_b: cluster_res/lifetime/1/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/3/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/3/assignment.dat, file_b: cluster_res/distance/3/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/2/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/2/assignment.dat, file_b: cluster_res/distance/2/assignment.dat, errors:-1 This file doesn't exist at all: cluster_res/distance/1/assignment.dat. This probably means that CONAN could not run at all. file_a: correct_output/cluster_res/distance/1/assignment.dat, file_b: cluster_res/distance/1/assignment.dat, errors:-1 Test 4: Residue-wise cluster analysis.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: blocking/block_out.txt. This probably means that CONAN could not run at all. file_a: correct_output/blocking/block_out.txt, file_b: blocking/block_out.txt, errors:-1 Test 5: Blocking analysis.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: pca/pc.10.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.10.dat, file_b: pca/pc.10.dat, errors:-1 This file doesn't exist at all: pca/pc.5.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.5.dat, file_b: pca/pc.5.dat, errors:-1 This file doesn't exist at all: pca/pc.2.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.2.dat, file_b: pca/pc.2.dat, errors:-1 This file doesn't exist at all: pca/pc.6.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.6.dat, file_b: pca/pc.6.dat, errors:-1 This file doesn't exist at all: pca/pc.9.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.9.dat, file_b: pca/pc.9.dat, errors:-1 This file doesn't exist at all: pca/pc.4.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.4.dat, file_b: pca/pc.4.dat, errors:-1 This file doesn't exist at all: pca/pc.8.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.8.dat, file_b: pca/pc.8.dat, errors:-1 This file doesn't exist at all: pca/pc.3.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.3.dat, file_b: pca/pc.3.dat, errors:-1 This file doesn't exist at all: pca/pca_projections.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pca_projections.dat, file_b: pca/pca_projections.dat, errors:-1 This file doesn't exist at all: pca/pca_output.txt. This probably means that CONAN could not run at all. file_a: correct_output/pca/pca_output.txt, file_b: pca/pca_output.txt, errors:-1 This file doesn't exist at all: pca/pc.1.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.1.dat, file_b: pca/pc.1.dat, errors:-1 This file doesn't exist at all: pca/pc.7.dat. This probably means that CONAN could not run at all. file_a: correct_output/pca/pc.7.dat, file_b: pca/pc.7.dat, errors:-1 Test 6: Principal component analysis.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00007_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007_dr.init.dat, file_b: matrices/00007_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00009_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009_dr.init.dat, file_b: matrices/00009_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00003_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003_dr.init.dat, file_b: matrices/00003_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00009_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009_dr.prev.dat, file_b: matrices/00009_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00004_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004_dr.prev.dat, file_b: matrices/00004_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 This file doesn't exist at all: matrices/00006_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006_dr.prev.dat, file_b: matrices/00006_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00008_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008_dr.init.dat, file_b: matrices/00008_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00001_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001_dr.prev.dat, file_b: matrices/00001_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00005_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005_dr.prev.dat, file_b: matrices/00005_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00001_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001_dr.init.dat, file_b: matrices/00001_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00005_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005_dr.init.dat, file_b: matrices/00005_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00008_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008_dr.prev.dat, file_b: matrices/00008_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00002_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002_dr.prev.dat, file_b: matrices/00002_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00004_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004_dr.init.dat, file_b: matrices/00004_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00002_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002_dr.init.dat, file_b: matrices/00002_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00010_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010_dr.prev.dat, file_b: matrices/00010_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00003_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003_dr.prev.dat, file_b: matrices/00003_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00006_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006_dr.init.dat, file_b: matrices/00006_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00007_dr.prev.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007_dr.prev.dat, file_b: matrices/00007_dr.prev.dat, errors:-1 This file doesn't exist at all: matrices/00010_dr.init.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010_dr.init.dat, file_b: matrices/00010_dr.init.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 Test 7: Rereading of sparse files.... FAILED sh: 1: Syntax error: Bad fd number This file doesn't exist at all: aggregate/timeline.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/timeline.dat, file_b: aggregate/timeline.dat, errors:-1 This file doesn't exist at all: aggregate/native_contacts.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/native_contacts.dat, file_b: aggregate/native_contacts.dat, errors:-1 This file doesn't exist at all: aggregate/total_interactions.y.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/total_interactions.y.dat, file_b: aggregate/total_interactions.y.dat, errors:-1 This file doesn't exist at all: aggregate/total_interactions.x.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/total_interactions.x.dat, file_b: aggregate/total_interactions.x.dat, errors:-1 This file doesn't exist at all: aggregate/time_mdmat_rmsd.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/time_mdmat_rmsd.dat, file_b: aggregate/time_mdmat_rmsd.dat, errors:-1 This file doesn't exist at all: aggregate/mdmat_average_rmsf.dat. This probably means that CONAN could not run at all. file_a: correct_output/aggregate/mdmat_average_rmsf.dat, file_b: aggregate/mdmat_average_rmsf.dat, errors:-1 This file doesn't exist at all: matrices/00010.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00010.dat, file_b: matrices/00010.dat, errors:-1 This file doesn't exist at all: matrices/00008.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00008.dat, file_b: matrices/00008.dat, errors:-1 This file doesn't exist at all: matrices/00001.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00001.dat, file_b: matrices/00001.dat, errors:-1 This file doesn't exist at all: matrices/00003.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00003.dat, file_b: matrices/00003.dat, errors:-1 This file doesn't exist at all: matrices/00002.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00002.dat, file_b: matrices/00002.dat, errors:-1 This file doesn't exist at all: matrices/00004.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00004.dat, file_b: matrices/00004.dat, errors:-1 This file doesn't exist at all: matrices/00005.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00005.dat, file_b: matrices/00005.dat, errors:-1 This file doesn't exist at all: matrices/00007.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00007.dat, file_b: matrices/00007.dat, errors:-1 This file doesn't exist at all: matrices/00000.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00000.dat, file_b: matrices/00000.dat, errors:-1 This file doesn't exist at all: matrices/00009.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00009.dat, file_b: matrices/00009.dat, errors:-1 This file doesn't exist at all: matrices/00006.dat. This probably means that CONAN could not run at all. file_a: correct_output/matrices/00006.dat, file_b: matrices/00006.dat, errors:-1 Test 8: Asymmetric mode.... FAILED 7 test(s) failed. The output of the failed tests has been preserved. It is possible that the deviations are minor. The failures are in the following folders: 2_Pearson 3_ClusterTraj 4_ClusterRes 5_Blocking 6_PCA 7_Reread 8_Asymmetric — You are receiving this because you modified the open/close state. 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Answer 14 · 2019-05-20T08:07:13.000Z

Thank you, Its working fine now.