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kbaseattic / assembly

An extensible framework for genome assembly.
MIT License
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fix incoherency about running jobs in various pieces #305

Open sebhtml opened 9 years ago

sebhtml commented 9 years ago

The REST endpoint for listing running jobs is /admin/system/jobs.

I don't think that this is used by any piece in the client.

My test machine is seb-kbase-devel.mcs.anl.gov.

The plan is to reproduce the problem first.

sebhtml commented 9 years ago

List of jobs with the current code:

http://seb-kbase-devel.mcs.anl.gov:8000/admin/system/jobs

sebhtml commented 9 years ago

I am not able to reproduce the issue on a all-in-one installation.

I tried these scenarios:

Further, I am getting this Spades error, with an instance with 22 GB...

0:05:56.854 16M / 3G INFO General (kmer_index.hpp : 351) K-mer counting done. There are 393029508 kmers in total. 0:05:56.854 16M / 3G INFO General (kmer_index.hpp : 353) Merging temporary buckets. 0:06:10.578 16M / 3G INFO K-mer Index Building (kmer_index.hpp : 476) Building perfect hash indices 0:09:14.109 148M / 3G INFO General (kmer_index.hpp : 371) Merging final buckets. 0:09:20.101 148M / 3G INFO K-mer Index Building (kmer_index.hpp : 515) Index built. Total 135963681 bytes occupied (2.7675 bits per kmer). 0:09:20.102 148M / 3G ERROR K-mer Counting (kmer_data.cpp : 260) The reads contain too many k-mers to fit into available memory limit. Increase memory limit and restart

I will thus switch to a smaller dataset since this error is not the one I am working on right now.