Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Not clear why KINC-nf not running cond-test #7

Open
JohnHadish opened this issue Oct 17, 2022 · 0 comments
Open

Not clear why KINC-nf not running cond-test #7

JohnHadish opened this issue Oct 17, 2022 · 0 comments

Comments

@JohnHadish
Copy link

JohnHadish commented Oct 17, 2022

I run KINC-nf with the following arguments:

nextflow run systemsgenetics/kinc-nf \
	-r master \
	-profile singularity,kamiak  \
	--input_dir "GEM.GEM.TPM_clean" \
	--graph_name "Gala_Apple" \
	--data_missing_val "NA" \
	--similarity_clusmethod "gmm" \
        --similarity_minsamp 12 \
	--similarity_maxclus 6 \
	--condtest_feat_tests "Treatment.ID.P,Short_Long,MCP,CA,Days.Postharvest" \
	--condtest_feat_types "Days.Postharvest:ordinal" \
	--max_cpus 100 \
	--max_gpus 0 

and the output log says that condtest will be ran:

cond-test
  enabled:        true
  chunks:         4
  feat_tests:     Treatment.ID.P,Short_Long,MCP,CA,Days.Postharvest
  feat_types:     Days.Postharvest:ordinal
  alpha:          0.001
  power:          0.8

But condtest is not ran and KINC-nf completes without any errors:

[-        ] process > import_emx                    -
[-        ] process > similarity_chunk              -
[-        ] process > similarity_merge              -
[2d/ce094a] process > corrpower (GEM.GEM.TPM_clean) [100%] 1 of 1 ✔
[-        ] process > condtest                      -
[-        ] process > extract                       -
Completed at: 16-Oct-2022 19:38:07
Duration    : 3h 32m 37s
CPU hours   : 3.5
Succeeded   : 1

Request: if KINC-nf is not able to run condtest for some reason, it should fail and tell the user why it failed

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant