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DeepRescore: rescore PSMs leveraging deep learning-derived peptide features

Nextflow 58.63% R 41.37%

proteomics msms deep-learning peptide-identification machine-learning

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deeprescore's Issues

GPU usage

Dear developers,

DeepRescore does not use the GPU on our server. How do I get him to see our graphic cards?
I assume I need to pass the parameters to Docker --runtime=nvidia --NVIDIA_VISIBLE_DEVICES=all, but due to the fact that I am using nextflow, I don't understand how to do this.

Thanks in advance.

Polina

Question regarding transfer learning approach

Hello!

Thanks for developing this tool. It is nice to see this rescoring approach finally packaged in an easily distributed and reproducible manner.

I have a question regarding the fragment ion intensity prediction model. Are you using the pre-trained model provided with pDeep2 as it is? Or is the model fine-tuned using the high-confidence PSMs (i.e. like AutoRT is) before predicting all the spectra?

Best wishes,
Kevin

'Sequential' object has no attribute '_layers'

Dear developers,

Thank you for providing this tool.
I tried to run your tool on test data, but I got an error 'Sequential' object has no attribute '_layers'. I guess that you fixed this problem on your repository by commenting out the linereturn model._layers[0]._batch_input_shape[1] on the def get_peptide_length_from_model function https://github.com/bzhanglab/AutoRT/blame/master/autort/RTModels.py#L640, but you didn't do that on the Docker files.

I pasted below the whole log message from nextflow.

log message from nextflow

N E X T F L O W  ~  version 21.04.1
Launching `DeepRescore.nf` [cranky_goldwasser] - revision: 20cb1fa1d6
executor >  local (6)
[e9/59e411] process > calc_basic_features (d2)            [100%] 1 of 1 ✔
[02/613b3c] process > pga_fdr_control (d2)                [100%] 1 of 1 ✔
[0c/2bdb1a] process > generate_train_prediction_data (d2) [100%] 1 of 1 ✔
[1f/43767c] process > run_pdeep2 (d2)                     [100%] 1 of 1 ✔
[59/023114] process > process_pDeep2_results (d2)         [100%] 1 of 1 ✔
[6e/34ab7b] process > train_autoRT (d2)                   [100%] 1 of 1, failed: 1 ✘
[-        ] process > predicte_autoRT                     -
[-        ] process > generate_percolator_input           -
[-        ] process > run_percolator                      -
[-        ] process > generate_pdv_input                  -
Error executing process > 'train_autoRT (d2)'

Caused by:
  Process `train_autoRT (d2)` terminated with an error exit status (1)

Command executed:

  #!/bin/sh
  set -e
  mkdir -p ./autoRT_models
  for file in autoRT_train/*.txt
  do
      fraction=`basename ${file} .txt`
      mkdir -p ./autoRT_models/${fraction}
      python /opt/AutoRT/autort.py train         -i $file         -o ./autoRT_models/${fraction}         -e 40         -b 64         -u m         -m /opt/AutoRT/models/base_models_PXD006109/model.json         -rlr         -n 10
  done
  wait

Command exit status:
  1

Command output:
  Scaling method: min_max
  Transfer learning ...

  Deep learning model: 0
  Load aa coding data from file /opt/AutoRT/models/base_models_PXD006109/aa.tsv
  AA types: 21
  Longest peptide in training data: 24

  Use test file ./autoRT_models/AC20171011_Broad_HLA_A1101_R1_Rep01/validation.tsv
  Longest peptide in test data: 20
  ['1', 'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']
  RT range: 0 - 98

  X_train shape:
  (1651, 48, 21)
  X_test shape:
  (184, 48, 21)
  Modeling start ...

