sanger-tol / treeval

Pipelines for the production of Treeval data
https://pipelines.tol.sanger.ac.uk/treeval
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Some resource equations are not parsed correctly #278

Closed DLBPointon closed 7 months ago

DLBPointon commented 7 months ago

Description of the bug

Some of the base.config equations are being parsed incorrectly, for instance: Miniprot_index has the config

memory = { check_max( 1.GB     * ( fasta.size() < 2e9 ? 30 : Math.ceil( reference.size() / 1e+9 * 50 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }

With a genome of 1.4Gb is being resolved as 351MB

Needs further investigation, perhaps adding a round up if something is being resolved. as a 0.3 and acting as a division rather than multiplier

Command used and terminal output

TERM_MEMLIMIT: job killed after reaching LSF memory usage limit.
  Exited with exit code 130.

  Resource usage summary:

      CPU time :                                   0.10 sec.
      Max Memory :                                 351 MB
      Average Memory :                             122.33 MB
      Total Requested Memory :                     -
      Delta Memory :                               -
      Max Swap :                                   -
      Max Processes :                              15
      Max Threads :                                29
      Run time :                                   4 sec.
      Turnaround time :                            5 sec.

Relevant files

No response

System information

No response

DLBPointon commented 7 months ago

Also occuring with Minimap2_align

        memory = { check_max( 1.GB     * ( reference.size() < 2e9 ? 30 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }

Resolved to 115MB

I think this is an edge case with certain genome sizes causing the error