`"` in the fasta file broke the program.

DRock420 commented 2 years ago

Hi there

I am running a non-specific peptidome search and it runs fine when I set the variable mods to 0 (actually there are no identifications but I am working on that) , however, if I set the variable mods to 1 or more I get an XML syntax error: panic: Cannot decode packed binary. XML syntax error on line 11083: expected attribute name in element goroutine 51 [running]: philosopher/lib/msg.callLogrus({0xc0000ffaa0, 0x5f}, {0x8612c0, 0x1?}) /workspace/philosopher/lib/msg/msg.go:319 +0x354 philosopher/lib/msg.DecodeMsgPck({0x9b0040?, 0xc0002bb740?}, {0x8612c0, 0x5}) /workspace/philosopher/lib/msg/msg.go:120 +0x6e philosopher/lib/spc.(PepXML).Parse(0xc000167a50, {0xc0000b4200, 0x77}) /workspace/philosopher/lib/spc/spc.go:63 +0x1c6 philosopher/lib/id.(PepXML).Read(0xc0000ce2c0, {0xc0000b4200, 0x77}) /workspace/philosopher/lib/id/pep.go:207 +0x105 philosopher/lib/id.ReadPepXMLInput.func1(0x1, {0xc0000b4200, 0x77}) /workspace/philosopher/lib/id/pep.go:386 +0x105 philosopher/lib/id.ReadPepXMLInput.func2(0x0?, {0xc0000b4200, 0x77}) /workspace/philosopher/lib/id/pep.go:422 +0xa2 created by philosopher/lib/id.ReadPepXMLInput /workspace/philosopher/lib/id/pep.go:419 +0x978 Process 'PhilosopherFilter' finished, exit code: 2 Process returned non-zero exit code, stopping ERRO[11:41:11] Cannot decode packed binary. XML syntax error on line 11083: expected attribute name in element

If I open the temp xml file and go to line 11083 it looks like this: peptide="ISPFVARPADDGAFGAKCMGSGNDVVLAAVDDDCM" massdiff="1.981689453125" calc_neutral_pep_mass="3513.5671" peptide_next_aa="V" " num_missed_cleavages="0" num_tol_term="0" protein_descr="40S ribosomal protein S3 OS=Manduca sexta OX=7130 GN=RpS3 PE=2 SV=1" num_tot_proteins="1" tot_num_ions="136" hit_rank="1" num_matched_ions="26" protein="rev_sp|P48153|RS3_MANSE" peptide_prev_aa="V" is_rejected="0" num_missed_cleavages="0">

The software has written an extra " after peptide_next_aa="V" causing a syntax error

Would you have any suggestions?

Running 18.0, 3.5, 4.4.0

Thanks in advance

Derek

fcyu commented 2 years ago

Can you send us the log file?

Thanks,

Fengchao

DRock420 commented 2 years ago

HI Fengchao

Please see attached

Derek

From: Fengchao @. Sent: September 13, 2022 12:16 PM To: Nesvilab/FragPipe @.> Cc: Derek Smith @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] XML Syntax error (Issue #826)

Can you send us the log file?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/826#issuecomment-1245852589, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AOX3MZLDMJGZ7HCHOWCBJFDV6DHILANCNFSM6AAAAAAQLXOUME. You are receiving this because you authored the thread.Message ID: @.**@.>>

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 18.0 MSFragger version 3.5 Philosopher version 4.4.0

LCMS files: Experiment/Group:

Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.raw DDA

14 commands to execute: CheckCentroid C:\Fragpipe\fragpipe\jre\bin\java.exe -Xmx41G -cp "C:\Fragpipe\fragpipe\lib\fragpipe-18.0.jar;C:\Fragpipe\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.raw 23 WorkspaceCleanInit [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\derek\AppData\Local\Temp\c32b46d0-9c2e-42f1-80cd-8b9909a9b22e MSFragger [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx41G C:\Fragpipe\fragpipe\tools\MSFragger-3.5\MSFragger-3.5.jar Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\fragger.params Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.raw MSFragger move pepxml C:\Fragpipe\fragpipe\jre\bin\java.exe -cp C:\Fragpipe\fragpipe\lib\fragpipe-18.0.jar;/C:/Fragpipe/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.pepXML Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\20220902_REC-2401_Sample_01_IT.pepXML MSFragger move pin C:\Fragpipe\fragpipe\jre\bin\java.exe -cp C:\Fragpipe\fragpipe\lib\fragpipe-18.0.jar;/C:/Fragpipe/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.pin Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\20220902_REC-2401_Sample_01_IT.pin PeptideProphet: Workspace init [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\fragpipe-20220902_REC-2401_Sample_01_IT.pepXML-temp] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\derek\AppData\Local\Temp\e19c8fc6-1aeb-4014-a3d3-3e501a24fa68 PeptideProphet [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\fragpipe-20220902_REC-2401_Sample_01_IT.pepXML-temp] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev --database Y:\data\Adamo\2022-09-09-decoys-ManducaSexta_taxonomy_id7130_uniprot2022.09.07.fasta.fas ..\20220902_REC-2401_Sample_01_IT.pepXML PeptideProphet: Delete temp C:\Fragpipe\fragpipe\jre\bin\java.exe -cp C:\Fragpipe\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\fragpipe-20220902_REC-2401_Sample_01_IT.pepXML-temp Rewrite pepxml [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\jre\bin\java.exe -cp C:\Fragpipe\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.raw PhilosopherDbAnnotate [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate Y:\data\Adamo\2022-09-09-decoys-ManducaSexta_taxonomy_id7130uniprot2022.09.07.fasta.fas --prefix rev PhilosopherFilter [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windowsamd64\philosopher.exe filter --tag rev --pepxml Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger PhilosopherReport [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report WorkspaceClean [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]
    Cmd: [CheckCentroid], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]
    Cmd: [WorkspaceCleanInit], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]
    Cmd: [MSFragger], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]
    Cmd: [PeptideProphet], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]
    Cmd: [PhilosopherDbAnnotate], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]
    Cmd: [PhilosopherFilter], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]
    Cmd: [PhilosopherReport], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]
    Cmd: [WorkspaceClean], Work dir: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger]

>rev_sp|B0FHH8|ML1P_MANSE MD-2-related lipid-recognition protein OS=Manduca sexta OX=7130 PE=1 SV=1
>rev_sp|Q9U0S4|VATD_MANSE V-type proton ATPase subunit D OS=Manduca sexta OX=7130 PE=2 SV=1
>rev_tr|A0A3G1VCH1|A0A3G1VCH1_MANSE Serpin-12 OS=Manduca sexta OX=7130 PE=2 SV=1
>rev_tr|A0A5K8B123|A0A5K8B123_MANSE Olfactory receptor 79 (Fragment) OS=Manduca sexta OX=7130 GN=OR-79 PE=2 SV=1
>rev_tr|A0A6G6XDQ6|A0A6G6XDQ6_MANSE CLIP domain-containing serine protease OS=Manduca sexta OX=7130 PE=2 SV=1
>rev_tr|D1LYK8|D1LYK8_MANSE 40S ribosomal protein S24 OS=Manduca sexta OX=7130 GN=rps24 PE=2 SV=1
>rev_tr|E5PST6|E5PST6_MANSE Cytochrome c oxidase subunit 1 (Fragment) OS=Manduca sexta paphus OX=1104469 GN=COI PE=3 SV=1
>rev_tr|O96991|O96991_MANSE Scolexin B (Fragment) OS=Manduca sexta OX=7130 GN=SCB1 PE=2 SV=1
>rev_tr|Q3LB55|Q3LB55_MANSE Uncharacterized protein OS=Manduca sexta OX=7130 PE=2 SV=1
>rev_tr|Q8I8Y1|Q8I8Y1_MANSE Laccase 1 OS=Manduca sexta OX=7130 PE=2 SV=1
>rev_tr|Q9U9K3|Q9U9K3_MANSE Ecdysis-triggering hormone OS=Manduca sexta OX=7130 GN=eth PE=4 SV=1
>sp|Q86RS3|DFP_MANSE Putative defense protein Hdd11-like OS=Manduca sexta OX=7130 PE=2 SV=1
>tr|A0A0S2Z3V6|A0A0S2Z3V6_MANSE CRAL-TRIO domain-containing protein (Fragment) OS=Manduca sexta OX=7130 PE=2 SV=1
>tr|A0A5K8B0X6|A0A5K8B0X6_MANSE Odorant receptor OS=Manduca sexta OX=7130 GN=OR-32 PE=2 SV=1
>tr|A0A5K8B5Q5|A0A5K8B5Q5_MANSE Olfactory receptor 84 (Fragment) OS=Manduca sexta OX=7130 GN=OR-84 PE=2 SV=1
>tr|D1LYJ8|D1LYJ8_MANSE Ribosomal protein S19 OS=Manduca sexta OX=7130 GN=rps19 PE=2 SV=1
>tr|D8VD27|D8VD27_MANSE Sterol carrier protein 2 OS=Manduca sexta OX=7130 GN=SCP2 PE=2 SV=1
>tr|O76960|O76960_MANSE Nicotinic acetylcholine receptor beta 1 subunit (Fragment) OS=Manduca sexta OX=7130 PE=2 SV=1
>tr|Q32XW9|Q32XW9_MANSE Ecdysis triggering hormone receptor subtype-A OS=Manduca sexta OX=7130 PE=2 SV=1
>tr|Q86M98|Q86M98_MANSE Antimicrobial protein attacin 2 (Fragment) OS=Manduca sexta OX=7130 PE=2 SV=1
>tr|Q9U5A9|Q9U5A9_MANSE Transporter OS=Manduca sexta OX=7130 GN=CAATCH1 PE=2 SV=1

