reprint report contain only 0's

[chrishuges]

Hi,
I am trying to use Philosopher (v3.4.13) to do an AP-MS analysis with Reprint. I use the pipeline functionality:

# Philosopher pipeline configuration file.
#
# The pipeline mode automates the processing done by Philosopher and other tools. First, check
# the steps you want to execute in the commands section and change them to
# 'yes'. For each selected command, go to its section and adjust the parameters
# accordingly to your analysis.
#
# If you want to include MSFragger and TMT-Integrator into your analysis, you will
# have to download them separately, and then add their location in their
# configuration section.
#
# Usage:
# philosopher pipeline --config <this_configuration_file> [list_of_data_set_folders]

analytics: true                                  # reports when a workspace is created for usage statistics
slackToken:                                      # specify the Slack API token (how to generate a token: https://api.slack.com/legacy/custom-integrations/legacy-tokens)
slackChannel:                                    # specify the channel name, or
slackUserID:                                     # specify a user ID for a direct message

Steps:
  Database Search: yes                           # peptide to spectrum matching with Comet or MSFragger
  Peptide Validation: yes                         # peptide assignment validation with PeptideProphet
  PTM Localization: no                           # PTM site localization with PTMProphet
  Protein Inference: yes                          # protein identification validation with ProteinProphet
  Label-Free Quantification: yes                  # precursor label-free quantification inspired by moFF
  Isobaric Quantification: no                    # isobaric labeling-based relative quantification for TMT and iTRAQ
  Bio Cluster Quantification: no                 # protein report based on Uniprot protein clusters
  FDR Filtering: yes                              # statistical filtering, validation and false discovery r ates assessment
  Individual Reports: yes                         # multi-level reporting for both narrow-searches and open-searches
  Integrated Reports: yes                         # combined analysis of LC-MS/MS results inspired by Abacus
  Integrated Isobaric Quantification: no         # integrates channel abundances from multiple isobaric-tagged samples with TMT-Integrator

