Closed jd690764 closed 5 years ago
fcyu
commented
5 years ago Hi,
Thanks for your interest in FragPipe/MSFragger. It looks like your issue was caused by language setting in your Linux.
BTW, the number reported by MSFragger looks weird. May I suggest you trying to convert the .d file to mzML rather than mzXML? We have a recommend MSConvert setting for timsTOF data. I can share it with you if you want.
Bests,
Fengchao
jd690764
commented
5 years ago Hi Fengchao,
Thanks for your reply,
I am sorry, can you be a bit more specific? Here is my setting:
locale
LANG=en_US.UTF-8 LC_CTYPE="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_PAPER="en_US.UTF-8" LC_NAME="en_US.UTF-8" LC_ADDRESS="en_US.UTF-8" LC_TELEPHONE="en_US.UTF-8" LC_MEASUREMENT="en_US.UTF-8" LC_IDENTIFICATION="en_US.UTF-8" LC_ALL= localectl System Locale: LANG=en_US.UTF-8 VC Keymap: us X11 Layout: us
What should I change about them?
I am actually using mzML - not mzXML. I used ProteoWizard to do the conversion with their 'pasef mgf' preset - which may not have been the right option? If you can send me the correct settings I'd really appreciate it.
Thank you. Janos
On Thu, Jun 13, 2019 at 12:16 PM Fengchao notifications@github.com wrote:
Hi,
Thanks for your interest in FragPipe/MSFragger. It looks like your issue was caused by language setting in your Linux.
BTW, the number reported by MSFragger looks weird. May I suggest you trying to convert the .d file to mzML rather than mzXML? We have a recommend MSConvert setting for timsTOF data. I can share it with you if you want.
Bests,
Fengchao
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/119?email_source=notifications&email_token=ACP7QYYS53X3VXUL6AU3MUDP2KMHVA5CNFSM4HX4SBLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXUYGJI#issuecomment-501842725, or mute the thread https://github.com/notifications/unsubscribe-auth/ACP7QYYQZXBPN5XQZOPXZPLP2KMHVANCNFSM4HX4SBLA .
fcyu
commented
5 years ago Hi Janos,
Your locate looks good. We noticed that there is one more strange message in your log:
2019/06/12 21:22:30.933342 cmd_run.go:375: restoring default SELinux context of /mnt/driveB/jdemeter/snapwhich may relate to Philosopher. We assigned this issue to @prvst now.
As to your data conversion, the pasef mgf should be fine.
Bests,
Fengchao
prvst
commented
5 years ago Why are you running the program from /var/ ?
Can you deactivate SELinux and try again ?
jd690764
commented
5 years ago Hi Fengchao,
I am using fedora 29 and I think SELinux comes with that. Currently it is in permissive mode, but if you think that would be better, I can deactivate it. Similarly, on fedora snap apparently is supposed to go there:
https://docs.snapcraft.io/installing-snap-on-fedora
Thanks, Janos
prvst
commented
5 years ago Hey, this is Felipe, not Fengchao,
Try disabling it then, it should be enough to make it work.
jd690764
commented
5 years ago Hi Felipe,
I disabled SELinux, re-ran MSFragger using the same data file and got the same error message. Please, see attached log.
Thank you, Janos
On Mon, Jun 17, 2019 at 2:05 PM Felipe Leprevost notifications@github.com wrote:
Hey, this is Felipe, not Fengchao,
Try disabling it then, it should be enough to make it work.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/119?email_source=notifications&email_token=ACP7QY7K6FY3YIUDJ3YT3NLP274BBA5CNFSM4HX4SBLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODX4OIZA#issuecomment-502850660, or mute the thread https://github.com/notifications/unsubscribe-auth/ACP7QYZT54OGXDGJ5H6QE3DP274BBANCNFSM4HX4SBLA .
