Unable to access jarfile /code/encyclopedia.jar

[animesh]

I am running the pipeline via WSL2 setup and getting the following error

./nextflow run TalusBio/nf-encyclopedia -r latest --input input.csv --dlib proteins.dlib --fasta proteins.fasta
N E X T F L O W  ~  version 22.10.2
Launching `https://github.com/TalusBio/nf-encyclopedia` [dreamy_minsky] DSL2 - revision: 63c5d914a2 [latest]
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[fe/53691a] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)             [100%] 2 of 2, failed: 2 ✘
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (2)'

Caused by:
  Process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (2)` terminated with an error exit status (1)

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_058.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_058.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window \
       \
  | tee mz600-604.210712_ratio_22m_01_058.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_058.mzML.features.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error: Unable to access jarfile /code/encyclopedia.jar

Work dir:
  /home/ash022/work/eb/9560810abcdc8abe743dda3e406ae4

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`

The inputs are from base repo folder https://github.com/TalusBio/nf-encyclopedia/tree/main/tests/data

cat input.csv
file, chrlib
mz600-604.210712_ratio_22m_01_046.mzML.gz, false
mz600-604.210712_ratio_22m_01_058.mzML.gz, false

Any ideas how to proceed?

[wfondrie]

Hi @animesh 👋

Thanks for giving nf-encyclopedia a try! To fix the error you're seeing here, you'll need to specify encyclopedia.jar parameter to point to your local EncyclopeDIA jar file. The edited command will look something like this, with /my/encyclopedia/path.jar replaced with your actual EncyclopeDIA jar file path:

./nextflow run TalusBio/nf-encyclopedia -r latest --input input.csv --dlib proteins.dlib --fasta proteins.fasta --encyclopedia.jar /my/encyclopedia/path.jar

However, I would highly recommend using our provided Docker container! To use the Dockerized version of the workflow, please verify that you first have Docker installed and running. Then you can run the workflow by adding the -with-docker flag:

./nextflow run TalusBio/nf-encyclopedia -r latest -with-docker --input input.csv --dlib proteins.dlib --fasta proteins.fasta 

[animesh]

Thanks @wfondrie for tips! I could not make it work though :( first command i didn't really understand? Do i need to download jar file for encyclopedia separately and specify its path with switch --encycopedia.jar?

Second command seems to have failed with following message

 ./nextflow run TalusBio/nf-encyclopedia -r latest -with-docker --input input.csv --dlib proteins.dlib --fasta proteins.fasta
N E X T F L O W  ~  version 22.10.2
Launching `https://github.com/TalusBio/nf-encyclopedia` [gloomy_volhard] DSL2 - revision: 63c5d914a2 [latest]
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[58/ebd4e8] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (2)             [  0%] 0 of 2
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)'

Caused by:
  Missing output file(s) `mz600-604.210712_ratio_22m_01_046.mzML.elib` expected by process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)`

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_046.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_046.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window \
       \
  | tee mz600-604.210712_ratio_22m_01_046.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_046.mzML.features.txt

Command exit status:
  0

Command output:
  [10:06:36] Parsed 65%
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  [10:06:37] Finalizing mz600-604.210712_ratio_22m_01_046.dia ...
  [10:06:38] Finished writing mz600-604.210712_ratio_22m_01_046.dia!
  [10:06:38] Calculating features...
  [10:06:38] Processing precursors scans...
  [10:06:38] Constructing writer for mz600-604.210712_ratio_22m_01_046.mzML.features.txt.unsorted
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[e1/24980f] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)             [ 50%] 1 of 2, failed: 1
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)'

Caused by:
  Missing output file(s) `mz600-604.210712_ratio_22m_01_046.mzML.elib` expected by process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)`

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_046.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_046.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window \
       \
  | tee mz600-604.210712_ratio_22m_01_046.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_046.mzML.features.txt

Command exit status:
  0

Command output:
  [10:06:36] Parsed 65%
  [10:06:36] Parsed 66%
  [10:06:36] Parsed 67%
  [10:06:36] Parsed 68%
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  [10:06:36] Parsed 98%
  [10:06:36] Parsed 99%
  [10:06:37] Finalizing mz600-604.210712_ratio_22m_01_046.dia ...
  [10:06:38] Finished writing mz600-604.210712_ratio_22m_01_046.dia!
  [10:06:38] Calculating features...
  [10:06:38] Processing precursors scans...
  [10:06:38] Constructing writer for mz600-604.210712_ratio_22m_01_046.mzML.features.txt.unsorted
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[58/ebd4e8] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (2)             [100%] 2 of 2, failed: 2 ✘
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)'

Caused by:
  Missing output file(s) `mz600-604.210712_ratio_22m_01_046.mzML.elib` expected by process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)`

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_046.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_046.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window \
       \
  | tee mz600-604.210712_ratio_22m_01_046.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_046.mzML.features.txt

Command exit status:
  0

Command output:
  [10:06:36] Parsed 65%
  [10:06:36] Parsed 66%
  [10:06:36] Parsed 67%
  [10:06:36] Parsed 68%
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  [10:06:36] Parsed 99%
  [10:06:37] Finalizing mz600-604.210712_ratio_22m_01_046.dia ...
  [10:06:38] Finished writing mz600-604.210712_ratio_22m_01_046.dia!
  [10:06:38] Calculating features...
  [10:06:38] Processing precursors scans...
  [10:06:38] Constructing writer for mz600-604.210712_ratio_22m_01_046.mzML.features.txt.unsorted
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[58/ebd4e8] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (2)             [100%] 2 of 2, failed: 2 ✘
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)'

Caused by:
  Missing output file(s) `mz600-604.210712_ratio_22m_01_046.mzML.elib` expected by process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)`

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_046.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_046.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window \
       \
  | tee mz600-604.210712_ratio_22m_01_046.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_046.mzML.features.txt

