I encountered some errors for a Ribo-seq run that contained matched Ribo-seq and RNA-seq data, failed for 4 separate processes that all appear to use the same command: 1: Name

NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE (all_samples)

Command

template 'summarizedexperiment.r'

Status

Exit: 1 (FAILED) Attempt: 1 (action: FINISH)

2: Name

NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (all_samples)

Command

template 'summarizedexperiment.r'

3: Name

NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples)

Command

template 'summarizedexperiment.r'

Status

Exit: 1 (FAILED) Attempt: 1 (action: FINISH)

4: Name

NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (all_samples)

Command

template 'summarizedexperiment.r'

In addition: Warning messages:
1: In file(file, "rt") :
  'raw = FALSE' but 'samplesheet_matched_Ribo-seq.csv' is not a regular file
2: In file(file, "rt") :
  cannot open file 'samplesheet_matched_Ribo-seq.csv': it is a directory
Execution halted

Hi Felix, if you can give me something I can reproduce, I'll debug

it is a public dataset, I could try to downsample some files and see if it reproduces?

The test profile has matched ribo + rna, so we know this works, the bug must be related to something different in the way you've configured this run. What config/ params have you supplied?

ok, it might just me being a muppet - please ignore for now. I am running a new test (for context I accidentally specified the input also as the output (which works on S3), and this might subsequently look like a directory if linked via fusion (

samplesheet_matched_Ribo-seq.csv

and

samplesheet_matched_Ribo-seq.csv/)

.

Ahh yes, that sounds fishy. I'll take a stab if it turns out to be real

It was indeed it!

You're the customer, you're always right, complain if you feel sufficiently motivated 🙂

Ok, I filed a low priority moan :)