Pangenome script benchmark

[ccbaumler]

The time -v output of the non-abund pangenome database curation suggesting the resources should be set to ~20GB and 2hrs per database.

        Command being timed: "./make-pangenome-sketches.py /home/baumlerc/2022-database-covers/dbs/gtdb-rs214-k21.zip -t /home/baumlerc/2022-database-covers/dbs/gtdb-rs214.lineages.sqldb -o test-no-abund.zip -k 21
 -r species --csv the-csv-file-you-desire_no-abund.csv"
        User time (seconds): 4469.89
        System time (seconds): 566.98
        Percent of CPU this job got: 83%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 1:39:58
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 17040560
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 96200
        Minor (reclaiming a frame) page faults: 88823161
        Voluntary context switches: 5672989
        Involuntary context switches: 60363
        Swaps: 0
        File system inputs: 51679104
        File system outputs: 5437344
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

When running the script with all the bells and whistles this time -v output suggests that the slurm resources should be set to >40GB and >2hrs.

        Command being timed: "./make-pangenome-sketches.py /home/baumlerc/2022-database-covers/dbs/gtdb-rs214-k21.zip -t /home/baumlerc/2022-database-covers/dbs/gtdb-rs214.lineages.sqldb -o test.zip -k 21 -r species -a --csv the-csv-file-you-desire.csv"
        User time (seconds): 5800.88
        System time (seconds): 717.47
        Percent of CPU this job got: 87%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 2:04:42
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 39818112
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 96751
        Minor (reclaiming a frame) page faults: 162501748
        Voluntary context switches: 5673639
        Involuntary context switches: 67568
        Swaps: 0
        File system inputs: 51784920
        File system outputs: 5634248
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0