Command exit status:
  0

Command output:
  [10:06:36] Parsed 65%
  [10:06:36] Parsed 66%
  [10:06:36] Parsed 67%
  [10:06:36] Parsed 68%
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  [10:06:36] Parsed 98%
  [10:06:36] Parsed 99%
  [10:06:37] Finalizing mz600-604.210712_ratio_22m_01_046.dia ...
  [10:06:38] Finished writing mz600-604.210712_ratio_22m_01_046.dia!
  [10:06:38] Calculating features...
  [10:06:38] Processing precursors scans...
  [10:06:38] Constructing writer for mz600-604.210712_ratio_22m_01_046.mzML.features.txt.unsorted
  [10:06:38] Processing 600.5 to 604.5 m/z, (2.9209983 second duty cycle)
  [10:06:38] 44 peptides remaining for 600.5 to 604.5...
  [10:06:38] 10 peptides remaining for 600.5 to 604.5...
  [10:06:39] Sorting results into mz600-604.210712_ratio_22m_01_046.mzML.features.txt
  [10:06:39] Sorted feature file in 0.05 seconds wall clock time
  [10:06:39] File size check: 60247 vs 60247 (diff: 0)
  Removing temp file mz600-604.210712_ratio_22m_01_046.mzML.features.txt.unsorted
  [10:06:39] 192 total peptides processed.
  [10:06:39] Running Percolator...
  [10:06:39] Executing [/tmp/Percolator-v3-01-3480874396419944307.exe --results-peptides mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.txt --weights mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.txt.1.weights --decoy-results-peptides mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.decoy.txt -y --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 mz600-604.210712_ratio_22m_01_046.mzML.features.txt]

Command error:
  56640fe7cea2: Download complete
  ef996253d333: Verifying Checksum
  ef996253d333: Download complete
  3f055c837894: Pull complete
  4f4fb700ef54: Verifying Checksum
  4f4fb700ef54: Download complete
  f9ca97a837d0: Pull complete
  64170d9f5c7d: Verifying Checksum
  64170d9f5c7d: Download complete
  2a6c6283796f: Pull complete
  22ac1ad915f7: Verifying Checksum
  22ac1ad915f7: Download complete
  3ede8a82856b: Verifying Checksum
  3ede8a82856b: Download complete
  93fadfa63681: Verifying Checksum
  93fadfa63681: Download complete
  aac34a9042fa: Download complete
  543e5e3d2623: Download complete
  84f0835b58f6: Download complete
  84f0835b58f6: Pull complete
  35b5bc2179a2: Pull complete
  4ddd2f7ee17a: Pull complete
  56640fe7cea2: Pull complete
  7988b915bfa1: Pull complete
  ee1d87909854: Pull complete
  ef996253d333: Pull complete
  4f4fb700ef54: Pull complete
  64170d9f5c7d: Pull complete
  22ac1ad915f7: Pull complete
  3ede8a82856b: Pull complete
  93fadfa63681: Pull complete
  aac34a9042fa: Pull complete
  4697359a5d79: Verifying Checksum
  4697359a5d79: Download complete
  4697359a5d79: Pull complete
  543e5e3d2623: Pull complete
  Digest: sha256:703e8e7b02a514ab9dbbd25e9a0e46179f7b31d48c150b885e0a97b9168479a6
  Status: Downloaded newer image for ghcr.io/talusbio/nf-encyclopedia:latest
  Picked up _JAVA_OPTIONS: -Djava.awt.headless=true
  [10:06:39] Fatal Error: Percolator exited with non-zero status: 139
  [10:06:39] Sorry, not feeling well today! Try again tomorrow!
  [10:06:39] Encountered Fatal Error!
  [10:06:39] edu.washington.gs.maccoss.encyclopedia.utils.EncyclopediaException: Percolator exited with non-zero status: 139
        edu.washington.gs.maccoss.encyclopedia.algorithms.percolator.PercolatorExecutor.checkResult(PercolatorExecutor.java:172)
        edu.washington.gs.maccoss.encyclopedia.algorithms.percolator.PercolatorExecutor.executePercolatorTSV(PercolatorExecutor.java:123)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.percolatePeptides(Encyclopedia.java:431)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runTop5Search(Encyclopedia.java:237)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runSearch(Encyclopedia.java:224)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runSearch(Encyclopedia.java:214)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.main(Encyclopedia.java:174)

Work dir:
  /home/ash022/work/e1/24980f25ba547055299525de65721f

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Any ideas how to proceed over this?

Docker is running via WSL2

docker -v
Docker version 20.10.21, build baeda1f

[wfondrie]

Do i need to download jar file for encyclopedia separately and specify its path with switch --encycopedia.jar?

This is only needed when running nf-encyclopedia without using Docker. The default value for encyclopedia.jar points to the location of the EncyclopeDIA executable within our container.

As for the other error you encountered, I didn't see that you were using our test files in your original post. These files only contain one DIA window from a very short gradient, so there aren't enough detected peptides for Percolator to run successfully with the default parameters. Instead, for our tests we change the following in the pipeline configuration:

params {
     encyclopedia.args = '-percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.9 -percolatorThreshold 0.9 -percolatorProteinThreshold 0.9'
}

You can also specify this from the command line:

./nextflow run TalusBio/nf-encyclopedia -r latest -with-docker \
    --input input.csv \
    --dlib proteins.dlib \
    --fasta proteins.fasta \
    --encyclopedia.args '-percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.9 -percolatorThreshold 0.9 -percolatorProteinThreshold 0.9'

[animesh]

Thanks again @wfondrie 👍🏽 Sorry for this noob q's, I think the command is working fine now but not sure what is the error in the end and where is the final result written?