Database Search:                                 # MSFragger 3.1 & Comet
  protein_database: /mnt/Data/chughes/projectsRepository/sorensenLab/relatedToDlg2/proteomics20210726_dlg2IpmsEwsCells/2021-07-26-decoys-reviewed-contam-UP000005640.fas                             # path to the target-decoy protein database
  decoy_tag: rev_                                # prefix tag used added to decoy sequences
  search_engine: msfragger                           # search engine options include "comet" and "msfragger"
  comet:                                         # Comet v2019011
    noindex: true                                # skip mzML file indexing
    param:                                       # comet parameter file (default "comet.params.txt")
    raw: mzML                                    # format of the spectra file
  msfragger:                                     # MSFragger v3.0
    path: /home/chughes/softwareTools/msfragger-3.2/MSFragger-3.2/MSFragger-3.2.jar                                       # path to MSFragger jar
    memory: 8                                    # how much memory in GB to use
    param:                                       # MSFragger parameter file
    raw: mzML                                    # spectra format
    num_threads: 0                               # 0=poll CPU to set num threads; else specify num threads directly (max 64)
    precursor_mass_lower: -50                    # lower bound of the precursor mass window
    precursor_mass_upper: 50                     # upper bound of the precursor mass window
    precursor_mass_units: 1                      # 0=Daltons, 1=ppm
    precursor_true_tolerance: 20                 # true precursor mass tolerance (window is +/- this value)
    precursor_true_units: 1                      # 0=Daltons, 1=ppm
    fragment_mass_tolerance: 0.05                  # fragment mass tolerance (window is +/- this value)
    fragment_mass_units: 0                       # fragment mass tolerance units (0 for Da, 1 for ppm)
    calibrate_mass: 2                            # 0=Off, 1=On, 2=On and find optimal parameters
    deisotope: 1                                 # activates deisotoping.
    isotope_error: 0/1/2                         # 0=off, 0/1/2 (standard C13 error)
    mass_offsets: 0                              # allow for additional precursor mass window shifts. Multiplexed with isotope_error. mass_offsets = 0/79.966 can be used as a restricted ‘open’ search that looks for unmodified and phosphorylated peptides (on any residue)
    precursor_mass_mode: selected                # selected or isolated
    localize_delta_mass: 0                       # this allows shifted fragment ions - fragment ions with mass increased by the calculated mass difference, to be included in scoring
    delta_mass_exclude_ranges: (-1.5,3.5)        # exclude mass range for shifted ions searching
    fragment_ion_series: b,y                     # ion series used in search
    search_enzyme_name: Trypsin                  # name of enzyme to be written to the pepXML file
    search_enzyme_cutafter: KR                   # residues after which the enzyme cuts
    search_enzyme_butnotafter: P                 # residues that the enzyme will not cut before
    num_enzyme_termini: 2                        # 2 for enzymatic, 1 for semi-enzymatic, 0 for nonspecific digestion
    allowed_missed_cleavage: 1                   # maximum value is 5
    clip_nTerm_M: 1                              # specifies the trimming of a protein N-terminal methionine as a variable modification (0 or 1)
    variable_mod_01: 15.99490 M 3                # variable modification
    variable_mod_02: 42.01060 [^ 1               # variable modification
    variable_mod_03:                             # variable modification
    variable_mod_04:                             # variable modification
    variable_mod_05:                             # variable modification
    variable_mod_06:                             # variable modification
    variable_mod_07:                             # variable modification
    allow_multiple_variable_mods_on_residue: 0   # static mods are not considered
    max_variable_mods_per_peptide: 3             # maximum of 5
    max_variable_mods_combinations: 5000         # maximum of 65534, limits number of modified peptides generated from sequence
    output_file_extension: pepXML                # file extension of output files
    output_format: pepXML                        # file format of output files (pepXML or tsv)
    output_report_topN: 1                        # reports top N PSMs per input spectrum
    output_max_expect: 50                        # suppresses reporting of PSM if top hit has expectation greater than this threshold
    report_alternative_proteins: 0               # 0=no, 1=yes
    precursor_charge: 1 4                        # assume range of potential precursor charge states. Only relevant when override_charge is set to 1
    override_charge: 0                           # 0=no, 1=yes to override existing precursor charge states with precursor_charge parameter
    digest_min_length: 7                         # minimum length of peptides to be generated during in-silico digestion
    digest_max_length: 50                        # maximum length of peptides to be generated during in-silico digestion
    digest_mass_range: 500.0 5000.0              # mass range of peptides to be generated during in-silico digestion in Daltons
    max_fragment_charge: 2                       # maximum charge state for theoretical fragments to match (1-4)
    track_zero_topN: 0                           # in addition to topN results, keep track of top results in zero bin
    zero_bin_accept_expect: 0                    # boost top zero bin entry to top if it has expect under 0.01 - set to 0 to disable
    zero_bin_mult_expect: 1                      # disabled if above passes - multiply expect of zero bin for ordering purposes (does not affect reported expect)
    add_topN_complementary: 0                    # inserts complementary ions corresponding to the top N most intense fragments in each experimental spectra
    minimum_peaks: 15                            # required minimum number of peaks in spectrum to search (default 10)
    use_topN_peaks: 100                          # pre-process experimental spectrum to only use top N peaks
    min_fragments_modelling: 2                   # minimum number of matched peaks in PSM for inclusion in statistical modeling
    min_matched_fragments: 4                     # minimum number of matched peaks for PSM to be reported
    minimum_ratio: 0.01                          # filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity
    clear_mz_range: 0.0 0.0                      # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range
    remove_precursor_peak: 0                     # remove precursor peaks from tandem mass spectra. 0=not remove; 1=remove the peak with precursor charge; 2=remove the peaks with all charge states.
    remove_precursor_range: -1.5,1.5             # m/z range in removing precursor peaks. Unit: Da.
    intensity_transform: 0                       # transform peaks intensities with sqrt root. 0=not transform; 1=transform using sqrt root.
    mass_diff_to_variable_mod: 0                                   # Put mass diff as a variable modification. 0 for no; 1 for yes and change the original mass diff and the calculated mass accordingly; 2 for yes but do not change the original mass diff.
    labile_search_mode: "off"                    # type of search (nglycan, labile, or off). Off means non-labile/typical search.
    restrict_deltamass_to: all                   # Specify amino acids on which delta masses (mass offsets or search modifications) can occur. Allowed values are single letter codes (e.g. ACD), must
    diagnostic_intensity_filter: 0                               # [nglycan/labile search_mode only]. Minimum relative intensity for SUM of all detected oxonium ions to achieve for spectrum to contain diagnostic fragment evidence. Calculated relative to spectrum base peak. 0 <= value.
    Y_type_masses:                               # [nglycan/labile search_mode only]. Specify fragments of labile mods that are commonly retained on intact peptides (e.g. Y ions for glycans). Only used if 'Y' is included in fragment_ion_series.
    diagnostic_fragments:                        # [nglycan/labile search_mode only]. Specify diagnostic fragments of labile mods that appear in the low m/z region. Only used if diagnostic_intensity_filter > 0.
    add_Cterm_peptide: 0.000000                  # c-term peptide fixed modifications
    add_Cterm_protein: 0.000000                  # c-term protein fixed modifications
    add_Nterm_peptide: 0.000000                  # n-term peptide fixed modifications
    add_Nterm_protein: 0.000000                  # n-term protein fixed modifications
    add_A_alanine: 0.000000                      # alanine fixed modifications
    add_C_cysteine: 0.000000                    # cysteine fixed modifications
    add_D_aspartic_acid: 0.000000                # aspartic acid fixed modifications
    add_E_glutamic_acid: 0.000000                # glutamic acid fixed modifications
    add_F_phenylalanine: 0.000000                # phenylalanine fixed modifications
    add_G_glycine: 0.000000                      # glycine fixed modifications
    add_H_histidine: 0.000000                    # histidine fixed modifications
    add_I_isoleucine: 0.000000                   # isoleucine fixed modifications
    add_K_lysine: 0.000000                       # lysine fixed modifications
    add_L_leucine: 0.000000                      # leucine fixed modifications
    add_M_methionine: 0.000000                   # methionine fixed modifications
    add_N_asparagine: 0.000000                   # asparagine fixed modifications
    add_P_proline: 0.000000                      # proline fixed modifications
    add_Q_glutamine: 0.000000                    # glutamine fixed modifications
    add_R_arginine: 0.000000                     # arginine fixed modifications
    add_S_serine: 0.000000                       # serine fixed modifications
    add_T_threonine: 0.000000                    # threonine fixed modifications
    add_V_valine: 0.000000                       # valine fixed modifications
    add_W_tryptophan: 0.000000                   # tryptophan fixed modifications
    add_Y_tyrosine: 0.000000                     # tyrosine fixed modifications

Peptide Validation:                              # PeptideProphet v5.2
  concurrent: false                              # Concurrent execution of multiple instaces
  extension: pepXML                              # pepXML file extension
  clevel: 0                                      # set Conservative Level in neg_stdev from the neg_mean, low numbers are less conservative, high numbers are more conservative
  accmass: true                                  # use Accurate Mass model binning
  decoyprobs: true                               # compute possible non-zero probabilities for Decoy entries on the last iteration
  enzyme: trypsin                                # enzyme used in sample (optional)
  exclude: false                                 # exclude deltaCn*, Mascot*, and Comet* results from results (default Penalize * results)
  expectscore: true                              # use expectation value as the only contributor to the f-value for modeling
  forcedistr: false                              # bypass quality control checks, report model despite bad modeling
  glyc: false                                    # enable peptide Glyco motif model
  icat: false                                    # apply ICAT model (default Autodetect ICAT)
  instrwarn: false                               # warn and continue if combined data was generated by different instrument models
  leave: false                                   # leave alone deltaCn*, Mascot*, and Comet* results from results (default Penalize * results)
  maldi: false                                   # enable MALDI mode
  masswidth: 5                                   # model mass width (default 5)
  minpeplen: 7                                   # minimum peptide length not rejected (default 7)
  minpintt: 2                                    # minimum number of NTT in a peptide used for positive pI model (default 2)
  minpiprob: 0.9                                 # minimum probability after first pass of a peptide used for positive pI model (default 0.9)
  minprob: 0.05                                  # report results with minimum probability (default 0.05)
  minrtntt: 2                                    # minimum number of NTT in a peptide used for positive RT model (default 2)
  minrtprob: 0.9                                 # minimum probability after first pass of a peptide used for positive RT model (default 0.9)
  neggamma: false                                # use Gamma distribution to model the negative hits
  noicat: false                                  # do no apply ICAT model (default Autodetect ICAT)
  nomass: false                                  # disable mass model
  nonmc: false                                   # disable NMC missed cleavage model
  nonparam: true                                 # use semi-parametric modeling, must be used in conjunction with --decoy option
  nontt: false                                   # disable NTT enzymatic termini model
  optimizefval: false                            # (SpectraST only) optimize f-value function f(dot,delta) using PCA
  phospho: false                                 # enable peptide Phospho motif model
  pi: false                                      # enable peptide pI model
  ppm: true                                      # use PPM mass error instead of Dalton for mass modeling
  zero: false                                    # report results with minimum probability 0

PTM Localization:                                # PTMProphet v6.0
  autodirect: false                              # use direct evidence when the lability is high, use in combination with LABILITY
  cions:                                         # use specified C-term ions, separate multiple ions by commas (default: y for CID, z for ETD)
  direct: false                                  # use only direct evidence for evaluating PTM site probabilities
  em: 2                                          # set EM models to 0 (no EM), 1 (Intensity EM Model Applied) or 2 (Intensity and Matched Peaks EM Models Applied)
  static: false                                  # use static fragppmtol for all PSMs instead of dynamically estimates offsets and tolerances
  fragppmtol: 15                                 # when computing PSM-specific mass_offset and mass_tolerance, use specified default +/- MS2 mz tolerance on fragment ions
  ifrags: false                                  # use internal fragments for localization
  keepold: false                                 # retain old PTMProphet results in the pepXML file
  lability: false                                # compute Lability of PTMs
  massdiffmode: false                            # use the Mass Difference and localize
  excludemassdiffmin: 0                          # Minimum mass difference excluded for MASSDIFFFMODE analysis (default=0)
  excludemassdiffmax: 0                          # Maximun mass difference excluded for MASSDIFFFMODE analysis (default=0)
  massoffset: 0                                  # adjust the massdiff by offset (0 = use default)
  maxfragz: 0                                    # limit maximum fragment charge (default: 0=precursor charge, negative values subtract from precursor charge)
  maxthreads: 4                                  # use specified number of threads for processing
  mino: 0                                        # use specified number of pseudo-counts when computing Oscore (0 = use default)
  minprob: 0                                     # use specified minimum probability to evaluate peptides
  mods:                                          # specify modifications
  nions:                                         # use specified N-term ions, separate multiple ions by commas (default: a,b for CID, c for ETD)
  nominofactor: false                            # disable MINO factor correction when MINO= is set greater than 0 (default: apply MINO factor correction)
  ppmtol: 1                                      # use specified +/- MS1 ppm tolerance on peptides which may have a slight offset depending on search parameters
  verbose: false                                 # produce Warnings to help troubleshoot potential PTM shuffling or mass difference issues

