error when generating images from a VCF file

[Eugenia-L]

Hi,

I’ve been trying to run SVplaudit using a VCF but I’ve got the following error. It generates some images and then the error comes. How can I fix it?

Traceback (most recent call last): File "Samplot/src/samplot.py", line 2140, in max_coverage)
File "Samplot/src/samplot.py", line 1698, in plot_samples if curr_max_insert_size > max_insert_size: TypeError: '>' not supported between instances of 'NoneType' and 'int'

Thanks in advance Best regards

[jbelyeu]

Apologies for the slow response. SV-plaudit uses two sub-tools, plotcritic and samplot. Samplot has progressed dramatically since the last SV-plaudit update, so for now I would recommend referring to the samplot repository and installing with conda (conda install -c bioconda samplot).

I will prioritize updating plotcritic and sv-plaudit to reflect these changes in the next week or so

[Michaelll123]

Hi Dr. jbelyeu, I installed the package of samplot as you instructed, however, there was still the same error, TypeError: '>' not supported between instances of 'NoneType' and 'int'. So we revised the script of samplot.py with the following sentences:

if not curr_max_insert_size: print("curr_max_insert_size is NONE") else: if curr_max_insert_size > max_insert_size: max_insert_size = curr_max_insert_size print("ok1")

Then the message of 'curr_max_insert_size is NONE' always appeared when the program was running.

By the way, the summary report is like the attached file, and all of the supports are 100% and the total scores are 1. I am not sure why they are so identical? Then how should we filter the SVs based on the supports and scores? Thanks for your patience and reply.

Jiantao

[jbelyeu]

Can you share your samplot version?

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