$HOME/nextflow run TalusBio/nf-encyclopedia -r latest -with-docker     --input $HOME/input.csv     --dlib proteins.dlib     --fasta proteins.fasta     --encyclopedia.args '-percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.9 -percolatorThreshold 0.9 -percolatorProteinThreshold 0.9'
N E X T F L O W  ~  version 22.10.2
Launching `https://github.com/TalusBio/nf-encyclopedia` [hungry_cuvier] DSL2 - revision: 63c5d914a2 [latest]
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[3f/1056fa] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (2)             [  0%] 0 of 2
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)'

Caused by:
  Missing output file(s) `mz600-604.210712_ratio_22m_01_046.mzML.elib` expected by process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)`

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_046.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_046.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.9 -percolatorThreshold 0.9 -percolatorProteinThreshold 0.9 \
       \
  | tee mz600-604.210712_ratio_22m_01_046.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_046.mzML.features.txt

Command exit status:
  0

Command output:
  [12:23:15] Parsed 65%
  [12:23:15] Parsed 66%
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[b4/7becb1] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)             [ 50%] 1 of 2, failed: 1
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)'

Caused by:
  Missing output file(s) `mz600-604.210712_ratio_22m_01_046.mzML.elib` expected by process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)`

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_046.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_046.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.9 -percolatorThreshold 0.9 -percolatorProteinThreshold 0.9 \
       \
  | tee mz600-604.210712_ratio_22m_01_046.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_046.mzML.features.txt

Command exit status:
  0

Command output:
  [12:23:15] Parsed 65%
  [12:23:15] Parsed 66%
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[3f/1056fa] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (2)             [100%] 2 of 2, failed: 2 ✘
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)'

Caused by:
  Missing output file(s) `mz600-604.210712_ratio_22m_01_046.mzML.elib` expected by process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)`

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_046.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_046.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.9 -percolatorThreshold 0.9 -percolatorProteinThreshold 0.9 \
       \
  | tee mz600-604.210712_ratio_22m_01_046.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_046.mzML.features.txt

Command exit status:
  0

Command output:
  [12:23:15] Parsed 65%
  [12:23:15] Parsed 66%
executor >  local (2)
[-        ] process > CONVERT_TO_MZML:MSCONVERT                         -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH    -
[-        ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[3f/1056fa] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (2)             [100%] 2 of 2, failed: 2 ✘
[-        ] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE              -
[-        ] process > MSSTATS                                           -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)'

Caused by:
  Missing output file(s) `mz600-604.210712_ratio_22m_01_046.mzML.elib` expected by process `PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1)`

Command executed:

  gzip -df mz600-604.210712_ratio_22m_01_046.mzML.gz
  java -Djava.aws.headless=true -Xmx31G -jar /code/encyclopedia.jar \
      -i mz600-604.210712_ratio_22m_01_046.mzML \
      -f proteins.fasta \
      -l proteins.dlib \
      -percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.9 -percolatorThreshold 0.9 -percolatorProteinThreshold 0.9 \
       \
  | tee mz600-604.210712_ratio_22m_01_046.mzML.local.log
  gzip mz600-604.210712_ratio_22m_01_046.mzML.features.txt

Command exit status:
  0

Command output:
  [12:23:15] Parsed 65%
  [12:23:15] Parsed 66%
  [12:23:15] Parsed 67%
  [12:23:15] Parsed 68%
  [12:23:15] Parsed 69%
  [12:23:15] Parsed 70%
  [12:23:15] Parsed 71%
  [12:23:15] Parsed 72%
  [12:23:15] Parsed 73%
  [12:23:15] Parsed 74%
  [12:23:15] Parsed 75%
  [12:23:15] Parsed 76%
  [12:23:15] Parsed 77%
  [12:23:15] Parsed 78%
  [12:23:15] Parsed 79%
  [12:23:15] Parsed 80%
  [12:23:15] Parsed 81%
  [12:23:15] Parsed 82%
  [12:23:15] Parsed 83%
  [12:23:15] Parsed 84%
  [12:23:15] Parsed 85%
  [12:23:15] Parsed 86%
  [12:23:15] Parsed 87%
  [12:23:15] Parsed 88%
  [12:23:15] Parsed 89%
  [12:23:15] Parsed 90%
  [12:23:15] Parsed 91%
  [12:23:15] Parsed 92%
  [12:23:15] Parsed 93%
  [12:23:15] Parsed 94%
  [12:23:15] Parsed 95%
  [12:23:15] Parsed 96%
  [12:23:15] Parsed 97%
  [12:23:15] Parsed 98%
  [12:23:15] Parsed 99%
  [12:23:15] Finalizing mz600-604.210712_ratio_22m_01_046.dia ...
  [12:23:15] Finished writing mz600-604.210712_ratio_22m_01_046.dia!
  [12:23:15] Calculating features...
  [12:23:15] Processing precursors scans...
  [12:23:15] Constructing writer for mz600-604.210712_ratio_22m_01_046.mzML.features.txt.unsorted
  [12:23:15] Processing 600.5 to 604.5 m/z, (2.9209983 second duty cycle)
  [12:23:16] 44 peptides remaining for 600.5 to 604.5...
  [12:23:16] 10 peptides remaining for 600.5 to 604.5...
  [12:23:17] Sorting results into mz600-604.210712_ratio_22m_01_046.mzML.features.txt
  [12:23:17] Sorted feature file in 0.05 seconds wall clock time
  [12:23:17] File size check: 60247 vs 60247 (diff: 0)
  Removing temp file mz600-604.210712_ratio_22m_01_046.mzML.features.txt.unsorted
  [12:23:17] 192 total peptides processed.
  [12:23:17] Running Percolator...
  [12:23:17] Executing [/tmp/Percolator-v3-01-6819644626685235672.exe --results-peptides mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.txt --weights mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.txt.1.weights --decoy-results-peptides mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.decoy.txt -y --no-terminate -N 0 --testFDR 0.01 --trainFDR 0.9 mz600-604.210712_ratio_22m_01_046.mzML.features.txt]

