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Peregrine: Fast Genome Assembler Using SHIMMER Index
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What's `pypeflow.simple_pwatcher_bridge:(slept for another 1100.0s -- another 110 loop iterations)` #35

Closed SHuang-Broad closed 4 years ago

SHuang-Broad commented 4 years ago

Hi Jason,

My assembly experiment is running a bit longer than expected (~50x, haploid, human-sized genome with canu-corrected CLR reads), and I'm seeing the following a lot

pypeflow.simple_pwatcher_bridge:(slept for another 1100.0s -- another 110 loop iterations)

while memory usage is high throughout.

What does the error message mean? Is it stuck?

Thanks! Steve

SHuang-Broad commented 4 years ago

I think I got this figured out. The input I gave peregrine was a fasta.gz. Switched to fasta and the process went much faster.