Monitoring

Monitoring ParGenes run

ParGenes will write the most important logs in OUTPUT_DIR/pargenes_logs.txt, where OUTPUT_DIR is specified with -o. At each step (parsing, modeltest, ML search etc.), ParGenes will redirect the logs to another file (indicated in pargenes_logs.txt). When opening this other log file, you will find how many jobs where already processed.

For instance, if pargenes_logs.txt contains:

[...]
Logs will be redirected to /home/you/pargenes/pargenes_run/mlsearch_run/logs.txt

Then you should open this file and see (for instance):

[...]
  End of msa150_fasta after 457720ms  (170/5885)
  ## Started msa171_fasta on [66:69]
  End of msa84_fasta after 221887ms  (171/5885)
  ## Started msa271_fasta on [154:157]
  End of msa53_fasta after 227789ms  (172/5885)
  ## Started msa12_fasta on [122:122]
  End of msa37_fasta after 458738ms  (173/5885)

## Started msa171_fasta on [66:69] means that ParGenes started to analyse the msa msa171.fasta on 4 cores (with ranks 66 to 69)`

End of msa150_fasta after 457720ms (170/5885) Means that ParGenes finished to analysed the msa msa150.fasta after 457s, and that 170 commands out of 5885 finished.

ParGenes always tries to start with the longest jobs, and to finish with the shorter ones (although there is no way of knowing that for sure in advance).