nukaemon
commented
2 years ago I just realized that my identification file not including any decoy sequences. I recreated my identification file by providing a fasta including decoy sequence to X!tandem, then the error went away.
I used DecoyPYrat to generate a decoy sequence fasta. It can specify prefix for decoy entries and actually sets "XXX_" prefix by default.
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 --decoyprefix 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 (lukall@u.washington.edu) 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