Command error:
  Picked up _JAVA_OPTIONS: -Djava.awt.headless=true
  [12:23:17] Fatal Error: Percolator exited with non-zero status: 139
  [12:23:17] Sorry, not feeling well today! Try again tomorrow!
  [12:23:17] Encountered Fatal Error!
  [12:23:17] edu.washington.gs.maccoss.encyclopedia.utils.EncyclopediaException: Percolator exited with non-zero status: 139
        edu.washington.gs.maccoss.encyclopedia.algorithms.percolator.PercolatorExecutor.checkResult(PercolatorExecutor.java:172)
        edu.washington.gs.maccoss.encyclopedia.algorithms.percolator.PercolatorExecutor.executePercolatorTSV(PercolatorExecutor.java:123)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.percolatePeptides(Encyclopedia.java:431)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runTop5Search(Encyclopedia.java:237)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runSearch(Encyclopedia.java:224)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runSearch(Encyclopedia.java:214)
        edu.washington.gs.maccoss.encyclopedia.Encyclopedia.main(Encyclopedia.java:174)

Work dir:
  /home/ash022/work/b4/7becb1144783119e9d48b4ae315a59

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[wfondrie]

No worries @animesh!

The "missing output" messages is NextFlow complaining that EncyclopeDIA did not produce the expected output files, in this case, because of an error. It looks like Percolator is failing for some reason while EncyclopeDIA is running:

  [12:23:17] Fatal Error: Percolator exited with non-zero status: 139
  [12:23:17] Sorry, not feeling well today! Try again tomorrow!

How much memory does your system have? I'm wondering if this could be the problem.

[animesh]

How much memory is needed @wfondrie? Currently i have allocated ~64G to WSL

cat /proc/meminfo
MemTotal:       65810824 kB
MemFree:        62117724 kB
MemAvailable:   63867012 kB
Buffers:          310088 kB
Cached:          1991440 kB
SwapCached:            0 kB
Active:           794936 kB
Inactive:        2266992 kB
Active(anon):       1516 kB
Inactive(anon):   776716 kB
Active(file):     793420 kB
Inactive(file):  1490276 kB
Unevictable:           0 kB
Mlocked:               0 kB
SwapTotal:      16777216 kB
SwapFree:       16777216 kB
Dirty:                 0 kB
Writeback:             0 kB
AnonPages:        687184 kB
Mapped:           293668 kB
Shmem:             17832 kB
KReclaimable:     109188 kB
Slab:             274396 kB
SReclaimable:     109188 kB
SUnreclaim:       165208 kB
KernelStack:       15264 kB
PageTables:         8208 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:    49682628 kB
Committed_AS:    4308868 kB
VmallocTotal:   34359738367 kB
VmallocUsed:       40536 kB
VmallocChunk:          0 kB
Percpu:            11424 kB
AnonHugePages:    485376 kB
ShmemHugePages:        0 kB
ShmemPmdMapped:        0 kB
FileHugePages:         0 kB
FilePmdMapped:         0 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
Hugetlb:               0 kB
DirectMap4k:       68608 kB
DirectMap2M:    10375168 kB
DirectMap1G:    66060288 kB

[wfondrie]

How much memory is needed @wfondrie? Currently i have allocated ~64G to WSL

That should be more than enough! We test our pipeline with 6.5 Gb memory allocated.

@cia23 - did you have to do anything noteworthy to run nf-encyclopedia on Windows using the Linux subsystem?

[cia23]

That should definitely be enough memory to run the pipeline. I didn't run into any issues like this when running on Windows. However, I have seen that Percolator error when a file is not found. What output files are you getting @animesh?

[animesh]

I see the two directories, reports and work being created @cia23 , following is their tree structure

tree reports/
reports/
├── execution_report_2022-11-17_11-32-55.html
├── execution_report_2022-11-17_11-34-43.html
├── execution_report_2022-11-17_11-35-37.html
├── execution_report_2022-11-17_11-37-55.html
├── execution_report_2022-11-17_11-39-32.html
├── execution_report_2022-11-18_11-02-23.html
├── execution_report_2022-11-18_11-03-43.html
├── execution_report_2022-11-19_13-22-34.html
├── execution_report_2022-11-20_13-23-06.html
├── execution_timeline_2022-11-17_11-32-55.html
├── execution_timeline_2022-11-17_11-34-43.html
├── execution_timeline_2022-11-17_11-35-37.html
├── execution_timeline_2022-11-17_11-37-55.html
├── execution_timeline_2022-11-17_11-39-32.html
├── execution_timeline_2022-11-18_11-02-23.html
├── execution_timeline_2022-11-18_11-03-43.html
├── execution_timeline_2022-11-19_13-22-34.html
├── execution_timeline_2022-11-20_13-23-06.html
├── execution_trace_2022-11-17_11-30-50.txt
├── execution_trace_2022-11-17_11-32-55.txt
├── execution_trace_2022-11-17_11-34-43.txt
├── execution_trace_2022-11-17_11-35-37.txt
├── execution_trace_2022-11-17_11-37-55.txt
├── execution_trace_2022-11-17_11-39-32.txt
├── execution_trace_2022-11-18_11-02-23.txt
├── execution_trace_2022-11-18_11-03-43.txt
├── execution_trace_2022-11-19_13-22-34.txt
├── execution_trace_2022-11-20_13-23-06.txt
├── pipeline_dag_2022-11-17_11-32-55.html
├── pipeline_dag_2022-11-17_11-34-43.html
├── pipeline_dag_2022-11-17_11-35-37.html
├── pipeline_dag_2022-11-17_11-37-55.html
├── pipeline_dag_2022-11-17_11-39-32.html
├── pipeline_dag_2022-11-18_11-02-23.html
├── pipeline_dag_2022-11-18_11-03-43.html
├── pipeline_dag_2022-11-19_13-22-34.html
└── pipeline_dag_2022-11-20_13-23-06.html