Protein Inference:                               # ProteinProphet v5.2
  accuracy: false                                # equivalent to --minprob 0
  allpeps: false                                 # consider all possible peptides in the database in the confidence model
  confem: false                                  # use the EM to compute probability given the confidence
  delude: false                                  # do NOT use peptide degeneracy information when assessing proteins
  excludezeros: false                            # exclude zero prob entries
  fpkm: false                                    # model protein FPKM values
  glyc: false                                    # highlight peptide N-glycosylation motif
  icat: false                                    # highlight peptide cysteines
  instances: false                               # use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment
  iprophet: false                                # input is from iProphet
  logprobs: false                                # use the log of the probabilities in the Confidence calculations
  maxppmdiff: 20                                 # maximum peptide mass difference in PPM (default 20)
  minprob: 0.05                                  # peptideProphet probabilty threshold (default 0.05)
  mufactor: 1                                    # fudge factor to scale MU calculation (default 1)
  nogroupwts: false                              # check peptide's Protein weight against the threshold (default: check peptide's Protein Group weight against threshold)
  nonsp: false                                   # do not use NSP model
  nooccam: false                                 # non-conservative maximum protein list
  noprotlen: false                               # do not report protein length
  normprotlen: false                             # normalize NSP using Protein Length
  protmw: false                                  # get protein mol weights
  softoccam: false                               # peptide weights are apportioned equally among proteins within each Protein Group (less conservative protein count estimate)
  unmapped: false                                # report results for UNMAPPED proteins

Label-Free Quantification:                       # Freequant
  peakTimeWindow: 0.4                            # specify the time windows for the peak (minute) (default 0.4)
  retentionTimeWindow: 3                         # specify the retention time window for xic (minute) (default 3)
  tolerance: 10                                  # m/z tolerance in ppm (default 10)

Isobaric Quantification:                         # Labelquant
  bestPSM: false                                 # select the best PSMs for protein quantification
  level: 2                                       # ms level for the quantification
  minProb: 0.7                                   # only use PSMs with a minimum probability score
  plex:                                          # number of channels
  purity: 0.5                                    # ion purity threshold (default 0.5)
  removeLow: 0.0                                 # ignore the lower 3% PSMs based on their summed abundances
  tolerance: 20                                  # m/z tolerance in ppm (default 20)
  uniqueOnly: false                              # report quantification based on only unique peptides
  brand: tmt                                     # isobaric labeling brand (tmt, itraq)

Bio Cluster Quantification:                      # BioQuant
  organismUniProtID:                             # UniProt proteome ID
  level: 0.9                                     # cluster identity level (default 0.9)

FDR Filtering:                                   # Filter
  psmFDR: 0.01                                   # psm FDR level (default 0.01)
  peptideFDR: 0.01                               # peptide FDR level (default 0.01)
  ionFDR: 0.01                                   # peptide ion FDR level (default 0.01)
  proteinFDR: 0.01                               # protein FDR level (default 0.01)
  peptideProbability: 0.7                        # top peptide probability threshold for the FDR filtering (default 0.7)
  proteinProbability: 0.5                        # protein probability threshold for the FDR filtering (not used with the razor algorithm) (default 0.5)
  peptideWeight: 1                               # threshold for defining peptide uniqueness (default 1)
  razor: false                                   # use razor peptides for protein FDR scoring
  picked: false                                  # apply the picked FDR algorithm before the protein scoring
  mapMods: false                                 # map modifications acquired by an open search
  models: false                                  # print model distribution
  sequential: false                              # alternative algorithm that estimates FDR using both filtered PSM and Protein lists

Individual Reports:                              # Report
  msstats: false                                 # create an output compatible to MSstats
  withDecoys: false                              # add decoy observations to reports
  mzID: false                                    # create a mzID output

Integrated Reports:                              # Abacus
  protein: true                                  # global level protein report
  peptide: true                                  # global level peptide report
  proteinProbability: 0.9                        # minimum protein probability (default 0.9)
  peptideProbability: 0.5                        # minimum peptide probability (default 0.5)
  uniqueOnly: false                              # report TMT quantification based on only unique peptides
  reprint: true                                 # create abacus reports using the Reprint format

