I ran the PBS job script that involves nf-core/rnasplice pipeline, and I’m getting this error message:

Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (contrast_NORMAL.csv)'

Caused by:
 Process `NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (contrast_NORMAL.csv)` terminated with an error exit status (1)

Command executed:

 check_contrastsheet.py contrast_NORMAL.csv contrastsheet.valid.csv
 cat <<-END_VERSIONS > versions.yml
 "NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK":
     python: $(python --version | sed 's/Python //g')
 END_VERSIONS

Command exit status:
 1

Command output:
 (empty)

Command error:
 [CRITICAL] The contrast sheet **must** contain these column headers: treatment, control, contrast.

Work dir:
 /home/tud03125/pipeline/normal_human_liver_rnasplice/work/b0/288550aa2bea6b4761e1e6a744953b

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Just in case, this’s inside my contrast sheet: condition contrast NORMAL NORMAL According to their instructions: https://nf-co.re/rnasplice/1.0.4/docs/usage/, their format’s like this: contrast,treatment,control TREATMENT_CONTROL,TREATMENT,CONTROL Or, in Excel sheet format: contrast treatment control TREATMENT_CONTROL TREATMENT CONTROL But still, I’m not doing Control/Treatment experiment. I’m just making a test experiment. So, what’s mine suppose to be? Like this? contrast treatment control NORMAL_NORMAL NORMAL NORMAL

Hi @Michael Levin did you find a solution to this? I am getting the same message even though my contrastsheet.csv looks like this: treatment,control,contrast NaCot,ContCot,NaCotvsContCot I tried changing the order of the columns but this too did not resolve the issue.

@Kilian For this one, I ended up this sheet to have it successful:

contrast	treatment	control
NORMAL_Total_RNA_seq_NORMAL_polyA_RNA	NORMAL_Total_RNA_seq	NORMAL_polyA_RNA

That said, this was still “Normal vs. Normal,” which gave

nf-core/rnasplice

some “stress” to differentiate it. They're only different by labs, which's experimental or batch effect rather than biological differences. That would require higher RAM than usual. I eventually moved to “Normal vs. Diseased” one here:

contrast	treatment	control
HCD_FASTED	HCD	FASTED
HCD_MK2206_FASTED	HCD_MK2206	FASTED
HCD_SPHINX31_FASTED	HCD_SPHINX31	FASTED

That one worked fine, and “less stress” for

nf-core/rnasplice

since that one should biologically differentiate. Not too memory-intensive RAM required for this one.

@Kilian, maybe check that your contrast sheet doesn't have any stray invisible characters, like CR (

\r

) from Windows editors in line endings. You can see these with

less -U

(shows up as

^M

), and hex viewers/editors (e.g.

xxd

) should show you exactly what is there.

dos2unix

is the easiest way to fix the endings.

Hi @Michael Levin and @Thomas Danhorn thanks for your input. I think it was indeed the invisible characters in the file; or a return after the last column. After redownloading the example file and adding in my contrasts it seems to run; at least past this stage.