0 directories, 37 files


tree work/
work/
├── 13
│   ├── 463081cab748bbb9f9905e6b5a3f60
│   │   └── S01.raw -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/mz600-604.210712_ratio_22m_01_046.mzML.gz
│   └── dbcf67e5c9480fab2ed620b6cc2f0c
│       ├── mz600-604.210712_ratio_22m_01_046.mzML
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── 15
│   └── 449498decc51abddaf00c7c01a0d13
│       └── S02.raw -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/mz600-604.210712_ratio_22m_01_046.mzML.gz
├── 2d
│   └── a3a89ca9d132cfed6183c63ff8fbf4
│       ├── catalina.base_IS_UNDEFINED
│       │   └── logs
│       │       └── ddi-ws.log
│       ├── mz600-604.210712_ratio_22m_01_046.dia
│       ├── mz600-604.210712_ratio_22m_01_046.mzML
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.txt.log
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.features.txt.gz
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── 37
│   └── a76acbff4f400d154f3c8723a84ee3
│       ├── mz600-604.210712_ratio_22m_01_046.mzML
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── 3e
│   └── df836858934d94e0da57c25d9e821a
├── 3f
│   └── 1056fa484320f0d0c4bc0f47c3d292
│       ├── catalina.base_IS_UNDEFINED
│       │   └── logs
│       │       └── ddi-ws.log
│       ├── mz600-604.210712_ratio_22m_01_058.dia
│       ├── mz600-604.210712_ratio_22m_01_058.mzML
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.encyclopedia.txt.log
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.features.txt.gz
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── 46
│   └── 1cfa7f6e696deed35c752e38008c0b
│       └── S02.raw -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/mz600-604.210712_ratio_22m_01_046.mzML.gz
├── 4f
│   └── 911fe292b5ec627ecbd6d536d5e312
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       ├── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
│       ├── S01..mzML
│       └── S01..mzML.local.log
├── 58
│   └── ebd4e8516812da5bb7b416e0c55d81
│       ├── catalina.base_IS_UNDEFINED
│       │   └── logs
│       │       └── ddi-ws.log
│       ├── mz600-604.210712_ratio_22m_01_058.dia
│       ├── mz600-604.210712_ratio_22m_01_058.mzML
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.encyclopedia.txt.log
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.features.txt.gz
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── 5a
│   └── a6a5b88257ce8b1404d96701d03845
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       ├── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
│       ├── S01..mzML
│       └── S01..mzML.local.log
├── 5e
│   └── c792d07553674f40aa1ba2e8dc0a1b
│       ├── mz600-604.210712_ratio_22m_01_058.mzML
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── 7c
│   └── f0fa81508bc57e356c5806b6b48f26
├── 96
│   └── 9d9dba94216c28aeaa4c5f08ccae83
├── a0
│   └── 4c793e83e41ff255f9b6e2f9ec6fc5
│       ├── mz600-604.210712_ratio_22m_01_058.mzML
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── a5
│   └── 79dd3baac378d40c687f9def15ddf4
│       └── S01.raw -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/mz600-604.210712_ratio_22m_01_046.mzML.gz
├── aa
│   └── 28645a7fa9bd1c12dced1ead7c705e
│       ├── catalina.base_IS_UNDEFINED
│       │   └── logs
│       │       └── ddi-ws.log
│       ├── mz600-604.210712_ratio_22m_01_058.dia
│       ├── mz600-604.210712_ratio_22m_01_058.mzML
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.encyclopedia.txt.log
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.features.txt.gz
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── b4
│   └── 7becb1144783119e9d48b4ae315a59
│       ├── catalina.base_IS_UNDEFINED
│       │   └── logs
│       │       └── ddi-ws.log
│       ├── mz600-604.210712_ratio_22m_01_046.dia
│       ├── mz600-604.210712_ratio_22m_01_046.mzML
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.txt.log
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.features.txt.gz
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── d6
│   └── a974e2ea464aad48e90f428815a0bb
│       └── S02.raw -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/mz600-604.210712_ratio_22m_01_046.mzML.gz
├── dc
│   └── 0309751b8f0da38e9d2361f3dd5b9e
├── e1
│   └── 24980f25ba547055299525de65721f
│       ├── catalina.base_IS_UNDEFINED
│       │   └── logs
│       │       └── ddi-ws.log
│       ├── mz600-604.210712_ratio_22m_01_046.dia
│       ├── mz600-604.210712_ratio_22m_01_046.mzML
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.encyclopedia.txt.log
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.features.txt.gz
│       ├── mz600-604.210712_ratio_22m_01_046.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── eb
│   └── 9560810abcdc8abe743dda3e406ae4
│       ├── mz600-604.210712_ratio_22m_01_058.mzML
│       ├── mz600-604.210712_ratio_22m_01_058.mzML.local.log
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
├── ec
│   └── e6465ce01540906183bf155d655b82
├── f0
│   └── ec9049273235278f27c77b6ad90563
│       └── S01.raw -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/mz600-604.210712_ratio_22m_01_046.mzML.gz
├── f5
│   └── 82b4b27158087aaeb77550262424e2
│       ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
│       ├── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta
│       ├── S02..mzML
│       └── S02..mzML.local.log
└── fe
    └── 53691acdbf0cab84d4fd21f6572097
        ├── mz600-604.210712_ratio_22m_01_046.mzML
        ├── mz600-604.210712_ratio_22m_01_046.mzML.local.log
        ├── proteins.dlib -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.dlib
        └── proteins.fasta -> /mnt/f/OneDrive - NTNU/nf-encyclopedia/tests/data/small-yeast.fasta

63 directories, 90 files

[wfondrie]

Hi @animesh,

We're trying to troubleshoot this, but haven't been able to reproduce the problem yet. Can you share the contents of /home/ash022/work/eb/9560810abcdc8abe743dda3e406ae4/mz600-604.210712_ratio_22m_01_058.mzML.local.log?

