# Grid Jobs Benchmarking

**URL:** <https://forum.biobakery.org/t/grid-jobs-benchmarking/8542>\
**Category:** bioBakery workflows\
**Created:** [October 3, 2025, 6:27pm UTC](https://forum.biobakery.org/t/grid-jobs-benchmarking/8542 "2025-10-03T18:27:32Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![J\_Lemon](https://avatars.discourse-cdn.com/v4/letter/j/919ad9/32.png) [@J\_Lemon](https://forum.biobakery.org/u/J_Lemon)\
**Post date:** [October 3, 2025, 6:27pm UTC](https://forum.biobakery.org/t/grid-jobs-benchmarking/8542/1 "2025-10-03T18:27:32Z")

</div>

I’m testing out running grid-jobs with biobakery\_workflows on a computing cluster and have found that bench marking each step is really slowing down the analysis. Right now I’m testing out running grid jobs with one of the demo samples and have found that benchmarking each step is taking anywhere from 1~10 minutes before the next job is submitted. I’m mostly concerned that if I ran a big batch of samples the bench marking would balloon the analysis time. Is this typically the case, or could there be some issues on my end?

- Currently I’m using biobakery\_workflows 3.1 and anadama2 0.10.0

```auto
sbatch -c16 biobakery_workflows wmgx
 --input ./test_files --output ./biobake_output 
--functional-profiling-option='--bypass-translated-search' 
--threads 32 
--taxonomic-profiling-options "--bowtie2db 
miniconda3/envs/biobake/lib/python3.10/site-
packages/metaphlan/metaphlan_databases/ 
--index mpa_vJun23_CHOCOPhlAnSGB_202403" 
--grid slurm
 --grid-jobs 2 --grid-partition node
 --bypass-strain-profiling

```

Heres an example from the log:

```auto
2025-10-03 17:50:43,657 root
log_grid_output INFO: Grid 16 from task id return code:0

2025-10-03 17:50:43,658 LoggerReporter log_event       
INFO: task 16, humann_renorm_ecs_relab ____ HD32R1_subsample.gz : grid job id 4836412 has status Getting benchmarking data

2025-10-03 17:59:43,499 root get_queue_status       
INFO: Getting latest queue info to refresh job status
2025-10-03 17:59:43,566 root record_benchmark        
INFO: Benchmark information for job id 16:

```