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Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping #1244
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Hello, MSBooster only supports mzml and mgf files. Could you please convert your .d file to mzml instead and try again? Thanks, |
Thank you!, Trying now...
…________________________________
From: yangkl96 ***@***.***>
Sent: Tuesday, September 12, 2023 3:30 PM
To: Nesvilab/FragPipe ***@***.***>
Cc: Gu, PhD Xiaorong ***@***.***>; Author ***@***.***>
Subject: [EXT] Re: [Nesvilab/FragPipe] Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping (Issue #1244)
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________________________________
Hello,
MSBooster only supports mzml and mgf files. Could you please convert your .d file to mzml instead and try again?
Thanks,
Kevin
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|
Hi Kevin System OS: Windows 10, Architecture: AMD64 Version info: LCMS files:
16 commands to execute:
CheckCentroid
|
It seems that you did not add the Best, Fengchao |
Thank you! Trying it now, will keep you posted.
…________________________________
From: Fengchao ***@***.***>
Sent: Wednesday, September 13, 2023 9:22 AM
To: Nesvilab/FragPipe ***@***.***>
Cc: Gu, PhD Xiaorong ***@***.***>; Author ***@***.***>
Subject: [EXT] Re: [Nesvilab/FragPipe] Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping (Issue #1244)
CAUTION CYBER RISK: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender, expected to receive this content and trust that it’s safe. If you determine that the email isn’t from a trusted source, you can delete the email, submit it via the BlueFish button in Outlook for investigation or forward the email as an attachment to ***@***.******@***.***?subject=Report%20a%20Suspicious%20Email> if you don’t have the Bluefish button or are on a mobile device.
________________________________
H:\mzXML\Ingel_08282023_RP_E2.mzML has non-centroid scans. Please re-convert it with peakPeaking (https://fragpipe.nesvilab.org/docs/tutorial_convert.html<https://fragpipe.nesvilab.org/docs/tutorial_convert.html>).
It seems that you did not add the peakPicking filter when converting the file to mzML. You should use that to make the peak centroid. Please check our tutorial in detail: https://fragpipe.nesvilab.org/docs/tutorial_convert.html<https://fragpipe.nesvilab.org/docs/tutorial_convert.html>
Best,
Fengchao
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Reply to this email directly, view it on GitHub<#1244 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BCMRLYFWF2S6KED5GEC63W3X2GXRVANCNFSM6AAAAAA4VHEH4A>.
You are receiving this because you authored the thread.Message ID: ***@***.***>
Please consider the environment before printing this e-mail
Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
|
It worked. Thank you very much! |
No problem. Best, Fengchao |
I used MSConverter to convert Agilent .d file to .mzXML file. Then use Fragpipe for database searching.
The Run was stopped. Please help!
System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
.NET Core Info: N/A
Version info:
FragPipe version 20.0
MSFragger version 3.8
IonQuant version 1.9.8
Philosopher version 5.0.0
LCMS files:
Experiment/Group:
16 commands to execute:
CheckCentroid
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\lib\fragpipe-20.0.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid H:\mzXML\Ingel_08282023_RP_E2.mzXML 11
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gux\AppData\Local\Temp\56e75c33-1551-434e-a3a6-55f88505beb9
MSFragger [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx8G C:\fragpipe\lib\MSFragger-3.8\MSFragger-3.8.jar D:\XiaorongGu\Proteomics\MGF\fragger.params H:\mzXML\Ingel_08282023_RP_E2.mzXML
MSFragger move pepxml
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pepXML D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pepXML
MSFragger move pin
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pin D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pin
MSBooster [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\tools\msbooster-1.1.11.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList D:\XiaorongGu\Proteomics\MGF\msbooster_params.txt
Percolator [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 11 --results-psms Ingel_08282023_RP_E2_percolator_target_psms.tsv --decoy-results-psms Ingel_08282023_RP_E2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ Ingel_08282023_RP_E2_edited.pin
Percolator: Convert to pepxml [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML Ingel_08282023_RP_E2.pin Ingel_08282023_RP_E2 Ingel_08282023_RP_E2_percolator_target_psms.tsv Ingel_08282023_RP_E2_percolator_decoy_psms.tsv interact-Ingel_08282023_RP_E2 DDA 0.5 H:\mzXML\Ingel_08282023_RP_E2.mzXML
Percolator: Delete temp
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2_percolator_target_psms.tsv
Percolator: Delete temp
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2_percolator_decoy_psms.tsv
ProteinProphet [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\XiaorongGu\Proteomics\MGF\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate C:\fragpipe\bin\2023-09-12-decoys-contam-2023-09-06-decoys-reviewed-contam-UP000005640.fas.fas --prefix rev_
PhilosopherFilter [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev_ --pepxml D:\XiaorongGu\Proteomics\MGF --protxml D:\XiaorongGu\Proteomics\MGF\combined.prot.xml --razor
PhilosopherReport [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
CheckCentroid
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\lib\fragpipe-20.0.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid H:\mzXML\Ingel_08282023_RP_E2.mzXML 11
Done in 2.5 s.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck
INFO[14:02:44] Executing Workspace v5.0.0
INFO[14:02:44] Removing workspace
INFO[14:02:44] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\gux\AppData\Local\Temp\56e75c33-1551-434e-a3a6-55f88505beb9
INFO[14:02:45] Executing Workspace v5.0.0
INFO[14:02:45] Creating workspace
INFO[14:02:45] Done
Process 'WorkspaceCleanInit' finished, exit code: 0
MSFragger [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx8G C:\fragpipe\lib\MSFragger-3.8\MSFragger-3.8.jar D:\XiaorongGu\Proteomics\MGF\fragger.params H:\mzXML\Ingel_08282023_RP_E2.mzXML
MSFragger version MSFragger-3.8
Batmass-IO version 1.28.12
timsdata library version timsdata-2-21-0-4
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved.
