Workflow fails at run_polystest step

[gxerios]

Step to reproduce :

./nextflow run main.nf --raws "../../data/*.raw" --fasta "../../data/*.fasta" --precursor_mass_tolerance 10.0 --fragment_mass_tolerance 0.5 --miscleavages 2 --variable_mods "Acetylation of protein N-term" --experiment_design "../../data/pxd001819.txt" --lfq_param "../../data/lfq_param_file.txt" --max_cpus 16 --max_memory 60GB -profile docker -with-report -with-trace -with-timeline

Main error

Error in smooth.spline(lambda, pi0, df = smooth.df) :
    missing or infinite values in inputs are not allowed
  Calls: UnpairedDesign -> qvalue -> pi0est -> smooth.spline

Error log

Error executing process > 'run_polystest (1)'

Caused by:
  Process `run_polystest (1)` terminated with an error exit status (1)

Command executed:

  convertProline=$(which runPolySTestCLI.R)

  echo $convertProline
  convertProline=$(dirname $convertProline)

  echo $convertProline
  Rscript ${convertProline}/convertFromProline.R quant_exp_design.txt proline_results_2274b219-a96c-4237-9d62-f64558d6c667.xlsx

  sed -i "s/threads: 2/threads: 16/g" pep_param.yml
  sed -i "s/threads: 2/threads: 16/g" prot_param.yml

  runPolySTestCLI.R pep_param.yml
  runPolySTestCLI.R prot_param.yml

Command exit status:
  1

Command output:
  /opt/conda/envs/nf-core-proline-labelfree/bin/runPolySTestCLI.R
  /opt/conda/envs/nf-core-proline-labelfree/bin
  ****** Found 10 different experimental conditions with up to 3 replicates

  |Var1       | Freq|
  |:----------|----:|
  |12500amol  |    3|
  |125amol    |    3|
  |250000amol |    2|
  |25000amol  |    1|
  |2500amol   |    3|
  |250amol    |    3|
  |50000amol  |    3|
  |5000amol   |    3|
  |500amol    |    3|
  |50amol     |    3|
  Files pep_param.yml and peptides.txt written
  Files prot_param.yml and proteins.txt written
  [1] "Reading pep_param.yml"
  [1] "16"
  Getting R functions from files located in /opt/conda/envs/nf-core-proline-labelfree/bin
  [1] "Set number of threads to 16"

  Experimental setup as read:

  |            |Condition 1 |Condition 2 |Condition 3 |Condition 4 |Condition 5 |Condition 6 |Condition 7  |Condition 8   |Condition 9  |Condition 10 |
  |:-----------|:-----------|:-----------|:-----------|:-----------|:-----------|:-----------|:------------|:-------------|:------------|:------------|
  |Replicate 1 |X125amol.1  |X50amol.1   |X250amol.1  |X500amol.1  |X2500amol.1 |X5000amol.1 |X12500amol.1 |X250000amol.1 |X25000amol.1 |X50000amol.1 |
  |Replicate 2 |X125amol.2  |X50amol.2   |X250amol.2  |X500amol.2  |X2500amol.2 |X5000amol.2 |X12500amol.2 |X250000amol.2 |X25000amol.2 |X50000amol.2 |
  |Replicate 3 |X125amol.3  |X50amol.3   |X250amol.3  |X500amol.3  |X2500amol.3 |X5000amol.3 |X12500amol.3 |X250000amol.3 |X25000amol.3 |X50000amol.3 |

  All pairwise comparison between conditions:

