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Sina Majidian edited this page Jan 13, 2025 · 4 revisions 
$ ls .
in_folder  out_folder  run_qfo3  slurm-45302634.out  work
$ ls work/65/04e6df512e4b54eda611677fa00440
pickle_hogs  species_tree_checked.nwk

$ cd work/65/04e6df512e4b54eda611677fa00440
$ ls .c*
.command.begin  .command.err  .command.log  .command.out  .command.run  .command.sh  .exitcode

 $ tail .command.err 
2024-07-10 04:37:37 DEBUG    [<<class 'Bio.Align.MultipleSeqAlignment'> instance (3 records of length 774) at 7f23cdcd7c10>, <<class 'Bio.Align.MultipleSeqAlignment'> instance (5 records of length 663) at 7f23cd5254c0>]...
2024-07-10 04:37:37 DEBUG    max length is 774 .
2024-07-10 04:37:37 DEBUG    running mafft took 0.7974371910095215
2024-07-10 04:37:37 DEBUG    All sub-hogs are merged, merged_msa (8,784) for rhog: D0680561, taxonomic level: LUCA
2024-07-10 04:37:37 INFO     Filtering columns (gap_ratio threshold=0.5): keep 659/784
2024-07-10 04:37:37 INFO     Gap ratio distribution (percentiles 10, 25, 50, 75, 90): [0.    0.    0.    0.125 0.75 ]
2024-07-10 04:37:38 INFO     

      /-tr|H2MCK5|H2MCK5_ORYLA||ORYLA||1056019410
   /-|
  |   \-tr|A9V5V4|A9V5V4_MONBE||MONBE||1012006064
  |
--|      /-tr|E3KMD8|E3KMD8_PUCGT||PUCGT||1031007566
  |   /-|
  |  |  |   /-sp|P0CQ20|PMIP2_CRYNJ||CRYNJ||1036000754
  |  |   \-|
   \-|      \-sp|P0CQ18|PMIP1_CRYNJ||CRYNJ||1036000753
     |
     |   /-tr|C7G061|C7G061_DICDI||DICDI||1049000185
      \-|
        |   /-tr|B8LBW5|B8LBW5_THAPS||THAPS||1075010665
         \-|
            \-tr|A0A1D6GTY7|A0A1D6GTY7_MAIZE||MAIZE||1048007046
2024-07-10 04:37:38 INFO     All subHOGs for the rootHOG D0680561 as OrthoXML format is written in pickle_hogs/file_D0680561.pickle
$

$ tail  .command.log 
  |  |   \-|
   \-|      \-sp|P0CQ18|PMIP1_CRYNJ||CRYNJ||1036000753
     |
     |   /-tr|C7G061|C7G061_DICDI||DICDI||1049000185
      \-|
        |   /-tr|B8LBW5|B8LBW5_THAPS||THAPS||1075010665
         \-|
            \-tr|A0A1D6GTY7|A0A1D6GTY7_MAIZE||MAIZE||1048007046
2024-07-10 04:37:38 INFO     All subHOGs for the rootHOG D0680561 as OrthoXML format is written in pickle_hogs/file_D0680561.pickle

 $ cat .command.sh 
#!/bin/bash -euo pipefail
fastoma-infer-subhogs --input-rhog-folder /scratch/smajidi1/qfo4/work/e4/389469e036a8a64a3cb0f3a799fc3b/rhogs_rest/71                                --species-tree species_tree_checked.nwk                               --output-pickles pickle_hogs                               -vv                               --msa-filter-method col-row-threshold                               --gap-ratio-row 0.3                               --gap-ratio-col 0.5                               --number-of-samples-per-hog 5

 head -n 20 .command.run 
#!/bin/bash
#SBATCH -J nf-hog_rest_(25)
#SBATCH -o /scratch/smajidi1/qfo4/work/65/04e6df512e4b54eda611677fa00440/.command.log
#SBATCH --no-requeue
#SBATCH --signal B:USR2@30
#SBATCH -t 04:00:00
#SBATCH --mem 12288M
#SBATCH -p cpu
NXF_CHDIR=/scratch/ss/f/work/65/04e6df512e4b54eda611677fa00440
# NEXTFLOW TASK: hog_rest (25)
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}


nxf_sleep() {
  sleep $1 2>/dev/null || sleep 1;
}

Note

The file .command.run (shown above) includes the slurm job script that were executed by nextflow. Note this part #SBATCH -J nf-hog_rest_(25).

You can use sacct to print all the submitted jobs (e.g. during past 2 days):

$sacct --format=jobid%-15,jobname%40,partition%5octres%40,cputime,totalcpu,maxrss,submit,state%15,exitcode,elapsed --starttime now-2days

45302815.batch                                     batch         00:11:24  11:13.133    689932K 2024-07-10T04:20:12       COMPLETED      0:0   00:11:24 
45302815.extern                                   extern         00:11:24   00:00:00       932K 2024-07-10T04:20:12       COMPLETED      0:0   00:11:24 
45302816                                nf-hog_rest_(25)   cpu   00:27:21  27:08.707            2024-07-10T04:20:11       COMPLETED      0:0   00:27:21 
45302816.batch                                     batch         00:27:21  27:08.706   2111252K 2024-07-10T04:20:12       COMPLETED      0:0   00:27:21 
45302816.extern                                   extern         00:27:21   00:00:00       928K 2024-07-10T04:20:12       COMPLETED      0:0   00:27:21 
45302817                                 nf-hog_big_(19)   cpu   00:01:16  00:28.146            2024-07-10T04:20:11       COMPLETED      0:0   00:00:19 
45302817.batch                                     batch         00:01:16  00:28.145      1336K 2024-07-10T04:20:12       COMPLETED      0:0   00:00:19

you can grep the job name nf-hog_rest_(25) on sacct output, to see its job id (which is 45302816), then run seff on the job id as below

 $ seff  45302816
Job ID: 45302816
Cluster: cu
User/Group: sm/unig
State: COMPLETED (exit code 0)
Cores: 1
CPU Utilized: 00:27:09
CPU Efficiency: 99.27% of 00:27:21 core-walltime
Job Wall-clock time: 00:27:21
Memory Utilized: 2.01 GB
Memory Efficiency: 16.78% of 12.00 GB

here you can see whether this rootHOG went out of memory.

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