[animesh]

Thanks for looking into this @wfondrie 👍🏽 That file seems to be emptpy?

ls -ltrh /home/ash022/work/eb/9560810abcdc8abe743dda3e406ae4/mz600-604.210712_ratio_22m_01_058.mzML.local.log
-rw-r--r-- 1 ash022 ash022 0 Nov 17 11:39 /home/ash022/work/eb/9560810abcdc8abe743dda3e406ae4/mz600-604.210712_ratio_22m_01_058.mzML.local.log

[wfondrie]

Hi @animesh,

We're still having trouble reproducing this. Can you delete your work directory, the .nextflow directory (if it exists) and any .nextflow.log* files (if they exist)?

After deleting these, please try rerunning the pipeline and post any log files, both in the new work subdirectory and the new .nextflow.log that should be created. Thanks!

[animesh]

Looks like starting from scratch actually produced some sizeable files @wfondrie 👍🏽 Just to be sure, below is what to expect from this exercise?

ls -lrrh reports/
total 3.1M
-rw-r--r-- 1 ash022 ash022  10K Dec  3 11:55 pipeline_dag_2022-12-03_11-54-51.html
-rw-r--r-- 1 ash022 ash022  375 Dec  3 11:55 execution_trace_2022-12-03_11-54-51.txt
-rw-r--r-- 1 ash022 ash022 247K Dec  3 11:55 execution_timeline_2022-12-03_11-54-51.html
-rw-r--r-- 1 ash022 ash022 2.9M Dec  3 11:55 execution_report_2022-12-03_11-54-51.html

find work/ -iname mz600-604.210712_ratio_22m_01_058.mzML.local.log
cat work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.local.log

[10:54:59] EncyclopeDIA version 1.12.34
[10:54:59] Parameters:
[10:54:59]  -i /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML
[10:54:59]  -l /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/proteins.dlib
[10:54:59]  -o /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.encyclopedia.txt
[10:54:59]  -fixed
 -frag CID
 -ptol 10.0
 -ftol 10.0
 -lftol 10.0
 -ptolunits PPM
 -ftolunits PPM
 -lftolunits PPM
 -poffset 0.0
 -foffset 0.0
 -enzyme Trypsin
 -percolatorThreshold 0.9
 -percolatorVersion v3-01
 -percolatorTrainingSetSize 0
 -percolatorTrainingFDR 0.9
 -acquisition DIA
 -numberOfThreadsUsed 4
 -expectedPeakWidth 25.0
 -precursorWindowSize -1.0
 -numberOfQuantitativePeaks 5
 -minNumOfQuantitativePeaks 3
 -topNTargetsUsed -1
 -quantifyAcrossSamples true
 -numberOfExtraDecoyLibrariesSearched 0.0
 -verifyModificationIons true
 -minIntensity -1.0
 -scoringBreadthType window
 -localizationModification none
 -rtWindowInMin -1.0
 -filterPeaklists false
 -precursorIsolationRangeFile none
 -percolatorModelFile none

[10:54:59] Opening library proteins.dlib (version: 0.1.14)
[10:54:59] Getting count of protein accessions...
[10:54:59] Converting files...
[10:54:59] Indexing mz600-604.210712_ratio_22m_01_058.mzML ...
[10:54:59] Converting mz600-604.210712_ratio_22m_01_058.mzML ...
[10:54:59] Parsed 1%
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[10:55:00] Finalizing mz600-604.210712_ratio_22m_01_058.dia ...
[10:55:00] Finished writing mz600-604.210712_ratio_22m_01_058.dia!
[10:55:00] Calculating features...
[10:55:00] Processing precursors scans...
[10:55:00] Constructing writer for /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.features.txt.unsorted
[10:55:00] Processing 600.5 to 604.5 m/z, (2.9226315 second duty cycle)
[10:55:01] 44 peptides remaining for 600.5 to 604.5...
[10:55:01] 13 peptides remaining for 600.5 to 604.5...
[10:55:02] Sorting results into /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.features.txt
[10:55:02] Sorted feature file in 0.05 seconds wall clock time
[10:55:02] File size check: 60193 vs 60193 (diff: 0)
Removing temp file /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.features.txt.unsorted
[10:55:02] 192 total peptides processed.
[10:55:02] Running Percolator...
[10:55:02] Executing [/tmp/Percolator-v3-01-5337986839841879254.exe --results-peptides /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.encyclopedia.txt --weights /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.encyclopedia.txt.1.weights --decoy-results-peptides /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.encyclopedia.decoy.txt -y --no-terminate -N 0 --testFDR 0.01 --trainFDR 0.9 /home/ash022/work/65/bc35e20c73fb221bb6778ea44c5eaf/mz600-604.210712_ratio_22m_01_058.mzML.features.txt]

because the reports/execution_report_2022-12-03_11-54-51.html says

[ggokturkk]

@wfondrie | I think I have same issue with different error. First, I used below code to run pipeline:

First Trial

nextflow run TalusBio/nf-encyclopedia -r latest -with-docker --input input.csv --dlib small-yeast.dlib --fasta small-yeast.fasta --max_memory 30.GB --encyclopedia.args '-percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.9 -percolatorThreshold 0.9 -percolatorProteinThreshold 0.9'

My input csv:

input.csv

Nextflow Log:

nextflow.log

Error:

