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CCBR / RENEE

A comprehensive quality-control and quantification RNA-seq pipeline
https://CCBR.github.io/RENEE/
MIT License
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error in RNA report on test data: cannot open the connection #82

Closed slsevilla closed 10 months ago

slsevilla commented 10 months ago

Ran RENEE v2.5.9 from the GUI on the test data:

Process errored here: 

Error in file(con, "w") : cannot open the connection
Calls: <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
In addition: There were 16 warnings (use warnings() to see them)
Execution halted
[Fri Jan  5 12:31:59 2024]
Error in rule rna_report:
    jobid: 0
    input: /data/sevillas2/RENEE/2.5.9_v1/DEG_ALL/RSEM.genes.expected_counts.all_samples.reformatted.tsv, /data/sevillas2/RENEE/2.5.9_v1/DEG_ALL/combined_TIN.tsv, /data/sevillas2/RENEE/2.5.9_v1/Reports/multiqc_matrix.tsv
    output: /data/sevillas2/RENEE/2.5.9_v1/Reports/RNA_Report.html
    shell:

    # Avoids inheriting $R_LIBS_SITE
    # from local env variables
    R_LIBS_SITE=/usr/local/lib/R/site-library
    # Generate RNA QC Dashboard
    workflow/scripts/rNA.R         -m workflow/scripts/rNA_flowcells.Rmd         -r /data/sevillas2/RENEE/2.5.9_v1/DEG_ALL/RSEM.genes.expected_counts.all_samples.reformatted.tsv         -t /data/sevillas2/RENEE/2.5.9_v1/DEG_ALL/combined_TIN.tsv         -q /data/sevillas2/RENEE/2.5.9_v1/Reports/multiqc_matrix.tsv         -o /data/sevillas2/RENEE/2.5.9_v1/Reports         -f RNA_Report.html

Process completed with all steps except for writing the output report:

...
label: loadings-heatmap (with options) 
List of 2
 $ dpi       : num 300
 $ fig.height: num 6

  |..................................................................... |  98%
   inline R code fragments

  |......................................................................| 100%
label: session-info
slsevilla commented 10 months ago

Tested in R-Studio and was able to knit the report without an error.

slsevilla commented 10 months ago

Tested on the command line with '--mode local' and got the same error listed above.

kelly-sovacool commented 10 months ago

Oddly, this fails for you, Vishal, and others, but works for me with v2.5.10.

slsevilla commented 10 months ago

Found a similar error: https://github.com/boxuancui/DataExplorer/issues/20

It appears because I don't have write permission to the R library location, that invocation of the rule fails to create the knit files. All of the fixes I've tried so far haven't worked though. I'm still only able to create it within R studio but cannot create it using Snakemake or just calling the R file directly.

slsevilla commented 10 months ago

The /output/dir/workflow directory is being set to 'read-only' by RENEE at some point. This is causing the creation of the 'knit.md' file to be unable to save and causing the pipeline to fail at this rule. I am going to test with a clean pull of the repo to ensure this fixes the issue

kelly-sovacool commented 10 months ago

We need to add a line to change the permissions of the output Rmd subdir after copying it

slsevilla commented 10 months ago

Running test to ensure this is working with current main branch

./renee run --input .tests/*.gz --output /data/sevillas2/renee_2.5.11/ --genome hg38_30 --mode slurm
kelly-sovacool commented 10 months ago

Running test to ensure this is working with current main branch

./renee run --input .tests/*.gz --output /data/sevillas2/renee_2.5.11/ --genome hg38_30 --mode slurm

Will this work on the main branch when we haven't merged #91 yet?