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Pipeline stops with error for Integrated Report step (Abacus). #296

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fstein opened this issue Nov 25, 2021 · 15 comments
Closed

Pipeline stops with error for Integrated Report step (Abacus). #296

fstein opened this issue Nov 25, 2021 · 15 comments
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@prvst @sarah-haynes
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bug Something isn't working

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@fstein
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fstein commented Nov 25, 2021

Hello,

when running the pipeline command of philosopher on multiple folders containing the annotation.txt and mzML files, it quits with the error "RemoveAll .: invalid argument.

When setting the Integrated Report step to no, it runs through without any error.

Any idea what might be the reason?

Cheers,

Frank

PS:

Here is the pipeline.yml parameter file:
philosopher.yml.txt

Here is the command line output:
INFO[12:22:53] Executing Pipeline v4.1.1
INFO[12:22:53] Creating workspace
WARN[12:22:53] A meta data folder was found and will not be overwritten.
INFO[12:22:53] Initiating the workspace on Bert
INFO[12:22:53] Creating workspace
WARN[12:22:53] A meta data folder was found and will not be overwritten.
INFO[12:22:53] Initiating the workspace on Ernie
INFO[12:22:53] Creating workspace
WARN[12:22:53] A meta data folder was found and will not be overwritten.
INFO[12:22:53] Annotating the database
INFO[12:22:54] Running the Database Search
MSFragger version MSFragger-3.4
Batmass-IO version 1.23.6
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: 1.8.0_301, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 35 GB memory
Checking database...
Checking spectral files...
C:\MS_Test_Folder\Ernie\Ernie_200910_P0000_Ernie_TMTyeast_25ng_60min_R1.mzML: Scans = 15246
C:\MS_Test_Folder\Ernie\Ernie_170620_P0000_Ernie_TMTyeast_25ng_60min_R2.mzML: Scans = 15642
C:\MS_Test_Folder\Bert\Bert_200617_P0000_Bert_TMTyeast_25ng_60min_R1_20200617172353.mzML: Scans = 15498
FIRST SEARCH*
Parameters:
num_threads = 6
database_name = C:\MS_Test_Folder\2021-11-25-decoys-contam-Saccharomyces_cerrevisiae_UP000002311_05202016_6749entries.fasta.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 = 2
use_all_mods_in_first_search = false
write_calibrated_mgf = 0
isotope_error = 0/1
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 = 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 = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = tsv_pepxml_pin
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = false
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 6
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
deisotope = 1
deneutralloss = true
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 = 300
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
remove_precursor_peak = 0
remove_precursor_range = -1.5,1.5
clear_mz_range_low = 125.5
clear_mz_range_high = 131.5
excluded_scan_list_file =
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = true
variable_mod_01 = 15.99490 M 3
variable_mod_02 = 42.01060 [^ 1
variable_mod_06 = 229.162932 n^ 1
variable_mod_07 = 229.162932 S 1
add_A_alanine = 0.000000
add_C_cysteine = 57.021464
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_K_lysine = 229.162932
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_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_V_valine = 0.000000
add_W_tryptophan = 0.000000
add_Y_tyrosine = 0.000000
Number of unique peptides
of length 7: 78837
of length 8: 75741
of length 9: 72136
of length 10: 68146
of length 11: 67093
of length 12: 62465
of length 13: 59846
of length 14: 57010
of length 15: 53296
of length 16: 51570
of length 17: 48840
of length 18: 45946
of length 19: 42987
of length 20: 41461
of length 21: 39667
of length 22: 36662
of length 23: 34966
of length 24: 33155
of length 25: 30627
of length 26: 28936
of length 27: 27448
of length 28: 26064
of length 29: 24621
of length 30: 22713
of length 31: 21183
of length 32: 19853
of length 33: 18535
of length 34: 17441
of length 35: 16122
of length 36: 14832
of length 37: 14047
of length 38: 13200
of length 39: 12119
of length 40: 11170
of length 41: 10398
of length 42: 9194
of length 43: 7752
of length 44: 5719
of length 45: 3807
of length 46: 2181
of length 47: 1137
of length 48: 519
of length 49: 253
of length 50: 114
In total 1329809 peptides.
Generated 10607660 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.10 Da.
500281306 fragments to be searched in 1 slices (7.45 GB total)
Operating on slice 1 of 1:
Fragment index slice generated in 14.03 s
001. Bert_200617_P0000_Bert_TMTyeast_25ng_60min_R1_20200617172353.mzML 1.6 s | deisotoping 0.7 s
[progress: 15473/15473 (100%) - 4685 spectra/s] 3.3s | postprocessing 0.2 s
002. Ernie_170620_P0000_Ernie_TMTyeast_25ng_60min_R2.mzML 0.8 s | deisotoping 0.1 s
[progress: 15584/15584 (100%) - 24426 spectra/s] 0.6s | postprocessing 0.1 s
003. Ernie_200910_P0000_Ernie_TMTyeast_25ng_60min_R1.mzML 1.0 s | deisotoping 0.1 s
[progress: 15228/15228 (100%) - 23683 spectra/s] 0.6s | postprocessing 0.1 s
*FIRST SEARCH DONE IN 0.525 MIN