Command error:
  f515f4c1b074: Download complete
  16d3b8690ce0: Pull complete
  6688d484c18d: Pull complete
  50ef52d49cb7: Pull complete
  8e10381b8c57: Pull complete
  5befd987b36f: Verifying Checksum
  5befd987b36f: Download complete
  9505c0f2462c: Verifying Checksum
  9505c0f2462c: Download complete
  b60763d28bdf: Download complete
  a17548ca111b: Verifying Checksum
  a17548ca111b: Download complete
  3442d7bf8734: Verifying Checksum
  3442d7bf8734: Download complete
  bb9ccf0ce8ca: Verifying Checksum
  bb9ccf0ce8ca: Download complete
  6a0d7a40b288: Verifying Checksum
  6a0d7a40b288: Download complete
  e84a0c00918e: Download complete
  bbd63def3ec3: Verifying Checksum                                                                                                                                                                                                                                      
  bbd63def3ec3: Download complete
  e84a0c00918e: Pull complete
  a17548ca111b: Pull complete
  f515f4c1b074: Pull complete
  5befd987b36f: Pull complete
  9505c0f2462c: Pull complete
  b60763d28bdf: Pull complete
  bbd63def3ec3: Pull complete
  3442d7bf8734: Pull complete
  bb9ccf0ce8ca: Pull complete
  6a0d7a40b288: Pull complete
  Digest: sha256:1e8772488571f36ff29f061b6fec4778b154dfb23c5bee816e36b7e790d15c03
  Status: Downloaded newer image for proteomics/autort:latest
  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-s_x2f8jd because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to
speed up the import of Matplotlib and to better support multiprocessing.
  2021-07-07 11:50:33.324340: I tensorflow/stream_executor/platform/default/dso_loader.cc:53] Successfully opened dynamic library libcudart.so.11.0
  2021-07-07 11:50:35.951041: I tensorflow/stream_executor/platform/default/dso_loader.cc:53] Successfully opened dynamic library libcuda.so.1
  2021-07-07 11:50:35.951091: E tensorflow/stream_executor/cuda/cuda_driver.cc:328] failed call to cuInit: UNKNOWN ERROR (34)
  2021-07-07 11:50:35.951124: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:163] no NVIDIA GPU device is present: /dev/nvidia0 does not exist
  2021-07-07 11:50:35.951395: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 FMA
  To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
  Traceback (most recent call last):
    File "/opt/AutoRT/autort.py", line 133, in <module>
      main()
    File "/opt/AutoRT/autort.py", line 99, in main
      add_reverse=add_reverse,add_ReduceLROnPlateau=add_ReduceLROnPlateau)
    File "/opt/AutoRT/autort/RTModels.py", line 427, in ensemble_models
      print(get_peptide_length_from_model(new_model))
    File "/opt/AutoRT/autort/RTModels.py", line 640, in get_peptide_length_from_model
      return model._layers[0]._batch_input_shape[1]
  AttributeError: 'Sequential' object has no attribute '_layers'

Work dir:
  /home/pkudryavtseva/DeepRescore/work/6e/34ab7b8ad260035a03d13a482abdca

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

I would be grateful if you can fix this.

Best regards,
Polina

Compatibility with FragPipe

Hi,
Is DeepScore compatible with FragPipe as input. Can you also enhance the identification of tryptic peptides using DeepScore. How would this behave for very large datasets.

Best, Peer

Exception caught: Error: no decoy PSMs were provided.

Dear developers

In run_percolator process, I got an error Exception caught: Error: no decoy PSMs were provided.
I'm not sure if this is related with --decoy_prefix option, but I'm currently setting XXX_ because I don't know exactly what should be given to this option.

log message from nextflow

N E X T F L O W ~ version 20.10.0
Launching /home/centos/DeepRescore/DeepRescore.nf [goofy_hopper] - revision: 86e61de38a
executor > local (10)
[14/0f974e] process > xml2mzid (d2) [100%] 1 of 1 ✔
[a7/3c6ef2] process > calc_basic_features_xt (d2) [100%] 1 of 1 ✔
[70/8e7f0f] process > pga_fdr_control (d2) [100%] 1 of 1 ✔
[00/3a5478] process > generate_train_prediction_data (d2) [100%] 1 of 1 ✔
[3b/b226be] process > run_pdeep2 (d2) [100%] 1 of 1 ✔
[1c/c4d0de] process > process_pDeep2_results (d2) [100%] 1 of 1 ✔
[ac/b6b3cf] process > train_autoRT (d2) [100%] 1 of 1 ✔
[2c/f2da0f] process > predicte_autoRT (d2) [100%] 1 of 1 ✔
[ea/2a9ade] process > generate_percolator_input (d2) [100%] 1 of 1 ✔
[d2/be169a] process > run_percolator (d2) [ 0%] 0 of 1
[- ] process > generate_pdv_input -
Error executing process > 'run_percolator (d2)'