  |            |Comparison 1 |Comparison 2 |Comparison 3 |Comparison 4 |Comparison 5 |Comparison 6 |Comparison 7 |Comparison 8 |Comparison 9 |Comparison 10 |Comparison 11 |Comparison 12 |Comparison 13 |Comparison 14 |Comparison 15 |Comparison 16 |Comparison 17 |Comparison 18 |Comparison 19 |Comparison 20 |Comparison 21 |Comparison 22 |Comparison 23 |Comparison 24 |Comparison 25 |Comparison 26 |Comparison 27 |Comparison 28 |Comparison 29 |Comparison 30 |Comparison 31 |Comparison 32 |Comparison 33 |Comparison 34 |Comparison 35 |Comparison 36 |Comparison 37 |Comparison 38 |Comparison 39 |Comparison 40 |Comparison 41 |Comparison 42 |Comparison 43 |Comparison 44 |Comparison 45 |
  |:-----------|:------------|:------------|:------------|:------------|:------------|:------------|:------------|:------------|:------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|:-------------|
  |Condition A |X125amol.    |X125amol.    |X125amol.    |X125amol.    |X125amol.    |X125amol.    |X125amol.    |X125amol.    |X125amol.    |X50amol.      |X50amol.      |X50amol.      |X50amol.      |X50amol.      |X50amol.      |X50amol.      |X50amol.      |X250amol.     |X250amol.     |X250amol.     |X250amol.     |X250amol.     |X250amol.     |X250amol.     |X500amol.     |X500amol.     |X500amol.     |X500amol.     |X500amol.     |X500amol.     |X2500amol.    |X2500amol.    |X2500amol.    |X2500amol.    |X2500amol.    |X5000amol.    |X5000amol.    |X5000amol.    |X5000amol.    |X12500amol.   |X12500amol.   |X12500amol.   |X250000amol.  |X250000amol.  |X25000amol.   |
  |Condition B |X50amol.     |X250amol.    |X500amol.    |X2500amol.   |X5000amol.   |X12500amol.  |X250000amol. |X25000amol.  |X50000amol.  |X250amol.     |X500amol.     |X2500amol.    |X5000amol.    |X12500amol.   |X250000amol.  |X25000amol.   |X50000amol.   |X500amol.     |X2500amol.    |X5000amol.    |X12500amol.   |X250000amol.  |X25000amol.   |X50000amol.   |X2500amol.    |X5000amol.    |X12500amol.   |X250000amol.  |X25000amol.   |X50000amol.   |X5000amol.    |X12500amol.   |X250000amol.  |X25000amol.   |X50000amol.   |X12500amol.   |X250000amol.  |X25000amol.   |X50000amol.   |X250000amol.  |X25000amol.   |X50000amol.   |X25000amol.   |X50000amol.   |X50000amol.   |
  Running limma tests
  Running rank products and permutations tests ...
  ================================================================================

Command error:
  Error in smooth.spline(lambda, pi0, df = smooth.df) :
    missing or infinite values in inputs are not allowed
  Calls: UnpairedDesign -> qvalue -> pi0est -> smooth.spline
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  Execution halted

Work dir:
  /home/gelonch/dev/jupyterlab_root/wombatp/Proline-Workflow/Nextflow/work/b2/7bcdb51604277b6240c315b3d187f0

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`

[veitveit]

I think I identified the error:

|250000amol |    2|
  |25000amol  |    1|

Your file for the experimental design has some wrong numbers or labels. And PolySTest might fail when there is only one replicate

[pinaraltiner]

I have tried with different datasets, with the following experimental design; however, the error still is the same as previously.

mzdbfile    exp_cond
./OVEMB150205_12.mzDB   1fmol
./OVEMB150205_14.mzDB   1fmol
./OVEMB150205_16.mzDB   1fmol
./OVEMB150205_18.mzDB   1fmol
./OVEMB150205_21.mzDB   10fmol
./OVEMB150205_23.mzDB   10fmol
./OVEMB150205_25.mzDB   10fmol
./OVEMB150205_27.mzDB   10fmol

[veitveit]

Strange. Also with the original UPS dataset and the correct experimental design? Can you run another git pull to get the newest version (dev)? And get the most recent docker images via docker pull wombatp/proline-pipeline:dev

[pinaraltiner]

mzdbfile    exp_cond
./UPS1_125amol_R2.mzDB  125amol
./UPS1_125amol_R3.mzDB  125amol
./UPS1_50amol_R1.mzDB   50amol
./UPS1_50amol_R2.mzDB   50amol
./UPS1_50amol_R3.mzDB   50amol
./UPS1_125amol_R1.mzDB  125amol

I tried to run the subset of original UPS data (shown above) after pulling the updated version of the Proline pipeline; however, I faced another error as in the below.

Error executing process > 'run_polystest (1)'

Caused by:
  Process `run_polystest (1)` terminated with an error exit status (1)

Command error:
  Error in txtProgressBar(1, NumComps) : must have 'max' > 'min'
  Calls: UnpairedDesign -> txtProgressBar
  In addition: Warning message:
  Partial NA coefficients for 256 probe(s)
  Execution halted