Piranha crashing after latest update

[AShaw1802]

Hi, I've just been running PIRANHA with the test data after the latest update and it keeps crashing at generate_report: Error in rule generate_report: jobid: 0 input: /data/run_data/output/piranha_output/published_data/vp1_sequences.fasta, /tmp/tmpmve3kmel/barcode07/variation_info.json, /tmp/tmpmve3kmel/barcode07/masked_variants.csv, /tmp/tmpmve3kmel/barcode07/variants.csv, /tmp/tmpmve3kmel/preprocessing_config.yaml output: /data/run_data/output/piranha_output/barcode_reports/barcode07_report.html

I haven't been able to test this on another laptop as I've only one to hand, but could you please check if this is a general issue? Thanks, Alex

[aineniamh]

Could you provide the test data and what command you ran, and I'll run it here, because piranha is passing tests on the repo so it can run (and runs locally on my machine), but may be some edge case breaking!

[AShaw1802]

Test.zip I'm using the test data from Piranha (attached), but running it in the GUI which I think we may have narrowed down the problem to- Catherine has now also had the same problem with the GUI. The GUI just updated Piranha this morning, which is why I thought it might the the new edition from over the weekend. Maybe this is one for Corey instead?

[aineniamh]

Ah right! So the green tick that shows up on the piranha repo means that github has tested piranha on the test data and managed to run to completion. I'm not sure what the exact GUI issue might be- but it could be a versioning issue of some sort. If it runs to the report, that suggests to me that mako might be causing an issue.

@CorwinAnsley do you know what the issue might be?

[jolnack]

Hi, Also run the updated Piranha on command line using some data and got similar error. Screenshot here. you might need to zoom in to see the message as it quite hard to read.

Catherine just pointed out to me that the error I got using the command line might just be an issue with the data set that I used. I just now run the updated Piranha on the command line using the Test data and that work fine.

[aineniamh]

What was the data you used? If you share it (even by email) I can help debug your first test case

[jolnack]

I couldn’t send the data via email even as compressed file as it is bigger than the server allows. I will send you the dropbox link to access it :)

[AShaw1802]

The data that I used is attached to my earlier message- it's Test.zip. It's the test data from the Piranha repository.

[aineniamh]

We found the source of the issue! It was to do with the change that javier requested about the header format no longer including the snp string. Should be fixed now- will wait for tests to pass and then tag a new release

[aineniamh]

The data that I used is attached to my earlier message- it's Test.zip. It's the test data from the Piranha repository.

@AShaw1802, thanks I'd seen that- was asking Joyce for the data for her issue that time!

[aineniamh]

I believe this should be resolved now for Alex, will investigate what the issue for yours was @jolnack!

[AShaw1802]

We just downloaded and reran the analysis and it's all working fine now- thanks for the rapid fix!