Caused by:
Process run_percolator (d2) terminated with an error exit status (1)

Command executed:

percolator -r d2_pep.txt -m d2_psms.txt format.pin

Command exit status:
1

Command output:
(empty)

Command error:
Percolator version 3.04.0, Build Date Sep 19 2019 15:17:34
Copyright (c) 2006-9 University of Washington. All rights reserved.
executor > local (10)
[14/0f974e] process > xml2mzid (d2) [100%] 1 of 1 ✔
[a7/3c6ef2] process > calc_basic_features_xt (d2) [100%] 1 of 1 ✔
[70/8e7f0f] process > pga_fdr_control (d2) [100%] 1 of 1 ✔
[00/3a5478] process > generate_train_prediction_data (d2) [100%] 1 of 1 ✔
[3b/b226be] process > run_pdeep2 (d2) [100%] 1 of 1 ✔
[1c/c4d0de] process > process_pDeep2_results (d2) [100%] 1 of 1 ✔
[ac/b6b3cf] process > train_autoRT (d2) [100%] 1 of 1 ✔
[2c/f2da0f] process > predicte_autoRT (d2) [100%] 1 of 1 ✔
[ea/2a9ade] process > generate_percolator_input (d2) [100%] 1 of 1 ✔
[d2/be169a] process > run_percolator (d2) [100%] 1 of 1, failed: 1 ✘
[- ] process > generate_pdv_input -
Error executing process > 'run_percolator (d2)'

Caused by:
Process run_percolator (d2) terminated with an error exit status (1)

Command executed:

percolator -r d2_pep.txt -m d2_psms.txt format.pin

Command exit status:
1

Command output:
(empty)

Command error:
Percolator version 3.04.0, Build Date Sep 19 2019 15:17:34
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll ([email protected]) in the
Department of Genome Sciences at the University of Washington.
Issued command:
percolator -r d2_pep.txt -m d2_psms.txt format.pin
Started Wed Sep 8 07:59:18 2021
on 58ed86d6c6f8
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile format.pin

WARNING: Tab delimited input does not contain ScanNr column,
scan numbers will be assigned automatically.

Features:
Mass_Error Abs_Mass_Error Ln_Total_Intensity Match_Ions_Intensity Rel_Match_Ions_Intensity Max_Match_Ion_Intensity X!Tandem:expect X!Tandem:hyperscore Charge error similarity
Found 1165 PSMs
Concatenated search input detected, skipping both target-decoy competition and mix-max.
Train/test set contains 1165 positives and 0 negatives, size ratio=inf and pi0=1
Exception caught: Error: no decoy PSMs were provided.

Work dir:
/home/centos/Work/210908.F24Z019E/deep_rescore/work/d2/be169ae511d224425606f95f999982

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

CVS or TSV problem (commit 36e2455 problem)

Dear developers

In commit 36e2455, the extension of the output file in predicte_autoRT was changed from csv to tsv.
I previously noticed this issue and did the same modification by myself (and worked).

However, it seems like that AutoRT now uses csv extension and the current version of DeepRescore.nf fails at this point due to commit 36e2455.
Is this caused by any updates in AutoRT?

Spectrum not found

Dear developers,

I've got one more question. I tried to run your tool on our own data, but I got an error Exception in thread "main" java.io.IOException: Spectrum '20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.3515.3515.2 File:20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.raw, NativeID:controllerType=0 controllerNumber=1 scan=3515' in mgf file '20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.mgf' not found!

Now my titles in the mgf file look like this: TITLE=20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.5.5.2 File:"20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.raw", NativeID:"controllerType=0 controllerNumber=1 scan=5", but there are no " characters in the error message.

