get error when creating conda environments

[wangmhan]

Hi, Thanks for the nice pipeline!

I tried to set up the workflow on a big server. I managed to use mamba to set the environment and run smoothly with the test code: sh setup_test.sh. Then I get stuck when runing this code: snakemake --use-conda --cores $Ncores --configfile config/config.yml
I modified it by specify another profile: snakemake --profile ~/profiles/server-slurm --use-conda --cores 1 --configfile config/config.yml

Because the cluster nodes have no internet access, so can only run it on a login node with 1 core. Here is the profile settings:
default-resources: mem_mb=6000

cluster: "submit.py"
cluster-status: "check_status.sh"
cluster-cancel: "scancel"

max-jobs-per-second: 5
max-status-checks-per-second: 0.2
local-cores: 1
latency-wait: 120
jobs: 50
keep-going: True
rerun-incomplete: True
printshellcmds: True

Here is the log:
Workflow defines that rule bwaindex is eligible for caching between workflows (use the --cache argument to enable this).
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 50
Job stats:
job count min threads max threads

---

bin_pairs_library 8 1 1
chunk_fastq 4 1 1
default 1 1 1
download_fastqs 1 1 1
map_chunks_bwa_pipe 4 1 1
merge_dedup 4 1 1
merge_runs 5 1 1
merge_stats_libraries_into_groups 3 1 1
merge_zoom_library_group_coolers 6 1 1
parse_sort_chunks 4 1 1
scaling_pairs_library 4 1 1
zoom_library 8 1 1
total 52 1 1

Select jobs to execute...
WorkflowError:
Error grouping resources in group '744b017c-b3d8-4ed6-8e0a-ee3979e6939e': Not enough resources were provided. This error is typically caused by a Pipe group requiring too many resources. Note that resources are summed across every member of the pipe group, except for ['runtime'], which is calculated via max(). Excess Resources:
_cores: 2/1

Do you have any ideas how to solve it? Big thanks!

Best,
Menghan

[srinitha709]

The error occurs because Snakemake is trying to allocate more cores than available.
Limit cores per rule ensure each rule requests only the available cores (1 in your case) Add resources cores=1 to your rules in the Snakefile and also additionally
Adjust profile by modify the server-slurm profile to request 1 core by default or
Check resource requests ensure no rule is implicitly requesting more than 1 core.

[wangmhan]

Thank you! I will adjust the number of cores.