**MASS CALIBRATION AND PARAMETER OPTIMIZATION
-----|---------------|---------------|---------------|---------------
| MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New)
-----|---------------|---------------|---------------|---------------
Run | Median MAD | Median MAD | Median MAD | Median MAD
001 | 0.49 0.91 | -0.06 0.82 | -0.66 1.26 | 0.02 1.18
002 | 2.55 1.46 | -0.00 0.89 | 2.30 1.16 | 0.09 1.10
003 | 3.44 1.42 | -0.06 0.90 | 0.28 1.35 | 0.09 1.28
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50
-------|-------|-------|-------|-------|-------|-------|-------|-------
Count | 6680| 6703| 6658| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1
-------|-------|-------|-------|-------|-------|-------
Count | 6755| 6760| 6760| 6716| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
Int. | 1
-------|-------
Count | 6770
-------|-------
-------|-------
Rm P. | 1
-------|-------
Count | 6717
-------|-------
New fragment_mass_tolerance = 7 PPM
New use_topN_peaks = 175
New minimum_ratio = 0.000000
New intensity_transform = 1
New remove_precursor_peak = 0
***MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 2.510 MIN

MAIN SEARCH
output_format = tsv_pepXML_pin but report_alternative_proteins = 0. Change report_alternative_proteins to 1.
Checking database...
variable_mod_03 has an empty value.
variable_mod_04 has an empty value.
variable_mod_05 has an empty value.
Parameters:
num_threads = 6
database_name = C:\MS_Test_Folder\2021-11-25-decoys-contam-Saccharomyces_cerrevisiae_UP000002311_05202016_6749entries.fasta.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 = 7.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = false
write_calibrated_mgf = 0
isotope_error = -1/0/1/2/3
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 = 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 = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = tsv_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 = 6
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
deisotope = 1
deneutralloss = true
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 = 175
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 1
remove_precursor_peak = 0
remove_precursor_range = -1.5,1.5
clear_mz_range_low = 125.5
clear_mz_range_high = 131.5
excluded_scan_list_file =
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = true
variable_mod_01 = 15.99490 M 3
variable_mod_02 = 42.01060 [^ 1
variable_mod_06 = 229.162932 n^ 1
variable_mod_07 = 229.162932 S 1
add_A_alanine = 0.000000
add_C_cysteine = 57.021464
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_K_lysine = 229.162932
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_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_V_valine = 0.000000
add_W_tryptophan = 0.000000
add_Y_tyrosine = 0.000000
Number of unique peptides
of length 7: 78837
of length 8: 75741
of length 9: 72136
of length 10: 68146
of length 11: 67093
of length 12: 62465
of length 13: 59846
of length 14: 57010
of length 15: 53296
of length 16: 51570
of length 17: 48840
of length 18: 45946
of length 19: 42987
of length 20: 41461
of length 21: 39667
of length 22: 36662
of length 23: 34966
of length 24: 33155
of length 25: 30627
of length 26: 28936
of length 27: 27448
of length 28: 26064
of length 29: 24621
of length 30: 22713
of length 31: 21183
of length 32: 19853
of length 33: 18535
of length 34: 17441
of length 35: 16122
of length 36: 14832
of length 37: 14047
of length 38: 13200
of length 39: 12119
of length 40: 11170
of length 41: 10398
of length 42: 9194
of length 43: 7752
of length 44: 5719
of length 45: 3807
of length 46: 2181
of length 47: 1137
of length 48: 519
of length 49: 253
of length 50: 114
In total 1329809 peptides.
Generated 10607660 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.03 Da.
500281306 fragments to be searched in 1 slices (7.45 GB total)
Operating on slice 1 of 1:
Fragment index slice generated in 12.50 s
001. Bert_200617_P0000_Bert_TMTyeast_25ng_60min_R1_20200617172353.mzBIN_calibrated 0.2 s
[progress: 15427/15427 (100%) - 11171 spectra/s] 1.4s | postprocessing 2.6 s
002. Ernie_170620_P0000_Ernie_TMTyeast_25ng_60min_R2.mzBIN_calibrated 0.2 s
[progress: 15535/15535 (100%) - 13675 spectra/s] 1.1s | postprocessing 1.9 s
003. Ernie_200910_P0000_Ernie_TMTyeast_25ng_60min_R1.mzBIN_calibrated 0.2 s
[progress: 15182/15182 (100%) - 15668 spectra/s] 1.0s | postprocessing 1.5 s
MAIN SEARCH DONE IN 0.445 MIN

TOTAL TIME 3.481 MIN*
INFO[12:26:26] Running the validation and inference on Bert
INFO[12:26:26] Executing PeptideProphet on Bert
file 1: C:\MS_Test_Folder\Bert\Bert_200617_P0000_Bert_TMTyeast_25ng_60min_R1_20200617172353.pepXML
processed altogether 11873 results
INFO: Results written to file: C:\MS_Test_Folder\Bert\interact.pep.xml

  • C:\MS_Test_Folder\Bert\interact.pep.xml

  • Searching the tree...