Integrated Isobaric Quantification:              # TMT-Integrator v1.1.10
  path:                                          # path to TMT-Integrator jar
  memory: 6                                      # memory allocation, in Gb
  output:                                        # the location of output files
  channel_num: 10                                # number of channels in the multiplex (e.g. 10, 11)
  ref_tag: Bridge                                # unique tag for identifying the reference channel (Bridge sample added to each multiplex)
  groupby: -1                                    # level of data summarization(0: PSM aggregation to the gene level; 1: protein; 2: peptide sequence; 3: PTM site; -1: generate reports at all levels)
  psm_norm: false                                # perform additional retention time-based normalization at the PSM level
  outlier_removal: true                          # perform outlier removal
  prot_norm: -1                                  # normalization (0: None; 1: MD (median centering); 2: GN (median centering + variance scaling); -1: generate reports with all normalization options)
  min_pep_prob: 0.9                              # minimum PSM probability threshold (in addition to FDR-based filtering by Philosopher)
  min_purity: 0.5                                # ion purity score threshold
  min_percent: 0.05                              # remove low intensity PSMs (e.g. value of 0.05 indicates removal of PSMs with the summed TMT reporter ions intensity in the lowest 5% of all PSMs)
  unique_pep: false                              # allow PSMs with unique peptides only (if true) or unique plus razor peptides (if false), as classified by Philosopher and defined in PSM.tsv files
  unique_gene: 0                                 # additional, gene-level uniqueness filter (0: allow all PSMs; 1: remove PSMs mapping to more than one GENE with evidence of expression in the dataset; 2:remove all PSMs mapping to more than one GENE in the fasta file)
  best_psm: true                                 # keep the best PSM only (highest summed TMT intensity) among all redundant PSMs within the same LC-MS run
  prot_exclude: none                             # exclude proteins with specified tags at the beginning of the accession number (e.g. none: no exclusion; sp|,tr| : exclude protein with sp| or tr|)
  allow_overlabel: true                          # allow PSMs with TMT on S (when overlabeling on S was allowed in the database search)
  allow_unlabeled: true                          # allow PSMs without TMT tag or acetylation on the peptide n-terminus
  mod_tag: none                                  # PTM info for generation of PTM-specific reports (none: for Global data; S[167],T[181],Y[243]: for Phospho; K[170]: for K-Acetyl)
  min_site_prob: -1                              # site localization confidence threshold (-1: for Global; 0: as determined by the search engine; above 0 (e.g. 0.75): PTMProphet probability, to be used with phosphorylation only)
  ms1_int: true                                  # use MS1 precursor ion intensity (if true) or MS2 summed TMT reporter ion intensity (if false) as part of the reference sample abundance estimation
  top3_pep: true                                 # use top 3 most intense peptide ions as part of the reference sample abundance estimation
  print_RefInt: false                            # print individual reference sample abundance estimates for each multiplex in the final reports (in addition to the combined reference sample abundance estimate)
  add_Ref: -1                                    # add an artificial reference channel if there is no reference channel (-1: don't add the reference; 0: use summation as the reference; 1: use average as the reference; 2: use median as the reference)
  max_pep_prob_thres: 0                          # the threshold for maximum peptide probability
  min_ntt: 0                                     # minimum allowed number of enzymatic termini

And the search, quantification, and reprint seems to complete fine without any errors. There are two reports created, reprint.int.tsv and reprint.spc.tsv. Both of these contain the correct sample names as headers and the protein accessions (Uniprot) as the first column, but all the values are 0, in both files. If I look at the combined-protein.tsv or peptides, there is plenty of data/SPCs/intensities reported. No individual reprint reports are created (e.g. per sample). Not sure if I just have a parameter wrong?

Thanks,
Chris

[anesvi]

Felipe is away this week, I believe, so need to wait for his response. Can you try with Philosopher version 4 that was just released? I myself run things via FragPipe, and there is no issue. I can see how one can possibly get 0 intensities (label-free command fails because of older mzML or something), but Spec Counts should always be there. So it is strange. But I never run reprint command via philosopher pipeline. Best Alexey

[chrishuges]

Thanks for the reply. I tried with version 4 of Philosopher using the same parameters, but it doesn't finish processing:

Computing MU for 1728 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO: mu=9.63282e-07, db_size=45491529
time="13:47:10" level=info msg="Protein inference results" decoy=93 target=1397
time="13:47:10" level=info msg="Converged to 1.08 % FDR with 1107 Proteins" decoy=12 threshold=0.9932 total=1119
time="13:47:11" level=fatal msg="Cannot read file. open .meta/razor.bin: no such file or directory"

I will try with FragPipe and see if I can get a result.