N E X T F L O W ~ version 23.04.1
Launching https://github.com/TalusBio/nf-encyclopedia [crazy_einstein] DSL2 - revision: fdf2570 [latest]
executor > local (4)
[- ] process > CONVERT_TO_MZML:MSCONVERT -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[da/ea4eb2] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1) [100%] 2 of 2 ✔
[39/907f39] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE (1) [100%] 1 of 1 ✔
[85/cca7ab] process > MSSTATS (1) [ 0%] 0 of 1
ERROR ~ Error executing process > 'MSSTATS (1)'
Caused by:
Process MSSTATS (1) terminated with an error exit status (1)
Command executed:
mkdir -p msstats reports logs results
msstats.R encyclopedia.quant.peptides.txt encyclopedia.quant.proteins.txt input.csv NO_FILE equalizeMedians false | tee logs/msstats.log
executor > local (4)
[- ] process > CONVERT_TO_MZML:MSCONVERT -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[da/ea4eb2] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1) [100%] 2 of 2 ✔
[39/907f39] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE (1) [100%] 1 of 1 ✔
[85/cca7ab] process > MSSTATS (1) [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'MSSTATS (1)'
Caused by:
Process MSSTATS (1) terminated with an error exit status (1)
Command executed:
mkdir -p msstats reports logs results
msstats.R encyclopedia.quant.peptides.txt encyclopedia.quant.proteins.txt input.csv NO_FILE equalizeMedians false | tee logs/msstats.log
executor > local (4)
[- ] process > CONVERT_TO_MZML:MSCONVERT -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[da/ea4eb2] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1) [100%] 2 of 2 ✔
[39/907f39] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE (1) [100%] 1 of 1 ✔
[85/cca7ab] process > MSSTATS (1) [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'MSSTATS (1)'
Caused by:
Process MSSTATS (1) terminated with an error exit status (1)
Command executed:
mkdir -p msstats reports logs results
msstats.R encyclopedia.quant.peptides.txt encyclopedia.quant.proteins.txt input.csv NO_FILE equalizeMedians false | tee logs/msstats.log
[ -f QCplot.pdf ] && mv QCplot.pdf reports/msstats.qc.pdf
echo "DONE!" # Needed for proper exit
Command exit status:
1
Command output:
[1] FALSE
Command error:
[1] FALSE
Error in check_join(., orig_rows, 0.75) :
<75% of peptides have associated protein.
Calls: main ... arrange -> rename -> mutate -> pivot_longer -> check_join
Execution halted
Work dir:
/home/ggokturk/Desktop/nf-encylopedia/nf-encyclopedia/work/85/cca7abfe084686081f84f731a9cfd8
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
-- Check '.nextflow.log' file for details

I guess this error occurred because the 'encyclopedia.quant.proteins.txt' file is empty.

Files:

encyclopedia.quant.peptides-1.txt
encyclopedia.quant.proteins-1.txt

Second Trial

nextflow run TalusBio/nf-encyclopedia -r latest -with-docker --input input.csv --dlib small-yeast.dlib --fasta small-yeast.fasta --max_memory 30.GB --encyclopedia.args '-percolatorVersion v3-01 -quantifyAcrossSamples true -scoringBreadthType window -percolatorTrainingSetSize 0 -percolatorTrainingFDR 0.95 -percolatorThreshold 0.95 -percolatorProteinThreshold 0.95'

I changed the parameters and it increased the number of findings but got a different error.