System info: System OS: Linux, Architecture: amd64 Java Info: 1.8.0_212, OpenJDK 64-Bit Server VM, Oracle Corporation
Version info: FragPipe version 9.4 MSFragger version 20190530 Philosopher version v1.0.1 (build 1558718856)
LCMS files: Experiment/Group:
11 commands to execute: Workspace [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher workspace --clean Workspace [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher workspace --init MsFragger [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] java -jar -Dfile.encoding=UTF-8 -Xmx100G /mnt/driveB/jdemeter/bin/msf/MSFragger-20190530/MSFragger-20190530.jar /mnt/driveB/jdemeter/bin/msf/tmp2/fragger.params /mnt/driveB/jdemeter/bin/msf/data/Jurkat_WCL_100_Slot1-48_1_1013.mzML MsFragger java -cp /mnt/driveB/jdemeter/bin/msf/lib/FragPipe-9.4.jar umich.msfragger.util.FileMove /mnt/driveB/jdemeter/bin/msf/data/Jurkat_WCL_100_Slot1-48_1_1013.pepXML /mnt/driveB/jdemeter/bin/msf/tmp2/Jurkat_WCL_100_Slot1-48_11013.pepXML ReportDbAnnotate [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher database --annotate /mnt/driveB/jdemeter/bin/msf/protlib/2019-06-07-td-rev-UP000005640.fas --prefix rev PeptideProphet [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database /mnt/driveB/jdemeter/bin/msf/protlib/2019-06-07-td-rev-UP000005640.fas Jurkat_WCL_100_Slot1-48_1_1013.pepXML ProteinProphet [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher proteinprophet --maxppmdiff 2000000 /mnt/driveB/jdemeter/bin/msf/tmp2/interact-Jurkat_WCL_100_Slot1-48_11013.pep.xml ReportFilter [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml /mnt/driveB/jdemeter/bin/msf/tmp2 --protxml /mnt/driveB/jdemeter/bin/msf/tmp2/interact.prot.xml ReportFreequant [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher freequant --ptw 0.4 --tol 10 --isolated --dir /mnt/driveB/jdemeter/bin/msf/data ReportReport [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher report Workspace [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher workspace --clean
Workspace [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2]
/var/lib/snapd/snap/bin/philosopher workspace --clean
time="15:25:03" level=info msg="Executing Workspace v1.0.1"
time="15:25:06" level=info msg="Removing workspace"
time="15:25:06" level=info msg=Done
Process 'Workspace' finished, exit code: 0
Workspace [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2]
/var/lib/snapd/snap/bin/philosopher workspace --init
time="15:25:06" level=info msg="Executing Workspace v1.0.1"
time="15:25:06" level=info msg="Creating workspace"
time="15:25:06" level=info msg=Done
Process 'Workspace' finished, exit code: 0
MsFragger [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2]
java -jar -Dfile.encoding=UTF-8 -Xmx100G /mnt/driveB/jdemeter/bin/msf/MSFragger-20190530/MSFragger-20190530.jar /mnt/driveB/jdemeter/bin/msf/tmp2/fragger.params /mnt/driveB/jdemeter/bin/msf/data/Jurkat_WCL_100_Slot1-48_1_1013.mzML
MSFragger version MSFragger-20190530
MSFTBX version 1.9.10
(c) University of Michigan
System OS: Linux, Architecture: amd64
Java Info: 1.8.0_212, OpenJDK 64-Bit Server VM, Oracle Corporation
JVM started with 91022 MB memory
***********************************FIRST SEARCH************************************
Parameters used in this search:
num_threads = 24
database_name = /mnt/driveB/jdemeter/bin/msf/protlib/2019-06-07-td-rev-UP000005640.fas
decoy_prefix = rev_
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
evaluate_mass_calibration = false
isotope_error = 0/1
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2
allowed_missed_cleavage = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_mod = 3
max_variable_mods_combinations = 5000
output_file_extension = pepXML
output_format = pepXML
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = false
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
variable_mod_03 = 79.96633 STY
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 69.42 GB.
6028106350 fragments to be searched in 2 slices (89.83 GB total)
Operating on slice 1 of 2:
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 322.3 s
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 322.3 s [progress: 12050/97833 (12.32%) - 2405.67 spectra/s]
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 322.3 s [progress: 72768/97833 (74.38%) - 7221.20 spectra/s]
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 322.3 s [progress: 97833/97833 (100.00%) - 8151.39 spectra/s] - completed 12.0 s
Operating on slice 2 of 2:
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 73.4 s
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 73.4 s [progress: 93781/97833 (95.86%) - 18648.04 spectra/s]
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 73.4 s [progress: 97833/97833 (100.00%) - 18013.81 spectra/s] - completed 5.4 s
***************************FIRST SEARCH DONE IN 9.329 MIN**************************
*********************************MASS CALIBRATION**********************************
-----|---------------|---------------|---------------|---------------
| MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New)
-----|---------------|---------------|---------------|---------------
Run | Median MAD | Median MAD | Median MAD | Median MAD
001 | Not enough data to perform mass calibration. Using the uncalibrated data.
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------
MS2 | 7 | 10 | 15 | 20 | 25 | 30
-------|-------|-------|-------|-------|-------|-------
Count | 1| 5| 20| 34| 148| 176
-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------
Peaks | 50_1 | 75_1 | 100_1 | 125_1 | 150_1
-------|-------|-------|-------|-------|-------
Count | 48| 76| 116| 146| 176
-------|-------|-------|-------|-------|-------
New fragment_mass_tolerance = 30 PPM
New use_topN_peaks = 150
New minimum_ratio = 0.010000
**************************MASS CALIBRATION DONE IN 42.094 MIN***********************
************************************MAIN SEARCH************************************
Parameters used in this search:
num_threads = 24
database_name = /mnt/driveB/jdemeter/bin/msf/protlib/2019-06-07-td-rev-UP000005640.fas
decoy_prefix = rev_
precursor_mass_lower = -50.0
precursor_mass_upper = 50.0
precursor_mass_units = 1
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 30.0
fragment_mass_units = 1
calibrate_mass = 2
evaluate_mass_calibration = false
isotope_error = 0/1/2
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2
allowed_missed_cleavage = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = true
max_variable_mods_per_mod = 3
max_variable_mods_combinations = 5000
output_file_extension = pepXML
output_format = pepXML
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = false
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 150
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
variable_mod_03 = 79.96633 STY
Selected fragment tolerance 0.15 Da and maximum fragment slice size of 69.41 GB.
