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<@UEM37TBAR> There is an error in the step `NONPAR...
# taxprofiler
l
@James Fellows Yates There is an error in the step 
NONPAREIL_CURVE
when running 
nextflow run <http://main.nf|main.nf> -profile test_noprofiling,singularity --outdir results
. I tried adding an extra argument `-d` to the process 
NONPAREIL
, but then it caused issues for other Illumina samples.
Copy code
ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:TAXPROFILER:NONPAREIL:NONPAREIL_CURVE (2613)'

Caused by:
  Missing output file(s) `*.png` expected by process `NFCORE_TAXPROFILER:TAXPROFILER:NONPAREIL:NONPAREIL_CURVE (2613)`

Command executed:

  #!/usr/bin/env Rscript
  library(Nonpareil)
  
  png(file='2613_ERR5766181.png')
  Nonpareil.curve('2613_ERR5766181.npo')
  dev.off()
  
  version_file_path <- "versions.yml"
  version_nonpareil <- paste(unlist(packageVersion("Nonpareil")), collapse = ".")
  f <- file(version_file_path, "w")
  writeLines('"NFCORE_TAXPROFILER:TAXPROFILER:NONPAREIL:NONPAREIL_CURVE":', f)
  writeLines("    nonpareil: ", f, sep = "")
  writeLines(version_nonpareil, f)
  close(f)

Command exit status:
  0

Command output:
  null device 
            1 

Command error:
  Warning message:
  In Nonpareil.curve("2613_ERR5766181.npo") :
    Insufficient resolution below 90% coverage, check parameters and re-run (e.g., increase the value of -d in nonpareil).
j
That's odd, we didn't have that issue in earlier tests did we?
What do you mean by you had issues for the other samples?
l
for instance 2612
j
But I mean what is the error for the other issues
l
wait a moment. I am re-running it
👍 1
Here is the error after adding 
-d 0.8
to the process nonpareil
Copy code
ERROR ~ Error executing process > 'NFCORE_TAXPROFILER:TAXPROFILER:NONPAREIL:NONPAREIL_NONPAREIL (2613)'

Caused by:
  Process `NFCORE_TAXPROFILER:TAXPROFILER:NONPAREIL:NONPAREIL_NONPAREIL (2613)` terminated with an error exit status (1)

Command executed:

  nonpareil \
      -s 2613_ERR5766181.merged.fastq.gz \
      -f fastq \
      -T kmer \
      -t 2 \
      -R 6144 \
      -b 2613_ERR5766181 \
      -d 0.8
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXPROFILER:TAXPROFILER:NONPAREIL:NONPAREIL_NONPAREIL":
      nonpareil: $(echo $(nonpareil -V 2>&1) | sed 's/Nonpareil v//' )
  END_VERSIONS

Command exit status:
  1

Command output:
  Nonpareil v3.5.5

Command error:
  Nonpareil v3.5.5
   [      0.0]   The file 2613_ERR5766181.merged.fastq.gz.enve-tmp.39 was created
   [      0.0]  Reading 2613_ERR5766181.merged.fastq.gz.enve-tmp.39
   [      0.0]   Picking 10000 random sequences
  Fatal error:
  Reads are required to have a minimum length of kmer size
   [      0.0] Fatal error: Reads are required to have a minimum length of kmer size
The default -d is 0.7
j
@Lili Andersson-Li where were you getting this error again?
l
Which error are you referring to: the first one or the second one?
j
just running 
test
on bounch_basenji or?
Both, they are sort of related
l
Yes, just run test 
nextflow run <http://main.nf|main.nf> -profile test_noprofiling,singularity --outdir results
After having the first error while running the test, I added 
-d 0.8
to the 
modules.config
file as indicated by the error message, which then led to the second error.
j
Interesting... I don't get that error locally
just straight 
test_noprofiling
works...
When running on bouncybasenji
l
Ok. I will run test again
j
I've opened the PR on GHA also to see if it happens there
💯 1
Rujnning a third time on my machine 🙂
exceptionallyfastparrot 1
Again fine on my mahcine
🙌 1
The only thing I can think of is
Copy code
[      0.0]   Picking 10000 random sequences
l
I am not sure why I got that error. I will re-run it anyway
j
Oh no wait
is it happening on BB?
Or on your module update branch?
With my latest versions of nonpareil?
Wait did I even update the pipeline...
Oh no I did
all good
So I think it's either a very occasioanl failure
Or random failrue on your end...
so something to monitor
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