RMARKDOWNNOTEBOOK - Error in \cor()\: ! supply both 'x' and 'y' or a matrix-like 'x'
#230
Labels
bug
Something isn't working
Comments
|
Hey there, thanks for the bug report! Without the dataset, I won't be able to look into this. Maybe someone else stumbles across this error as well and can share their data for reproducing :) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Description of the bug
Hello, I am a co-worker of olgabot and this issue is following issue 196. Running the nf-core/differentialabundance pipeline with the current dev version has resolved the
PLOT_EXPLORATORYstep issue but a potentially similar issue arises later on in the pipeline at theMAKE_REPORT_BUNDLEstep. In addition, although theSHINYNGS_APPstep succeeds and publishes a shiny app to shinyapp.io, it has errors and crashes.Command used and terminal output
The exit status of the task that caused the workflow execution to fail was: 1
Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (REDACTED-study_name)'
Caused by:
Essential container in task exited
Command executed:
Dump .params.yml heredoc (section will be empty if parametrization is disabled)
cat <<"END_PARAMS_SECTION" > ./.params.yml
cpus: 2
artifact_dir: artifacts
input_dir: ./
meta:
id: REDACTED-study_name
study_name: REDACTED-study_name
study_type: rnaseq
study_abundance_type: counts
report_file: /.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd
report_title: None
report_author: None
report_description: None
report_scree: true
report_round_digits: 4
observations_type: sample
observations_id_col: sample
observations_name_col: sample
features: matrix_as_anno.feature_metadata.tsv
features_type: gene
features_id_col: gene_id
features_name_col: gene_name
features_metadata_cols: gene_id,gene_name,gene_biotype
features_log2_assays: null
features_gtf_feature_type: transcript
features_gtf_table_first_field: gene_id
filtering_min_samples: 1
filtering_min_abundance: 1
filtering_min_proportion: null
filtering_grouping_var: null
exploratory_main_variable: auto_pca
exploratory_clustering_method: ward.D2
exploratory_cor_method: spearman
exploratory_n_features: 500
exploratory_whisker_distance: 1.5
exploratory_mad_threshold: -5
exploratory_assay_names: raw,normalised,variance_stabilised
exploratory_final_assay: variance_stabilised
exploratory_palette_name: Set1
differential_file_suffix: .deseq2.results.tsv
differential_feature_id_column: gene_id
differential_feature_name_column: gene_name
differential_fc_column: log2FoldChange
differential_pval_column: pvalue
differential_qval_column: padj
differential_min_fold_change: 2
differential_max_pval: 1
differential_max_qval: 0.05
differential_foldchanges_logged: true
differential_palette_name: Set1
differential_subset_to_contrast_samples: false
deseq2_test: Wald
deseq2_fit_type: parametric
deseq2_sf_type: ratio
deseq2_min_replicates_for_replace: 7
deseq2_use_t: false
deseq2_lfc_threshold: 0
deseq2_alt_hypothesis: greaterAbs
deseq2_independent_filtering: true
deseq2_p_adjust_method: BH
deseq2_alpha: 0.1
deseq2_minmu: 0.5
deseq2_vs_method: vst
deseq2_shrink_lfc: true
deseq2_cores: 1
deseq2_vs_blind: true
deseq2_vst_nsub: 1000
gene_sets_files: null
observations: REDACTED-file.tsv
raw_matrix: rsem.merged.gene_counts.assay.tsv
normalised_matrix: all.normalised_counts.tsv
variance_stabilised_matrix: all.vst.tsv
contrasts_file: REDACTED-file.tsv
versions_file: software_versions.yml
logo: nf-core-differentialabundance_logo_light.png
css: nf-core_style.css
citations: CITATIONS.md
END_PARAMS_SECTION
Create output directory
mkdir artifacts
Set parallelism for BLAS/MKL etc. to avoid over-booking of resources
export MKL_NUM_THREADS="2"
export OPENBLAS_NUM_THREADS="2"
export OMP_NUM_THREADS="2"
Work around rstudio/rmarkdown#1508
If the symbolic link is not replaced by a physical file
output- and temporary files will be written to the original directory.
mv "differentialabundance_report.Rmd" "differentialabundance_report.Rmd.orig"
cp -L "differentialabundance_report.Rmd.orig" "REDACTED-study_name.Rmd"
Render notebook
Rscript - <<EOF
params = yaml::read_yaml('.params.yml')
EOF
cat <<-END_VERSIONS > versions.yml
"NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK":
rmarkdown: $(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))")
END_VERSIONS
Command exit status:
1
Command output:
1/72
2/72 [unnamed-chunk-1]
3/72
4/72 [unnamed-chunk-2]
5/72
6/72 [unnamed-chunk-3]
7/72
8/72 [unnamed-chunk-4]
9/72
10/72 [setup]
11/72
12/72 [unnamed-chunk-5]
13/72
14/72 [unnamed-chunk-6]
15/72
16/72 [unnamed-chunk-7]
17/72
18/72 [unnamed-chunk-8]
19/72
20/72 [unnamed-chunk-9]
21/72
22/72 [unnamed-chunk-10]
23/72
24/72 [unnamed-chunk-11]
25/72
26/72 [unnamed-chunk-12]
27/72
28/72 [unnamed-chunk-13]
29/72
30/72 [unnamed-chunk-14]
31/72
32/72 [unnamed-chunk-15]
33/72
34/72 [unnamed-chunk-16]
35/72
36/72 [unnamed-chunk-17]
37/72
38/72 [unnamed-chunk-18]
39/72
40/72 [unnamed-chunk-19]
41/72
42/72 [unnamed-chunk-20]
43/72
44/72 [unnamed-chunk-21]
Command error:
(more omitted..)
7/72
8/72 [unnamed-chunk-4]
9/72
10/72 [setup]
11/72
12/72 [unnamed-chunk-5]
13/72
14/72 [unnamed-chunk-6]
15/72
16/72 [unnamed-chunk-7]
17/72
18/72 [unnamed-chunk-8]
19/72
20/72 [unnamed-chunk-9]
21/72
22/72 [unnamed-chunk-10]
23/72
24/72 [unnamed-chunk-11]
25/72
26/72 [unnamed-chunk-12]
27/72
28/72 [unnamed-chunk-13]
29/72
30/72 [unnamed-chunk-14]
31/72
32/72 [unnamed-chunk-15]
33/72
34/72 [unnamed-chunk-16]
35/72
36/72 [unnamed-chunk-17]
37/72
38/72 [unnamed-chunk-18]
39/72
40/72 [unnamed-chunk-19]
41/72
42/72 [unnamed-chunk-20]
43/72
44/72 [unnamed-chunk-21]
Quitting from lines 706-752 [unnamed-chunk-21] (REDACTED-study_name.Rmd)
Error in
cor():! supply both 'x' and 'y' or a matrix-like 'x'
Backtrace:
Execution halted
Work dir:
REDACTED-s3://path
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named
.command.shThe text was updated successfully, but these errors were encountered: