Error in Analysis stage

[vidyak2uiuc]

During the ANALYSIS stage of the pipeline, an error is displayed in the console output. However, this error is not logged into the pipeline_*.log. I am not sure about the impact of this error on the output of the analysis. Please find the diff between console output and the contents of the log file below.

Also, find the input json, console output file, log file and the analysis csv file for reference. pipeline_cit_hepph.json console_op_cit_hepph.txt cm_pipeline_cit_hepph.log k10_analysis.csv

[alessitomas]

I have received the same error while testing the pipeline with:

pipeline.json network.tsv

This is a screenshot of the terminal error after running the cm pipeline:

Error Origin

In the analysis section of the commands.sh file, it's possible to see that the first line (line 106) runs the analysis.R with two arguments.

Selected line (line 106):

Rscript /Users/tomasalessi/Workspace/UIUC/dashboard-cm/cm_pipeline/scripts/analysis.R /Users/tomasalessi/Workspace/UIUC/dashboard-cm/cm_pipeline/samples//example-20240629-17:47:27/S1_example_leiden.cleaned.tsv analysis/res0.001_i2_analysis.csv &

It's possible to identify that only two arguments are passed to analysis.R script:

...S1_example_leiden.cleaned.tsv analysis/res0.001_i2_analysis.csv

Analysis.R script

If the length of args is 0 the run stops and it's printed the following message "At least three arguments must be supplied...", but if the length of args is 2 the run continues.

In the case that only 2 arguments are passed to the script, algo_res will have length 0

The following for will still run, and when trying to fread on NA value, the terminal error will be generated

[MinhyukPark]

@alessitomas could you add more logs such as commands.sh or the result of ls on the output directories. If you are able to zip the entire output folder and upload it, that would work as well.

[alessitomas]

Sure, output folder zipped:

example-20240701-14:02:26.zip