I pasted below the whole log message from nextflow.

log message from nextflow

executor >  local (5)
[7e/fbce9b] process > calc_basic_features (d2)            [100%] 1 of 1 ✔
[aa/e8b050] process > pga_fdr_control (d2)                [100%] 1 of 1 ✔
[49/cb2f1c] process > generate_train_prediction_data (d2) [100%] 1 of 1 ✔
[e7/20a741] process > run_pdeep2 (d2)                     [100%] 1 of 1 ✔
[5d/b364fe] process > process_pDeep2_results (d2)         [100%] 1 of 1, failed: 1 ✘
[-        ] process > train_autoRT                        -
[-        ] process > predicte_autoRT                     -
[-        ] process > generate_percolator_input           -
[-        ] process > run_percolator                      -
[-        ] process > generate_pdv_input                  -
Error executing process > 'process_pDeep2_results (d2)'

Caused by:
  Process `process_pDeep2_results (d2)` terminated with an error exit status (2)

Command executed:

  #!/bin/sh
  mv d2_pdeep2_prediction_results.txt d2_pdeep2_prediction_results.txt.mgf
  Rscript /home/pkudryavtseva/DeepRescore/bin/format_pDeep2_titile.R d2_pdeep2_prediction.txt d2-rawPSMs.txt ./d2_format_titles.txt

  java -Xmx92g -cp /home/pkudryavtseva/DeepRescore/bin/PDV-1.6.1.beta.features/PDV-1.6.1.beta.features-jar-with-dependencies.jar PDVGUI.GenerateSpectrumTable         ./d2_format_titles.txt 20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.mgf d2_pdeep2_prediction_results.txt.m
gf ./d2_spectrum_pairs.txt comet
  mkdir sections sections_results
  Rscript /home/pkudryavtseva/DeepRescore/bin/similarity/devide_file.R ./d2_spectrum_pairs.txt 16 ./sections/
  for file in ./sections/*
  do
      name=`basename $file`
      Rscript /home/pkudryavtseva/DeepRescore/bin/similarity/calculate_similarity_SA.R $file ./sections_results/${name}_results.txt &
  done
  wait
  awk 'NR==1 {header=$_} FNR==1 && NR!=1 { $_ ~ $header getline; } {print}' ./sections_results/*_results.txt > ./d2_similarity_SA.txt

Command exit status:
  2

Command output:
  (empty)

Command error:
  Exception in thread "main" java.io.IOException: Spectrum '20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.3515.3515.2 File:20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.raw, NativeID:controllerType=0 controllerNumber=1 scan=3515' in mgf file '20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.mgf' not found!
  ✖ dplyat com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:788)
  ✖ dplyat com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:730)
  ✖ dplyat PDVGUI.GenerateSpectrumTable.process(GenerateSpectrumTable.java:84)
  ✖ dplyat PDVGUI.GenerateSpectrumTable.<init>(GenerateSpectrumTable.java:31)
  ✖ dplyat PDVGUI.GenerateSpectrumTable.main(GenerateSpectrumTable.java:21)
  Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
  Bioconductor version '3.10' is out-of-date; the current release version '3.13'
    is available with R version '4.1'; see https://bioconductor.org/install
  ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
  ✔ ggplot2 3.2.1     ✔ purrr   0.3.3
  ✔ tibble  2.1.3     ✔ dplyr   0.8.4
  ✔ tidyr   1.0.0     ✔ stringr 1.4.0
  ✔ readr   1.3.1     ✔ forcats 0.4.0
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ dplyr::filter() masks stats::filter()
  ✖ dplyr::lag()    masks stats::lag()

  Attaching package: ‘data.table’

  The following objects are masked from ‘package:dplyr’:

      between, first, last

  The following object is masked from ‘package:purrr’:

      transpose

  Warning message:
  In fread(args[1]) :
    File './d2_spectrum_pairs.txt' has size 0. Returning a NULL data.table.
  Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
  Bioconductor version '3.10' is out-of-date; the current release version '3.13'
    is available with R version '4.1'; see https://bioconductor.org/install
  ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
  ✔ ggplot2 3.2.1     ✔ purrr   0.3.3
  ✔ tibble  2.1.3     ✔ dplyr   0.8.4
  ✔ tidyr   1.0.0     ✔ stringr 1.4.0
  ✔ readr   1.3.1     ✔ forcats 0.4.0
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ dplyr::between()   masks data.table::between()
  ✖ dplyr::filter()    masks stats::filter()
  ✖ dplyr::first()     masks data.table::first()
  ✖ dplyr::lag()       masks stats::lag()
  ✖ dplyr::last()      masks data.table::last()
  ✖ purrr::transpose() masks data.table::transpose()
  Error in fread(args[1]) :
    File './sections/*' does not exist or is non-readable. getwd()=='/home/pkudryavtseva/DeepRescore/work/5d/b364fe3cd205d19732b749e111e7f8'
  Execution halted
  awk: cannot open ./sections_results/*_results.txt (No such file or directory)

