AssertionError

[CSouque]

Hi!

I have a weird error with roughly half of my samples when I run plASgraph2:

Traceback (most recent call last): File "/home/cs477/plASgraph2/src/plASgraph2_classify.py", line 149, in <module> main_gfa(**arg_dict) File "/home/cs477/plASgraph2/src/plASgraph2_classify.py", line 84, in main_gfa prediction_df = test_one('', graph_file, model, parameters, '.') File "/home/cs477/plASgraph2/src/plASgraph2_classify.py", line 91, in test_one G = create_graph.read_single_graph(file_prefix, graph_file, sample_id, parameters['minimum_contig_length']) File "/home/cs477/plASgraph2/src/create_graph.py", line 219, in read_single_graph read_graph(graph_file, None, sample_id, graph, minimum_contig_length) File "/home/cs477/plASgraph2/src/create_graph.py", line 124, in read_graph assert node_id not in graph AssertionError

Do you know what could be causing this and how to fix it?

Happy to provide a failing and succeeding assembly graph if this helps.

Best,

[cchauve]

I would welcome to have examples of assembly graphs.

[CSouque]

GCID-2726 worked but GCID-2587 failed Assembly_graphs.zip

[CSouque]

Hi!

I wanted to check if you had any inputs and if more examples would be useful. We are currently doing a plasmid tool benchmarking projects, and it would be great if I could have the full results for plasgraph2

Best,

[cchauve]

My apologies, I have not had time to deal with this. cedric chauve

---

From: CSouque @.***> Sent: May 17, 2024 12:22 To: cchauve/plASgraph2 Cc: Computational Methods for Comparative Genomics at Simon Fraser University; Comment Subject: Re: [cchauve/plASgraph2] AssertionError (Issue #3)

Hi!

I wanted to check if you had any inputs and if more examples would be useful. We are currently doing a plasmid tool benchmarking projects, and it would be great if I could have the full results for plasgraph2

Best,

— Reply to this email directly, view it on GitHubhttps://github.com/cchauve/plASgraph2/issues/3#issuecomment-2118214988, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACXV7DWAINDUE25MJXWKAFTZCZH2TAVCNFSM6AAAAABG6XECF2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJYGIYTIOJYHA. You are receiving this because you commented.Message ID: @.***>

[tvinar]

Could you please provide an input on which it fails? I can look into that.

[CSouque]

Hi! Thanks for coming back to me! I managed to fix it, and it seems some of my assemblies graphs had gotten corrupted while transferring them? (see picture and file attached). Getting back to the original assemblies graphs seems to have fixed it, so it seems the error was due to a faulty graph (still no idea how that did happen) DIV2357.gfa.zip

[JPWestley]

Hello CSouque.

I am interested in your plasmid tool benchmarking project. Would you be willing to share what tools you are looking at, and which appear to be performing best? I am currently trying to decide which tool(s) to use for a project myself. You can email me at jw1235@exeter.ac.uk if you would prefer that.

Many thanks in advance! Joe

[tvinar]

I would be interested as well ;)