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shendurelab / MPRAflow

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data
Apache License 2.0
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failed at calc_correlations step #50

Closed xunchen85 closed 3 years ago

xunchen85 commented 3 years ago

Hi Max,

When I ran count.nf function, I stuck at this step with the error of outputing *.png files. Following the messages, I was able to successfully run the Rscript independently and obtain corresponding correlation.txt and multiple png files as I attached.

I want to double-check with you whether I missed other downstream steps with this error? Do I really need to debug this error about outputting figures in the pipeline?

Thanks, Xun

image image

visze commented 3 years ago

Hi xun,

Sorry that your run into an error again. Calc correlation and make rnaster tables are the last steps. So it seems to be ok.

Maybe it is a runtime error. Creating these plots take sometimes ages an the job got killed. You can change the label to longtime here: https://github.com/shendurelab/MPRAflow/blob/3df34853904e0245507a361c700791c3e49a7e0e/count.nf#L607

Maybe this helps. But anyway you should have all the output files of the count workflow because you run the script by yourself.

Best, Max

Xun Chen @.***> schrieb am Mi., 21. Juli 2021, 08:41:

Hi Max,

When I ran count.nf function, I stuck at this step with the error of outputing *.png files. Following the messages, I was able to successfully run the Rscript independently and obtain corresponding correlation.txt and multiple png files as I attached.

I want to double-check with you whether I missed other downstream steps with this error? Do I really need to debug this error about outputting figures in the pipeline?

Thanks, Xun

[image: image] https://user-images.githubusercontent.com/9758589/126442306-6c8a67a1-c973-4ac5-bbf7-8178007d952e.png [image: image] https://user-images.githubusercontent.com/9758589/126443077-aa5587c1-4808-4ddf-b522-3c7ba8926cfa.png

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xunchen85 commented 3 years ago

Hi Max,

Thanks for your prompt reply. I guess the error is due to the Cairo, which I did not successfully set up in the environment. I tried but it failed. Anyhow, I'm glad it went through.

Thanks for your confirmation.

Best, Xun