# FragPipe v18.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=Y\:\\data\\Adamo\\2022-09-09-decoys-ManducaSexta_taxonomy_id7130_uniprot2022.09.07.fasta.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=0.01
diann.unrelated-runs=false
diann.use-predicted-spectra=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=C\:\\Fragpipe\\fragpipe\\tools\\IonQuant-1.8.0.jar
fragpipe-config.bin-msfragger=C\:\\Fragpipe\\fragpipe\\tools\\MSFragger-3.5\\MSFragger-3.5.jar
fragpipe-config.bin-philosopher=C\:\\Fragpipe\\fragpipe\\tools\\philosopher_v4.4.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=0
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=65
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=0.8
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=10000
msfragger.max_variable_mods_per_peptide=1
msfragger.min_fragments_modelling=3
msfragger.min_matched_fragments=5
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.00
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=12000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=nonspecific
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=0
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=-18.01056 79.96633
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=-
msfragger.search_enzyme_cut_2=-
msfragger.search_enzyme_name_1=nonspecific
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),false,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,2; 42.010600,[^,true,1; -17.026500,nQ,true,1; -18.010600,nE,true,1; -0.984020,c^,true,1; 4.025107,K,false,1; 6.020129,R,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=500
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 1
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=false
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=1
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=20
ptmshepherd.precursor_mass_units=1
ptmshepherd.precursor_tol=20
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
run-psm-validation=true
run-validation-tab=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=Y\:\\data\\Adamo\\REC-2401\\20220902_REC-2401_Adamo\\Derek_Fragger
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=23

CheckCentroid C:\Fragpipe\fragpipe\jre\bin\java.exe -Xmx41G -cp "C:\Fragpipe\fragpipe\lib\fragpipe-18.0.jar;C:\Fragpipe\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.raw 23 Done in 0 ms. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[11:33:42] Executing Workspace v4.4.0
INFO[11:33:42] Removing workspace
WARN[11:33:42] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[11:33:42] Done
WorkspaceCleanInit [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\derek\AppData\Local\Temp\c32b46d0-9c2e-42f1-80cd-8b9909a9b22e INFO[11:33:42] Executing Workspace v4.4.0
INFO[11:33:42] Creating workspace
INFO[11:33:42] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx41G C:\Fragpipe\fragpipe\tools\MSFragger-3.5\MSFragger-3.5.jar Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\fragger.params Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.raw MSFragger version MSFragger-3.5 Batmass-IO version 1.25.5 timsdata library version timsdata-2-8-7-1 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 41 GB memory Checking database... Deisotoping doesn't support low resolution tandem mass spectra. Changing deisotope to 0. deisotope = 0. Changing deneutralloss to 0. Checking spectral files... Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.raw: Scans = 47368