Work dir:
  /home/pkudryavtseva/DeepRescore/work/5d/b364fe3cd205d19732b749e111e7f8

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out

I would be grateful if you can help me with this problem.
Best regards,
Polina

Spectrum in mgf file not found

Dear developers

Thank you for providing this useful tool.
I setup DeepRescore in AWS(CentOS7) with GPU backend and it could run on test data successfully.

Now, I tried on my own data but encountered with an error at 'process_pDeep2_results' step.
The nextflow command executed is below which should be ok, and the identification file (output.2021_04_07_02_59_45.t.xml) was generated from the same mgf file(myown.mgf) using X!Tandem.

nextflow run ${DEEPRESCORE} --id_file output.2021_04_07_02_59_45.t.xml --ms_file myown.mgf --se xtandem --ms_instrument Lumos --ms_energy 0.34 --prefix d2 --decoy_prefix XXX_  --cpu 4 --mem 12

The command error message from nextflow tells that something wrong happened in Java execution

Command error:
  Exception in thread "main" java.io.IOException: Spectrum 'File: D:\Discoverer2_2Data\DiscovererDaemon\200611BPB\F24Z019E_1_5ul.raw; SpectrumID: 2220; scans: 2975' in mgf file 'myown.mgf' not found!
        at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:788)
        at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:730)
        at PDVGUI.GenerateSpectrumTable.process(GenerateSpectrumTable.java:84)
        at PDVGUI.GenerateSpectrumTable.<init>(GenerateSpectrumTable.java:31)
        at PDVGUI.GenerateSpectrumTable.main(GenerateSpectrumTable.java:21)

I looked at myown.mgf and there are actually entry lines related with SpectrumID: 2220; scans: 2975.

.
.
.
BEGIN IONS
TITLE=File: "D:\Discoverer2_2Data\DiscovererDaemon\200611BPB\F24Z019E_1_5ul.raw"; SpectrumID: "2220"; scans: "2975"
PEPMASS=496.76181 16035.10645
CHARGE=2+
RTINSECONDS=724
SCANS=2975
168.998 9.06042
171.242 47.312
176.236 15.0943
183.230 16.0298
186.481 12.8785
.
.
.

Also, SpectrumID "2220" shows up at the first line in 'd2_format_titles.txt', so it seems getting the error immediately on loading 'd2_format_titles.txt'.

I also manually tested each command executed in process_pDeep2_results step and confirmed that 'd2_spectrum_pairs.txt' was generated but empty after PDV-1.6.1.beta.features-jar-with-dependencies.jar.

Do you have any idea to solve this problem?
I paste below the whole log message from nextflow just in case.

log message from nextflow

[37/ea937f] process > xml2mzid (d2)                       [100%] 1 of 1 ✔
[1a/aa62b3] process > calc_basic_features_xt (d2)         [100%] 1 of 1 ✔
[89/0c6d10] process > pga_fdr_control (d2)                [100%] 1 of 1 ✔
[1d/7ff0ff] process > generate_train_prediction_data (d2) [100%] 1 of 1 ✔
[29/3b4f5d] process > run_pdeep2 (d2)                     [100%] 1 of 1 ✔
[f0/b0788f] process > process_pDeep2_results (d2)         [100%] 1 of 1, failed: 1 ✘
[-        ] process > train_autoRT                        -
[-        ] process > predicte_autoRT                     -
[-        ] process > generate_percolator_input           -
[-        ] process > run_percolator                      -
[-        ] process > generate_pdv_input                  -
Error executing process > 'process_pDeep2_results (d2)'

Caused by:
  Process `process_pDeep2_results (d2)` terminated with an error exit status (2)

Command executed:

