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foerstner-lab / READemption

A pipeline for the computational evaluation of RNA-Seq data
https://reademption.readthedocs.io
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Align subcommand mysteriously takes forever in some runs in ver. 2.0.0 #41

Closed elhossary closed 2 years ago

elhossary commented 2 years ago

Some of the runs went without problems. but there are some runs had issues with no error message produced. But the observation is: The alignment runs normally until segemehl log message "Goodbye." then the it abonormaly takes forever with no finsih, no matter the size of the data When I iterrupted the run, bam files produced but the stats files were not produced. Most propably, the program hangs at the endings of "concurrent" processes. may be the process pool does not close? I also got in one of the runs this message: concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

Tillsa commented 2 years ago

Can you please post the complete align command, the output of tree of the analysis folder before running align and the error message?

Tillsa commented 2 years ago

Fixed in version 2.0.2