System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
JVM started with 8 GB memory
Checking database...
Checking spectral files...
H:\mzXML\Ingel_08282023_RP_E2.mzXML: Scans = 5335
MAIN SEARCH
Checking database...
Parameters:
num_threads = 11
database_name = C:\fragpipe\bin\2023-09-12-decoys-contam-2023-09-06-decoys-reviewed-contam-UP000005640.fas.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 0
use_all_mods_in_first_search = 0
write_calibrated_mzml = 0
write_uncalibrated_mgf = 0
write_mzbin_all = 0
isotope_error = 0/1/2/3
mass_offsets = 0.0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = 0
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions =
search_enzyme_name = trypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = P
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = 1
allow_multiple_variable_mods_on_residue = 0
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = 1
override_charge = 0
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 1
deisotope = 1
deneutralloss = 1
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
activation_types = all
group_variable = 0
require_precursor = 1
reuse_dia_fragment_peaks = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file =
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = 1
variable_mod_01 = 15.9949 M 3
variable_mod_02 = 42.0106 [^ 1
add_A_alanine = 0.0
add_B_user_amino_acid = 0.0
add_C_cysteine = 57.02146
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.0
add_E_glutamic_acid = 0.0
add_F_phenylalanine = 0.0
add_G_glycine = 0.0
add_H_histidine = 0.0
add_I_isoleucine = 0.0
add_J_user_amino_acid = 0.0
add_K_lysine = 0.0
add_L_leucine = 0.0
add_M_methionine = 0.0
add_N_asparagine = 0.0
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.0
add_Q_glutamine = 0.0
add_R_arginine = 0.0
add_S_serine = 0.0
add_T_threonine = 0.0
add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da)
add_V_valine = 0.0
add_W_tryptophan = 0.0
add_X_user_amino_acid = 0.0
add_Y_tyrosine = 0.0
add_Z_user_amino_acid = 0.0
Selected fragment index width 0.10 Da.
314040894 fragments to be searched in 1 slices (4.68 GB total)
Operating on slice 1 of 1:
Fragment index slice generated in 5.22 s
001. Ingel_08282023_RP_E2.mzXML 4.2 s | deisotoping 0.6 s
[progress: 5335/5335 (100%) - 4271 spectra/s] 1.2s | remapping alternative proteins and postprocessing 2.3 s
MAIN SEARCH DONE IN 0.268 MIN
TOTAL TIME 0.416 MIN*
Process 'MSFragger' finished, exit code: 0
MSFragger move pepxml
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pepXML D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pepXML
Process 'MSFragger move pepxml' finished, exit code: 0
MSFragger move pin
C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err H:\mzXML\Ingel_08282023_RP_E2.pin D:\XiaorongGu\Proteomics\MGF\Ingel_08282023_RP_E2.pin
Process 'MSFragger move pin' finished, exit code: 0
MSBooster [Work dir: D:\XiaorongGu\Proteomics\MGF]
C:\fragpipe\jre\bin\java.exe -Xmx8G -cp "C:\fragpipe\tools\msbooster-1.1.11.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList D:\XiaorongGu\Proteomics\MGF\msbooster_params.txt
MSBooster v1.1.11
Using 11 threads
java.lang.IllegalArgumentException: No matching mzml/mgf file for Ingel_08282023_RP_E2.pin, please check that provided mzml/mgf directories contain proper mzml/mgf files.
at Features.PinMzmlMatcher.(PinMzmlMatcher.java:93)
at Features.MainClass.main(MainClass.java:507)
Process 'MSBooster' finished, exit code: 1
Process returned non-zero exit code, stopping
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