  #!/bin/sh
  mv d2_pdeep2_prediction_results.txt d2_pdeep2_prediction_results.txt.mgf
  Rscript /home/centos/DeepRescore/bin/format_pDeep2_titile.R d2_pdeep2_prediction.txt d2-rawPSMs.txt ./d2_format_titles.txt

  java -Xmx12g -cp /home/centos/DeepRescore/bin/PDV-1.6.1.beta.features/PDV-1.6.1.beta.features-jar-with-dependencies.jar PDVGUI.GenerateSpectrumTable         ./d2_format_titles.txt myown.mgf d2_pdeep2_prediction_results.txt.mgf ./d2_spectrum_pairs.txt xtandem
  mkdir sections sections_results
  Rscript /home/centos/DeepRescore/bin/similarity/devide_file.R ./d2_spectrum_pairs.txt 4 ./sections/
  for file in ./sections/*
  do
      name=`basename $file`
      Rscript /home/centos/DeepRescore/bin/similarity/calculate_similarity_SA.R $file ./sections_results/${name}_results.txt &
  done
  wait
  awk 'NR==1 {header=$_} FNR==1 && NR!=1 { $_ ~ $header getline; } {print}' ./sections_results/*_results.txt > ./d2_similarity_SA.txt

Command exit status:
  2

Command output:
  (empty)

Command error:
  Exception in thread "main" java.io.IOException: Spectrum 'File: D:\Discoverer2_2Data\DiscovererDaemon\200611BPB\F24Z019E_1_5ul.raw; SpectrumID: 2220; scans: 2975' in mgf file 'myown.mgf' not found!
        at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:788)
        at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:730)
        at PDVGUI.GenerateSpectrumTable.process(GenerateSpectrumTable.java:84)
        at PDVGUI.GenerateSpectrumTable.<init>(GenerateSpectrumTable.java:31)
        at PDVGUI.GenerateSpectrumTable.main(GenerateSpectrumTable.java:21)
  Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
  Bioconductor version '3.10' is out-of-date; the current release version '3.12'
    is available with R version '4.0'; see https://bioconductor.org/install
  ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
  ✔ ggplot2 3.2.1     ✔ purrr   0.3.3
  ✔ tibble  2.1.3     ✔ dplyr   0.8.4
  ✔ tidyr   1.0.0     ✔ stringr 1.4.0
  ✔ readr   1.3.1     ✔ forcats 0.4.0
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ dplyr::filter() masks stats::filter()
  ✖ dplyr::lag()    masks stats::lag()
  
  Attaching package: ‘data.table’
  
  The following objects are masked from ‘package:dplyr’:
  
      between, first, last
  
  The following object is masked from ‘package:purrr’:
  
      transpose
  
  Warning message:
  In fread(args[1]) :
    File './d2_spectrum_pairs.txt' has size 0. Returning a NULL data.table.
  Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
  Bioconductor version '3.10' is out-of-date; the current release version '3.12'
    is available with R version '4.0'; see https://bioconductor.org/install
  ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
  ✔ ggplot2 3.2.1     ✔ purrr   0.3.3
  ✔ tibble  2.1.3     ✔ dplyr   0.8.4
  ✔ tidyr   1.0.0     ✔ stringr 1.4.0
  ✔ readr   1.3.1     ✔ forcats 0.4.0
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ dplyr::between()   masks data.table::between()
  ✖ dplyr::filter()    masks stats::filter()
  ✖ dplyr::first()     masks data.table::first()
  ✖ dplyr::lag()       masks stats::lag()
  ✖ dplyr::last()      masks data.table::last()
  ✖ purrr::transpose() masks data.table::transpose()
  Error in fread(args[1]) : 
    File './sections/*' does not exist or is non-readable. getwd()=='/home/centos/Work/test/work/f0/b0788f2a27d40b620301bb2776920b'
  Execution halted
  awk: cannot open ./sections_results/*_results.txt (No such file or directory)

Work dir:
  /home/centos/Work/test/work/f0/b0788f2a27d40b620301bb2776920b

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

bzhanglab / deeprescore Goto Github PK

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deeprescore's Issues

GPU usage

Question regarding transfer learning approach

'Sequential' object has no attribute '_layers'

Compatibility with FragPipe

Exception caught: Error: no decoy PSMs were provided.

CVS or TSV problem (commit 36e2455 problem)

Spectrum not found

Spectrum in mgf file not found

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