****MAIN SEARCH**** Checking database... Deisotoping doesn't support low resolution tandem mass spectra. Changing deisotope to 0. deisotope = 0. Changing deneutralloss to 0. Parameters: num_threads = 23 database_name = Y:\data\Adamo\2022-09-09-decoys-ManducaSexta_taxonomy_id7130_uniprot2022.09.07.fasta.fas decoyprefix = 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 = 0.8 fragment_mass_units = 0 calibrate_mass = 0 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = 0/1/2 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = nonspecific search_enzyme_sense_1 = C search_enzyme_cut_1 = - search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 search_enzyme_sense_2 = C search_enzyme_cut_2 = - search_enzyme_nocut_2 = allowed_missed_cleavage_2 = 2 num_enzyme_termini = 0 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 1 max_variable_mods_combinations = 10000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 65 digest_mass_range_low = 500.0 digest_mass_range_high = 12000.0 max_fragment_charge = 2 deisotope = 0 deneutralloss = false 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 = 500 minIonsScoring = 3 min_matched_fragments = 5 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all 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 = true variable_mod_01 = 15.994900 M 2 variable_mod_02 = 42.010600 [^ 1 variable_mod_03 = -17.026500 nQ 1 variable_mod_04 = -18.010600 nE 1 variable_mod_05 = -0.984020 c^ 1 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 0.000000 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 add_Z_user_amino_acid = 0.000000 Number of unique peptides of length 7: 562290 of length 8: 566994 of length 9: 568728 of length 10: 569717 of length 11: 570193 of length 12: 570357 of length 13: 570288 of length 14: 570050 of length 15: 569655 of length 16: 569137 of length 17: 568525 of length 18: 567844 of length 19: 567100 of length 20: 566286 of length 21: 565436 of length 22: 564529 of length 23: 563593 of length 24: 562609 of length 25: 561596 of length 26: 560584 of length 27: 559553 of length 28: 558491 of length 29: 557405 of length 30: 556295 of length 31: 555163 of length 32: 554017 of length 33: 552853 of length 34: 551671 of length 35: 550483 of length 36: 549285 of length 37: 548077 of length 38: 546862 of length 39: 545650 of length 40: 544428 of length 41: 543186 of length 42: 541942 of length 43: 540694 of length 44: 539437 of length 45: 538172 of length 46: 536903 of length 47: 535632 of length 48: 534354 of length 49: 533072 of length 50: 531784 of length 51: 530494 of length 52: 529203 of length 53: 527907 of length 54: 526598 of length 55: 525292 of length 56: 523989 of length 57: 522681 of length 58: 521369 of length 59: 520053 of length 60: 518726 of length 61: 517389 of length 62: 516055 of length 63: 514725 of length 64: 513389 of length 65: 512047 In total 32260837 peptides. Generated 97742607 modified peptides. Number of peptides with more than 10000 modification patterns: 0 Selected fragment index width 0.80 Da. 7226248860 fragments to be searched in 4 slices (107.68 GB total) Operating on slice 1 of 4: Fragment index slice generated in 8.77 s

20220902_REC-2401_Sample_01_IT.raw 60.5 s [progress: 47368/47368 (100%) - 1867 spectra/s] 25.4s Operating on slice 2 of 4: Fragment index slice generated in 8.03 s
20220902_REC-2401_Sample_01_IT.raw 20.3 s [progress: 47368/47368 (100%) - 3968 spectra/s] 11.9s Operating on slice 3 of 4: Fragment index slice generated in 7.70 s
20220902_REC-2401_Sample_01_IT.raw 20.0 s [progress: 47368/47368 (100%) - 4562 spectra/s] 10.4s Operating on slice 4 of 4: Fragment index slice generated in 7.67 s
20220902_REC-2401_Sample_01_IT.raw 19.7 s [progress: 47368/47368 (100%) - 4101 spectra/s] 11.5s | ramaping alternative proteins and postprocessing 6.4 s MAIN SEARCH DONE IN 4.137 MIN

***TOTAL TIME 4.213 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\Fragpipe\fragpipe\jre\bin\java.exe -cp C:\Fragpipe\fragpipe\lib\fragpipe-18.0.jar;/C:/Fragpipe/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.pepXML Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\20220902_REC-2401_Sample_01_IT.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Fragpipe\fragpipe\jre\bin\java.exe -cp C:\Fragpipe\fragpipe\lib\fragpipe-18.0.jar;/C:/Fragpipe/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.pin Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\20220902_REC-2401_Sample_01_IT.pin Process 'MSFragger move pin' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\fragpipe-20220902_REC-2401_Sample_01_IT.pepXML-temp] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\derek\AppData\Local\Temp\e19c8fc6-1aeb-4014-a3d3-3e501a24fa68 INFO[11:37:57] Executing Workspace v4.4.0
INFO[11:37:57] Creating workspace
INFO[11:37:57] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\fragpipe-20220902_REC-2401_Sample_01_IT.pepXML-temp] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --nontt --nonmc --decoy rev --database Y:\data\Adamo\2022-09-09-decoys-ManducaSexta_taxonomy_id7130_uniprot2022.09.07.fasta.fas ..\20220902_REC-2401_Sample_01_IT.pepXML INFO[11:37:57] Executing PeptideProphet v4.4.0
Unknown file type. No file loaded.Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger/20220902_REC-2401_Sample_01_IT.raw Unknown file type. No file loaded.Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger/20220902_REC-2401_Sample_01_IT.raw file 1: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\20220902_REC-2401_Sample_01_IT.pepXML processed altogether 45319 results INFO: Results written to file: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml

Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml
Building Commentz-Walter keyword tree...error2 TETSVTDLDYSTIEDTDYTVTDSSTSSDETTGTDDKSSTTT vs YVYYANYSNSLVYNNEEQRLSYFTEDIGLNSYYYYFHSHLPFWWNSERYGALKSRRGEIYYYFYQ
Searching the tree...
Linking duplicate entries...
Printing results...using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Not using ntt model Not using nmc model Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem nonspecific PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) @.*** read in 0 1+, 9581 2+, 9797 3+, 8523 4+, 11324 5+, 6094 6+, and 0 7+ spectra. Found 22240 Decoys, and 23079 Non-Decoys MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10.........20...WARNING: Mixture model quality test failed for charge (1+).

WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 24 iterations INFO[11:41:09] Done
Process 'PeptideProphet' finished, exit code: 0 PeptideProphet: Delete temp C:\Fragpipe\fragpipe\jre\bin\java.exe -cp C:\Fragpipe\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\fragpipe-20220902_REC-2401_Sample_01_IT.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\jre\bin\java.exe -cp C:\Fragpipe\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\20220902_REC-2401_Sample_01_IT.raw Fixing pepxml: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml Writing output to: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml17996539353664058444.temp-rewrite Deleting file: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml Moving rewritten file to original location: [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml17996539353664058444.temp-rewrite] -> [Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate Y:\data\Adamo\2022-09-09-decoys-ManducaSexta_taxonomy_id7130uniprot2022.09.07.fasta.fas --prefix rev INFO[11:41:10] Executing Database v4.4.0
INFO[11:41:10] Annotating the database
INFO[11:41:10] Done
Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger] C:\Fragpipe\fragpipe\tools\philosopher_v4.4.0_windowsamd64\philosopher.exe filter --tag rev --pepxml Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger INFO[11:41:10] Executing Filter v4.4.0
INFO[11:41:10] Processing peptide identification files
INFO[11:41:10] Parsing Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml.tmp.a28584 INFO[11:41:10] Parsing Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml WARN[11:41:10] No PSM was found in data set. Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml panic: Cannot decode packed binary. XML syntax error on line 11083: expected attribute name in element

goroutine 51 [running]: philosopher/lib/msg.callLogrus({0xc0000ffaa0, 0x5f}, {0x8612c0, 0x1?}) /workspace/philosopher/lib/msg/msg.go:319 +0x354 philosopher/lib/msg.DecodeMsgPck({0x9b0040?, 0xc0002bb740?}, {0x8612c0, 0x5}) /workspace/philosopher/lib/msg/msg.go:120 +0x6e philosopher/lib/spc.(PepXML).Parse(0xc000167a50, {0xc0000b4200, 0x77}) /workspace/philosopher/lib/spc/spc.go:63 +0x1c6 philosopher/lib/id.(PepXML).Read(0xc0000ce2c0, {0xc0000b4200, 0x77}) /workspace/philosopher/lib/id/pep.go:207 +0x105 philosopher/lib/id.ReadPepXMLInput.func1(0x1, {0xc0000b4200, 0x77}) /workspace/philosopher/lib/id/pep.go:386 +0x105 philosopher/lib/id.ReadPepXMLInput.func2(0x0?, {0xc0000b4200, 0x77}) /workspace/philosopher/lib/id/pep.go:422 +0xa2 created by philosopher/lib/id.ReadPepXMLInput /workspace/philosopher/lib/id/pep.go:419 +0x978 Process 'PhilosopherFilter' finished, exit code: 2 Process returned non-zero exit code, stopping ERRO[11:41:11] Cannot decode packed binary. XML syntax error on line 11083: expected attribute name in element


Cancelling 3 remaining tasks

fcyu commented 2 years ago

Thanks for the log file.