[Bin-cc]

Hi chrishuges,

I had the same problem as you when I was running version 4.0.0, how did you solve it?

Best
Bin

[chrishuges]

Hi Bin,

I didn't end up solving it within Philosopher. I just went back to using Philosopher just for the search results and further processing results in SAINT directly with my own scripts. I actually went back to using Philospher 3.4.13 because I was having other issues with 4.0.0 as well (no values in TMT quant, failing runs because of inability to locate some razor.bin file that you can see above in the post you responded to, actually).

Sorry I couldn't be of help!

Chris

[chrishuges]

Just noticed this was marked answered. Is the solution to stop using this tool and switch to another? Should I be switching to FragPipe anyway (is Philosopher no longer supported)?

[prvst]

Hi Chris. The issue you reported could not be reproduced. It sometimes happens that people find errors or have difficulties because they are running a specific type of data, or they have troubles following the tutorials. We have an active user base, Philosopher is active and being maintained. The core filtering and quantification in FragPipe is actually from Philosopher, and we use internally daily, as many other people do. If you are having difficulties with the terminal version of the tool, I encourage you to try the graphical interface, once that several options and parameters are automatically set to help users. We also advise to always use the latest versions of our tools.

[chrishuges]

Fantastic. I think it is a great tool and I use it frequently, so I am happy to hear that. There was just no indication provided that an unsuccessful attempt was made to reproduce the error, so I was uncertain of what the status was when I saw it marked as answered.

I am happy to provide any files and configuration information that would support reproduction. I agree and do always try to use the latest versions of your tools, so I would be interested to learn if it is actually a problem with my system or related to my usage of the command-line version as it would be useful for me to track it down so I can correct it.

The GUI version does indeed work (I tried with GUI FragPipe after it was suggested above). But, saving a long-winded explanation, we would prefer to use the command-line version so were hoping to get it going.

I am not certain if the user, Bin, who commented above is having the same issue with REPRINT or if they are also observing this razor.bin error.

Thanks for your prompt reply.

[Bin-cc]

Hi Chris,

I also tried to use REPRINT to analyze the results file of philosopher, but I encountered the same error as you, so I switched to other methods for analysis. Please let me know if you have any further progress and I will be happy to try REPRINT again.

At the moment I haven't figured out how to fix the .meta/razor .bin problem, so I'm using the 3.4.0 version of philosopher for now, and if the problem of 4.0.0 version is fixed, I'll try that as well immediately.

Best regards,
Bin

[anesvi]

Sorry to hear about this. We will see if we can speed up the release of updated philosopher and FragPipe fixing this issue Alexey From: Bin-cc ***@***.***> Sent: Friday, October 8, 2021 11:17 PM To: Nesvilab/philosopher ***@***.***> Cc: Nesvizhskii, Alexey ***@***.***>; Comment ***@***.***> Subject: Re: [Nesvilab/philosopher] reprint report contain only 0's (Discussion #253) External Email - Use Caution Hi Chris, I also tried to use REPRINT to analyze the results file of philosopher, but I encountered the same error as you, so I switched to other methods for analysis. Please let me know if you have any further progress and I will be happy to try REPRINT again. At the moment I haven't figured out how to fix the .meta/razor .bin problem, so I'm using the 3.4.0 version of philosopher for now, and if the problem of 4.0.0 version is fixed, I'll try that as well immediately. Best regards, Bin — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#253 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM65XF2QSGLYV25FT3R3UF6X3FANCNFSM5BASEPSA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[prvst]

We have the next release under testing now, it should contain the solution for the meta/bin issue you encountered. Regarding the empty reprint files, we will need to follow up with some tests to try to reproduce it.