  • Linking duplicate entries...

  • Printing results...

  • Building Commentz-Walter keyword tree...using Accurate Mass Bins
    using PPM mass difference
    Using Decoy Label "rev_".
    Decoy Probabilities will be reported.
    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 trypsin
    MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 8673 2+, 3079 3+, 121 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 2685 Decoys, and 9188 Non-Decoys
Iterations: .........10.........20......
WARNING: Mixture model quality test failed for charge (1+).
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 27 iterations
INFO[12:26:57] Running the validation and inference on Ernie
INFO[12:26:57] Executing PeptideProphet on Ernie
file 1: C:\MS_Test_Folder\Ernie\Ernie_170620_P0000_Ernie_TMTyeast_25ng_60min_R2.pepXML
file 2: C:\MS_Test_Folder\Ernie\Ernie_200910_P0000_Ernie_TMTyeast_25ng_60min_R1.pepXML
processed altogether 22130 results
INFO: Results written to file: C:\MS_Test_Folder\Ernie\interact.pep.xml

  • C:\MS_Test_Folder\Ernie\interact.pep.xml

  • Searching the tree...

  • Linking duplicate entries...

  • Printing results...

  • Building Commentz-Walter keyword tree...using Accurate Mass Bins
    using PPM mass difference
    Using Decoy Label "rev_".
    Decoy Probabilities will be reported.
    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 trypsin
    MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
read in 0 1+, 18460 2+, 2865 3+, 805 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 4366 Decoys, and 17764 Non-Decoys
Iterations: .........10.........20......
WARNING: Mixture model quality test failed for charge (1+).
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 27 iterations
INFO[12:27:56] Running the validation and inference on Bert
INFO[12:27:56] Executing ProteinProphet on Bert
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
(no FPKM) (using degen pep info)
Reading in C:/MS_Test_Folder/Bert/interact.pep.xml...
...read in 0 1+, 4419 2+, 2069 3+, 90 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 6331 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database c:/MS_Test_Folder/2021-11-25-decoys-contam-Saccharomyces_cerrevisiae_UP000002311_05202016_6749entries.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.. Total: 13728
Computing degenerate peptides for 1821 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 1919 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1919 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 1919 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing 1635 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
Computing MU for 1919 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO: mu=2.64895e-05, db_size=12304840
INFO[12:28:00] Running the validation and inference on Ernie
INFO[12:28:00] Executing ProteinProphet on Ernie
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
(no FPKM) (using degen pep info)
Reading in C:/MS_Test_Folder/Ernie/interact.pep.xml...
...read in 0 1+, 12026 2+, 1832 3+, 87 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 8479 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database c:/MS_Test_Folder/2021-11-25-decoys-contam-Saccharomyces_cerrevisiae_UP000002311_05202016_6749entries.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.. Total: 13728
Computing degenerate peptides for 2374 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 2487 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 2487 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 2487 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 2487 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 2487 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 2487 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing 2126 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
Computing MU for 2487 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO: mu=3.17999e-05, db_size=12304840
INFO[12:28:08] Integrating peptide validation
Running FPKM NSS NRS NSE NSI NSM Model EM:
Computing NSS values ...

Creating 6 threads
Wait for threads to finish ...
........................ done
Computing NRS values ...

Creating 6 threads
Wait for threads to finish ...
0--------------------------------------------------50------------------------------------------------100%
..................................................................................................... done
Computing NSE values ...

Creating 6 threads
Wait for threads to finish ...
0--------------------------------------------------50------------------------------------------------100%
..................................................................................................... done
Computing NSI values ...

Creating 6 threads
Wait for threads to finish ...
0--------------------------------------------------50------------------------------------------------100%
..................................................................................................... done
Computing NSM values ...