Error

N E X T F L O W ~ version 23.04.1
Launching https://github.com/TalusBio/nf-encyclopedia [tender_tuckerman] DSL2 - revision: fdf2570 [latest]
executor > local (4)
[- ] process > CONVERT_TO_MZML:MSCONVERT -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[dc/f32c77] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1) [100%] 2 of 2 ✔
[fc/cdcac3] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE (1) [100%] 1 of 1 ✔
[68/2c7383] process > MSSTATS (1) [ 0%] 0 of 1
ERROR ~ Error executing process > 'MSSTATS (1)'
Caused by:
Process MSSTATS (1) terminated with an error exit status (1)
Command executed:
mkdir -p msstats reports logs results
msstats.R encyclopedia.quant.peptides.txt encyclopedia.quant.proteins.txt input.csv NO_FILE equalizeMedians false | tee logs/msstats.log
[ -f QCplot.pdf ] && mv QCplot.pdf reports/msstats.qc.pdf
echo "DONE!" # Needed for proper exit
Command exit status:
1
Command output:
[1] FALSE
INFO [2023-05-09 11:58:07] ** Raw data from Skyline imported successfully.
INFO [2023-05-09 11:58:07] ** Raw data from Skyline cleaned successfully.
INFO [2023-05-09 11:58:07] ** Using annotation extracted from quantification data.
INFO [2023-05-09 11:58:07] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-05-09 11:58:07] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
WARN [2023-05-09 11:58:07] StandardType not found in input columns.
INFO [2023-05-09 11:58:07] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN [2023-05-09 11:58:07] ** DetectionQValue not found in input columns.
INFO [2023-05-09 11:58:07] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-05-09 11:58:07] ** Features with all missing measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Shared peptides are removed.
INFO [2023-05-09 11:58:07] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-05-09 11:58:07] ** Features with one or two measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Run annotation merged with quantification data.
INFO [2023-05-09 11:58:07] ** Features with one or two measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Fractionation handled.
Command error:
[1] FALSE
INFO [2023-05-09 11:58:07] ** Raw data from Skyline imported successfully.
INFO [2023-05-09 11:58:07] ** Raw data from Skyline cleaned successfully.
INFO [2023-05-09 11:58:07] ** Using annotation extracted from quantification data.
INFO [2023-05-09 11:58:07] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-05-09 11:58:07] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
executor > local (4)
[- ] process > CONVERT_TO_MZML:MSCONVERT -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[dc/f32c77] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1) [100%] 2 of 2 ✔
[fc/cdcac3] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE (1) [100%] 1 of 1 ✔
[68/2c7383] process > MSSTATS (1) [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'MSSTATS (1)'
Caused by:
Process MSSTATS (1) terminated with an error exit status (1)
Command executed:
mkdir -p msstats reports logs results
msstats.R encyclopedia.quant.peptides.txt encyclopedia.quant.proteins.txt input.csv NO_FILE equalizeMedians false | tee logs/msstats.log
[ -f QCplot.pdf ] && mv QCplot.pdf reports/msstats.qc.pdf
echo "DONE!" # Needed for proper exit
Command exit status:
1
Command output:
[1] FALSE
INFO [2023-05-09 11:58:07] ** Raw data from Skyline imported successfully.
INFO [2023-05-09 11:58:07] ** Raw data from Skyline cleaned successfully.
INFO [2023-05-09 11:58:07] ** Using annotation extracted from quantification data.
INFO [2023-05-09 11:58:07] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-05-09 11:58:07] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
WARN [2023-05-09 11:58:07] StandardType not found in input columns.
INFO [2023-05-09 11:58:07] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN [2023-05-09 11:58:07] ** DetectionQValue not found in input columns.
INFO [2023-05-09 11:58:07] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-05-09 11:58:07] ** Features with all missing measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Shared peptides are removed.
INFO [2023-05-09 11:58:07] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-05-09 11:58:07] ** Features with one or two measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Run annotation merged with quantification data.
INFO [2023-05-09 11:58:07] ** Features with one or two measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Fractionation handled.
Command error:
[1] FALSE
INFO [2023-05-09 11:58:07] ** Raw data from Skyline imported successfully.
INFO [2023-05-09 11:58:07] ** Raw data from Skyline cleaned successfully.
INFO [2023-05-09 11:58:07] ** Using annotation extracted from quantification data.
INFO [2023-05-09 11:58:07] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-05-09 11:58:07] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
executor > local (4)
[- ] process > CONVERT_TO_MZML:MSCONVERT -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_SEARCH -
[- ] process > BUILD_CHROMATOGRAM_LIBRARY:ENCYCLOPEDIA_AGGREGATE -
[dc/f32c77] process > PERFORM_QUANT:ENCYCLOPEDIA_SEARCH (1) [100%] 2 of 2 ✔
[fc/cdcac3] process > PERFORM_QUANT:ENCYCLOPEDIA_AGGREGATE (1) [100%] 1 of 1 ✔
[68/2c7383] process > MSSTATS (1) [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'MSSTATS (1)'
Caused by:
Process MSSTATS (1) terminated with an error exit status (1)
Command executed:
mkdir -p msstats reports logs results
msstats.R encyclopedia.quant.peptides.txt encyclopedia.quant.proteins.txt input.csv NO_FILE equalizeMedians false | tee logs/msstats.log
[ -f QCplot.pdf ] && mv QCplot.pdf reports/msstats.qc.pdf
echo "DONE!" # Needed for proper exit
Command exit status:
1
Command output:
[1] FALSE
INFO [2023-05-09 11:58:07] ** Raw data from Skyline imported successfully.
INFO [2023-05-09 11:58:07] ** Raw data from Skyline cleaned successfully.
INFO [2023-05-09 11:58:07] ** Using annotation extracted from quantification data.
INFO [2023-05-09 11:58:07] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-05-09 11:58:07] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
WARN [2023-05-09 11:58:07] StandardType not found in input columns.
INFO [2023-05-09 11:58:07] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN [2023-05-09 11:58:07] ** DetectionQValue not found in input columns.
INFO [2023-05-09 11:58:07] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-05-09 11:58:07] ** Features with all missing measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Shared peptides are removed.
INFO [2023-05-09 11:58:07] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-05-09 11:58:07] ** Features with one or two measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Run annotation merged with quantification data.
INFO [2023-05-09 11:58:07] ** Features with one or two measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Fractionation handled.
Command error:
[1] FALSE
INFO [2023-05-09 11:58:07] ** Raw data from Skyline imported successfully.
INFO [2023-05-09 11:58:07] ** Raw data from Skyline cleaned successfully.
INFO [2023-05-09 11:58:07] ** Using annotation extracted from quantification data.
INFO [2023-05-09 11:58:07] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-05-09 11:58:07] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
WARN [2023-05-09 11:58:07] StandardType not found in input columns.
INFO [2023-05-09 11:58:07] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN [2023-05-09 11:58:07] ** DetectionQValue not found in input columns.
INFO [2023-05-09 11:58:07] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-05-09 11:58:07] ** Features with all missing measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Shared peptides are removed.
INFO [2023-05-09 11:58:07] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-05-09 11:58:07] ** Features with one or two measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Run annotation merged with quantification data.
INFO [2023-05-09 11:58:07] ** Features with one or two measurements across runs are removed.
INFO [2023-05-09 11:58:07] ** Fractionation handled.
Error in setnames(x, value) :
Can't assign 4 names to a 0 column data.table
Calls: main ... colnames<- -> names<- -> names<-.data.table -> setnames
Execution halted
Work dir:
/home/ggokturk/Desktop/nf-encylopedia/nf-encyclopedia/work/68/2c73839d788cca4bc294a3d87fe48e
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
-- Check '.nextflow.log' file for details

Nextflow Log:

nextflow2.log

Files:

encyclopedia.quant.peptides.txt
encyclopedia.quant.proteins.txt

[wfondrie]

Hi @ggokturkk - this appears to be a different issue.

From the first trial:

I guess this error occurred because the 'encyclopedia.quant.proteins.txt' file is empty.

Yes this is exactly right. These are tiny test files, so we don't really expect to find much of anything at all.

From the second trial:

I changed the parameters and it increased the number of findings but got a different error.

The MSstats error here occurs because both of the proteins only have one observed peptide.

My recommendation would be to try reanalyzing data from Searle et al. to get a full view of what nf-encyclopedia does.