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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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How to check if my custom database complete? #657

Open Sabrin2020 opened 1 year ago

Sabrin2020 commented 1 year ago

I got an error after building my custom database but the slurm script message said completed not failed

cat kraken_test1.err

Lmod is automatically replacing "hpc-uniol-env" with "hpc-env/8.3".

Loading database information... done. 96799063 sequences (29233.32 Mbp) processed in 4670.492s (1243.5 Kseq/m, 375.55 Mbp/m). 73330577 sequences classified (75.76%) 23468486 sequences unclassified (24.24%) slurmstepd: error: Exceeded step memory limit at some point. slurmstepd: error: Exceeded job memory limit at some point.

Does Exceeded job memory limit at some point means database could be corrupted?

Sabrin2020 commented 1 year ago

now when I run bracken-build I get same error but i ran kraken on a test sample before and it worked just fine!!

Loading database information...Failed attempt to allocate 569289122376bytes; you may not have enough free memory to load this database. If your computer has enough RAM, perhaps reducing memory usage from other programs could help you load this database? classify: unable to allocate hash table memory find: ‘cat’ terminated by signal 13

jenniferlu717 commented 1 year ago

It seems as if your system does not have enough memory for your run. It could be that when you ran it before there was enough RAM but you may have something else running on the same system that is now using the RAM