Error run_camsa.py

[navajeet123]

Hi,

I am getting an error while executing run_camsa.py Please suggest!

2020-04-12 20:48:48,149 - CAMSA.main - INFO - Starting the analysis 2020-04-12 20:48:48,149 - CAMSA.main - INFO - Processing input 2020-04-12 20:48:48,149 - CAMSA.main - INFO - Reading assembly points 2020-04-12 20:48:49,078 - CAMSA.main - INFO - Merging assembly points from different sources into a set of unique ones. 2020-04-12 20:48:49,819 - CAMSA.main - INFO - Processing assemblies' subgroups 2020-04-12 20:48:49,819 - CAMSA.main - INFO - Processing assembly points taking both order and orientation into account 2020-04-12 20:48:49,895 - CAMSA.main - INFO - Processing assembly points, taking just order into account 2020-04-12 20:48:50,768 - CAMSA.main - INFO - Computing assembly points conflicts 2020-04-12 20:48:55,288 - CAMSA.main - INFO - Obtaining a merged assembly, using maximal-matching strategy Traceback (most recent call last): File ".camsa-env/bin/run_camsa.py", line 252, in min_cw=args.c_merging_cw_min) File "camsa-env/lib/python3.7/site-packages/camsa/core/merging.py", line 131, in maximal_matching for cc in networkx.connected_component_subgraphs(G=cover_graph, copy=True): AttributeError: module 'networkx' has no attribute 'connected_component_subgraphs' (END)

Thanks

[aganezov]

Please advise if you are running conda/PyPi installation of CAMSA or the Github source one. There has been a lag in updating the conda /PyPi distribution in my part. I'll be correcting it shortly.

[navajeet123]

Hi Aganezov,

This is the Github source one.

Thanks

[aganezov]

That's rather strange, as the line 131 (as per you stack trace) in the Github master branch reads

        for cc in networkx.connected_components(G=cover_graph):

and not

for cc in networkx.connected_component_subgraphs(G=cover_graph, copy=True):

Note, sadly, the version numbering does not ideally separate the Github updated version from PyPi/conda one (I'm updating PyPi/conda distributions now to be inline with networkx 2.4 compatibility)

[navajeet123]

Dear Aganezov, many thanks for your response. Kindly let me know,once you are done with the update. I will install again and would be very much happy to execute once again.

[aganezov]

Hello! I've created a new version release 1.3 on Github (https://github.com/compbiol/CAMSA/releases/tag/1.3) from the most current master branch snapshot, and I've also updated the PyPi/conda distirbutions with it. Most recent Travis CI build (https://travis-ci.org/github/compbiol/CAMSA/builds/674439824) suggests that the release shall work fine, as it successfully ran on OSX/Linux with various vesions of python on several included examples. Let me know if this addresses your problem!

[navajeet123]

Dear Aganezov, Many thanks! run_camsa.py completed successfully.

Proceeded with down-line step. Error: Traceback (most recent call last): File "../camsa-env/bin/camsa_points2fasta.py", line 146, in for cc in networkx.connected_component_subgraphs(G=assembly_graph): AttributeError: module 'networkx' has no attribute 'connected_component_subgraphs'

Please share your views.

Thanks

[aganezov]

glad to hear the previous issue was resolved.

The problem you've outlined seems to be identical to the one mentioned above (i.e., outdated (w.r.t. most recent networkx library) code), but I've checked both the source code on Github as well as distributions on Github release, conda, and PyPi, and all have correct updated code, that would not produced such an issue.

Can it be, that while you've updated the camsa package to a newwer version, you have not rerun the actual installation process, and thus you have an outdated version of camsa_points2fasta.py script in your bin?

[navajeet123]

Dear Aganezov,

Thanks for helping me out! Re-installed again. All my queries are resolved. Got the merged assembly.

Regards Navajeet

[aganezov]

Glad to hear issues are now resolved!