get error when creating conda environments #18
Description
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