There is no ID from your data:

WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality test failed for charge (3+).
WARNING: Mixture model quality test failed for charge (4+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).

There are also some issue in your fasta file:

  - Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml
  - Building Commentz-Walter keyword tree...error2 TETSVTDLDYSTIEDTDYTVTDSSTSSDETTGTDDKSSTTT vs YVYYANYSNSLVYNNEEQRLSYFTEDIGLNSYYYYFHSHLPFWWNSERYGALKSRRGEIYYYFYQ

I don't know the reason since it is from PeptideProphet. Can you download a new fasta file using FragPipe and try again?

Best,

Fengchao

DRock420 commented 2 years ago

HI Fengchao

I only know one way to download it through Fragpipe, however the Uniprot Proteome site for that species is blank (contains no protein entries) which just gives me a java error when I try to download the fasta file.

https://www.uniprot.org/proteomes/UP000791440

Do you have any suggestions for a work around?

Thanks

Derek

From: Fengchao @. Sent: September 13, 2022 12:27 PM To: Nesvilab/FragPipe @.> Cc: Derek Smith @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] XML Syntax error (Issue #826)

Thanks for the log file.

There is no ID from your data:

WARNING: Mixture model quality test failed for charge (2+).

WARNING: Mixture model quality test failed for charge (3+).

WARNING: Mixture model quality test failed for charge (4+).

WARNING: Mixture model quality test failed for charge (5+).

WARNING: Mixture model quality test failed for charge (6+).

WARNING: Mixture model quality test failed for charge (7+).

There are also some issue in your fasta file:

Y:\data\Adamo\REC-2401\20220902_REC-2401_Adamo\Derek_Fragger\interact-20220902_REC-2401_Sample_01_IT.pep.xml
Building Commentz-Walter keyword tree...error2 TETSVTDLDYSTIEDTDYTVTDSSTSSDETTGTDDKSSTTT vs YVYYANYSNSLVYNNEEQRLSYFTEDIGLNSYYYYFHSHLPFWWNSERYGALKSRRGEIYYYFYQ

I don't know the reason since it is from PeptideProphet. Can you download a new fasta file using FragPipe and try again?

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/826#issuecomment-1245861970, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AOX3MZNOTO35HXFMNJDC4MLV6DIPXANCNFSM6AAAAAAQLXOUME. You are receiving this because you authored the thread.Message ID: @.**@.>>

fcyu commented 2 years ago

Hi Derek,

You can download the fasta file from https://www.uniprot.org/uniprotkb?facets=reviewed%3Atrue&query=%28taxonomy_id%3A7130%29, and then, adding decoys by clicking add decoy button in FragPipe.

At the meantime, can you send us your fasta file? You need to zip your file and upload it in GitHub. Replying the email would make GitHub truncate it.

Thanks,

Fengchao

DRock420 commented 2 years ago

HI Fengchao

That's how we created the original database. I have attached the .fas file with decoys and contaminants

Thanks

Derek

2022-09-09-decoys-contam-ManducaSexta_taxonomy_id7130_uniprot2022.09.07.fasta.zip

fcyu commented 2 years ago

Hi Derek,

Your fasta file has exactly the same issue as https://github.com/Nesvilab/FragPipe/issues/821#issuecomment-1245901552:

Best,

Fengchao

DRock420 commented 2 years ago

Thanks Fenchao, the search finishes with the new FASTA file. I don't know how it got corrupted.

The search still resulted in 0 psm and so I will try against a more general all species database to see if that improves anything

fcyu commented 2 years ago

Thanks for your feedback.

Please feel free to contact us if you have any further questions.

Best,

Fengchao

DRock420 commented 1 year ago

Sorry, yes we are working together to fix the problem

Derek

From: Fengchao @. Sent: September 13, 2022 1:22 PM To: Nesvilab/FragPipe @.> Cc: Derek Smith @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] XML Syntax error (Issue #826)

Hi Derek,

Your fasta file has exactly the same issue as #821 (comment)https://github.com/Nesvilab/FragPipe/issues/821#issuecomment-1245901552:

[image]https://user-images.githubusercontent.com/6926299/190001494-894079d3-ca51-4d31-a75d-dba2ba0d26b4.png

Best,

Fengchao

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Nesvilab / FragPipe

`"` in the fasta file broke the program. #826