ncbi / rapt

Read Assembly and Annotation Pipeline Tool
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How to know if RAPT is running? #6

Open rfcohen opened 3 years ago

rfcohen commented 3 years ago

I've had success running RAPT but not so much today. How to know if it's doing anything?

./run_rapt.py -a srr3496277
RAPT is now running, it may take a long time to finish. To see the progress, track the verbose log file /Users/rcohen/rapt/raptout_c7d9dee3bd/verbose.log.

No directory created with that name. And subsequently no output (logs or otherwise).

Trying:

./run_rapt.py --test       
RAPT is now running, it may take a long time to finish. To see the progress, track the verbose log file /Users/rcohen/rapt/raptout_436562b3bd/verbose.log.

No directory created with that name. And subsequently no output (logs or otherwise).

rcohen@iMac-Pro rapt % ./run_rapt.py -v
rcohen@iMac-Pro rapt % 

And well '-v' doesn't do anything.

Thanks.

techshine2018 commented 3 years ago

This silence mode behavior of RAPT is by design due to some feedback complaining the output to std is too lengthy and annoying. It could take some time (download the docker image) before the output directory is created and logs start to populate. But with -v option it should eventually print out version information (still, it needs to download and run the image).

That said, there is an undocumented switch, --do-verbose-std, to turn off the silence mode. Launch run_rapy.py with that switch will essentially fork the verbose log to the console along the way.

Sorry for the inconvenience and thank you very much to try our product. Please visit us frequently for new releases with more features and greater usability!

rfcohen commented 3 years ago

This silence mode behavior of RAPT is by design due to some feedback complaining the output to std is too lengthy and annoying. It could take some time (download the docker image) before the output directory is created and logs start to populate. But with -v option it should eventually print out version information (still, it needs to download and run the image).

That said, there is an undocumented switch, --do-verbose-std, to turn off the silence mode. Launch run_rapy.py with that switch will essentially fork the verbose log to the console along the way.

Sorry for the inconvenience and thank you very much to try our product. Please visit us frequently for new releases with more features and greater usability!

  • RAPT team

Really, no feedback is generally bad design. I don't know if it's working or not. It didn't even create the output directory after several hours. There was no obvious process running. IMO it was dead. I will try again with the --do-verbose-std flag. (Maybe that should be un-undocumented just to see if it's working/doing anything)

rfcohen commented 3 years ago

Turns out RAPT was crashing with no error reporting!

techshine2018 commented 3 years ago

No output even with --do-verbose-std ?

rfcohen commented 3 years ago

Didn't try with the --do-verbose-std. It started to work better and produce output. May have been a docker issue. Nonetheless, failing silently != good.