Spectrum not found

[kudpolser]

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.(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

[wenbostar]

Could you format your mgf files to only keep something like "20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.5.5.2" in titles of all spectra in your mgf file and then redo the peptide identification?

Before formatting: 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"

After formatting: TITLE=20150410_QE3_UPLC9_DBJ_SA_46fractions_Rep1_1.5.5.2

Bo

[kudpolser]

Thank you!