Creating 6 threads
Wait for threads to finish ...
0--------------------------------------------------50------------------------------------------------100%
..................................................................................................... done
FPKM values are unavailable ...
Iterations: .........done
INFO[12:28:31] Creating combined protein inference
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
(no FPKM) (using degen pep info)
Reading in C:/MS_Test_Folder/Bert/interact.pep.xml...
...read in 0 1+, 3886 2+, 1959 3+, 86 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Reading in C:/MS_Test_Folder/Ernie/interact.pep.xml...
...read in 0 1+, 10884 2+, 1731 3+, 73 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.9

Initializing 9968 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database c:/MS_Test_Folder/2021-11-25-decoys-contam-Saccharomyces_cerrevisiae_UP000002311_05202016_6749entries.fasta.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.. Total: 13728
Computing degenerate peptides for 1969 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 2058 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 2058 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 2058 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 2058 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100%
Computing 1797 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
Computing MU for 2058 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO: mu=3.81399e-06, db_size=12304840
INFO[12:28:36] Protein inference results decoy=165 target=1632
INFO[12:28:36] Converged to 1.00 % FDR with 1296 Proteins decoy=13 threshold=0.9913 total=1309
2021/11/25 12:28:37 RemoveAll .: invalid argument
@fstein
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fstein commented Nov 25, 2021

You can have a look at all files under the following link: https://oc.embl.de/index.php/s/IvjBCb9riEoZ07K

@prvst prvst self-assigned this Nov 25, 2021
@prvst prvst added the bug Something isn't working label Nov 25, 2021
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prvst commented Dec 3, 2021

@fstein I was able to go throught the data analysis using your pipeline script, and without any issues:

INFO[13:28:20] Processing combined file                     
INFO[13:28:23] Converged to 0.99 % FDR with 7907 Peptides    decoy=79 threshold=0.907935 total=7986
INFO[13:28:23] Restoring peptide results                    
INFO[13:28:24] collecting data from individual experiments  
INFO[13:28:24] summarizing the quantification               
INFO[13:28:26] Processing combined file                     
INFO[13:28:27] Converged to 1.00 % FDR with 1296 Proteins    decoy=13 threshold=0.9913 total=1309
INFO[13:28:28] Restoring protein results                    
INFO[13:28:30] Processing spectral counts                   
INFO[13:28:31] Processing peptide counts                    
INFO[13:28:32] Processing intensities                       
INFO[13:28:32] Done

Here's what I suggest you can try. Remove all hidden files from each data data folder, and remove the current workspace. Remove all pin files, pepindexes, and any temporary file you might have. Probably unrelated, but also change the Protein Inference option to no. This should be only used for individual analyzes, and not for combined ones.

Please, keep me posted.

@fstein
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fstein commented Dec 8, 2021

Dear Felipe,

thanks for looking into this. Unfortunately, none of your suggestions worked for me (I tried removing files and starting all over again in quite some attempts) and I keep getting the same error. I even downloaded a fresh philosopher and msfragger release. Again, same error.
Just to be sure, that I did not mess anything up, here is a link to the fragpipe folder that I use to start philosopher: https://oc.embl.de/index.php/s/8TaDyuU5k2d8gmH
philosopher is under fragpipe\tools\philosopher

Any other idea what might be the reasons?

Cheers,

Frank

@fstein
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fstein commented Dec 8, 2021

PS: Did you also try running it from scratch using my philosopher.yml file? When I did it, I had only the annotation.txt, the raw and the mzML files in the data data folders. In the data folder, I only had the fasta db (*.fas) and the philosopher.yml. All hidden files were removed.

@prvst
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prvst commented Dec 8, 2021

I'm getting the same as before. I'm asking @sarah-haynes to help me pinpoint the problem, she'll try to reproduce the error on her side.

@fstein
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fstein commented Dec 8, 2021

Thanks a lot. Let me know if I can help or try anything else.

@prvst
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prvst commented Jan 4, 2022

@fstein can you upload your yml file?

@sarah-haynes This might be the same from #295

@fstein
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fstein commented Jan 4, 2022

I did this already in my first comment. I renamed it to philosopher.yml.txt. Do you need it again?

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fstein commented Jan 4, 2022

It's also available under the following link: https://oc.embl.de/index.php/s/IvjBCb9riEoZ07K

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prvst commented Jan 4, 2022

@fstein We implemented a fix for your issue, a new version will be out soon. Thanks for reporting,

@prvst prvst closed this as completed Jan 4, 2022
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fstein commented Feb 4, 2022

This is great news that you found a bug. Do you already have a rough idea when the updated version of philopher might be available for download?

Thanks again.

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prvst commented Feb 4, 2022

we don't have a hard date yet, but it will be soon, we just need to finish working on some other changes.

@fstein
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fstein commented Mar 30, 2022

Dear Filipe,

I also tried the version that you shared with me on this particular data set. Unfortunately, I still get the same error. Or was this not bug that you mentioned not solved in the version you shared with me?

Also, in order to trigger the integrated report with Abacus, do you need to create any additional files? For example, do you need a manifest file (like with FragPipe).

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prvst commented Mar 31, 2022

You still get the RemoveALL error ?

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fstein commented Mar 31, 2022

Yes

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