pick_open_reference_otus.py does not notify about scarce memory

biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

GNU General Public License v2.0

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pick_open_reference_otus.py does not notify about scarce memory #1468

Open ElDeveloper opened 10 years ago

ElDeveloper commented 10 years ago

A forum user noted that when uclust runs out of memory, the log file generated by the workflow does not inform you about this but the uclust log does. If there's any way to integrate this information into the main log file that would be fantastic!

passdan commented 10 years ago

standard pipeline log:

cogent.app.util.ApplicationError: Error running usearch61. Possible causes are unsupported version (current supported version is usearch v6.1.544) is installed or improperly formatted input file was provided

usearch log:

    ---Fatal error---
    Out of memory, mymalloc(40606580), curr 4.08e+09 bytes

Also, would it be useful to flag that this is an 32 bit usearch problem and that 64 bit solves?

gregcaporaso commented 10 years ago

This would be so useful to have reported back via QIIME. Any takers on this? If this same mechanism would work for usearch as well, that would be fantastic.