6085215732 fragments to be searched in 2 slices (90.68 GB total)
Operating on slice 1 of 2:
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 68.3 s
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 68.3 s [progress: 59370/97833 (60.69%) - 11831.41 spectra/s]
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 68.3 s [progress: 97833/97833 (100.00%) - 10724.95 spectra/s] - completed 9.1 s
Operating on slice 2 of 2:
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 68.6 s
001. Jurkat_WCL_100_Slot1-48_1_1013.mzML 68.6 s [progress: 97833/97833 (100.00%) - 29964.17 spectra/s] - completed 3.3 s
***************************MAIN SEARCH DONE IN 3.958 MIN***************************
*******************************TOTAL TIME 55.381 MIN********************************
Process 'MsFragger' finished, exit code: 0
MsFragger
java -cp /mnt/driveB/jdemeter/bin/msf/lib/FragPipe-9.4.jar umich.msfragger.util.FileMove /mnt/driveB/jdemeter/bin/msf/data/Jurkat_WCL_100_Slot1-48_1_1013.pepXML /mnt/driveB/jdemeter/bin/msf/tmp2/Jurkat_WCL_100_Slot1-48_1_1013.pepXML
Process 'MsFragger' finished, exit code: 0
ReportDbAnnotate [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2]
/var/lib/snapd/snap/bin/philosopher database --annotate /mnt/driveB/jdemeter/bin/msf/protlib/2019-06-07-td-rev-UP000005640.fas --prefix rev_
time="16:20:40" level=info msg="Executing Database v1.0.1"
time="16:20:40" level=info msg="Processing database"
time="16:20:45" level=info msg=Done
Process 'ReportDbAnnotate' finished, exit code: 0
PeptideProphet [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2]
/var/lib/snapd/snap/bin/philosopher peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database /mnt/driveB/jdemeter/bin/msf/protlib/2019-06-07-td-rev-UP000005640.fas Jurkat_WCL_100_Slot1-48_1_1013.pepXML
time="16:20:45" level=info msg="Executing PeptideProphet v1.0.1"
WARNING: cannot open data file /mnt/driveB/jdemeter/bin/msf/tmp2/Jurkat_WCL_100_Slot1-48_1_1013.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file /mnt/driveB/jdemeter/bin/msf/tmp2/Jurkat_WCL_100_Slot1-48_1_1013.mzXML in msms_run_summary tag...
WARNING: cannot open data file /mnt/driveB/jdemeter/bin/msf/tmp2/Jurkat_WCL_100_Slot1-48_1_1013.mzML in msms_run_summary tag... trying .mzXML ...
WARNING: CANNOT correct data file /mnt/driveB/jdemeter/bin/msf/tmp2/Jurkat_WCL_100_Slot1-48_1_1013.mzXML in msms_run_summary tag...
file 1: /mnt/driveB/jdemeter/bin/msf/tmp2/Jurkat_WCL_100_Slot1-48_1_1013.pepXML
processed altogether 53386 results
INFO: Results written to file: /mnt/driveB/jdemeter/bin/msf/tmp2/interact-Jurkat_WCL_100_Slot1-48_1_1013.pep.xml
- /mnt/driveB/jdemeter/bin/msf/tmp2/interact-Jurkat_WCL_100_Slot1-48_1_1013.pep.xml
- Building Commentz-Walter keyword tree...
- 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.
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
PeptideProphet (TPP v5.2.0 Flammagenitus, Build 201903141531-exported (Linux-x86_64)) AKeller@ISB
read in 6415 1+, 45265 2+, 988 3+, 581 4+, 137 5+, 0 6+, and 0 7+ spectra.
Found 25947 Decoys, and 27439 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.........30..
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 33 iterations
time="16:23:25" level=info msg=Done
Process 'PeptideProphet' finished, exit code: 0
ProteinProphet [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2]
/var/lib/snapd/snap/bin/philosopher proteinprophet --maxppmdiff 2000000 /mnt/driveB/jdemeter/bin/msf/tmp2/interact-Jurkat_WCL_100_Slot1-48_1_1013.pep.xml
time="16:23:25" level=info msg="Executing ProteinProphet v1.0.1"
terminate called after throwing an instance of 'std::runtime_error'
what(): locale::facet::_S_create_c_locale name not valid
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.0 Flammagenitus, Build 201903151138-exported (Linux-x86_64))
2019/06/17 16:23:26 open /tmp/56d57430-ed48-417b-931f-3cc124d1f29f/interact.prot.xml: no such file or directory
Process 'ProteinProphet' finished, exit code: 1
Process returned non-zero exit code, stopping
ReportFilter [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2]
/var/lib/snapd/snap/bin/philosopher filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml /mnt/driveB/jdemeter/bin/msf/tmp2 --protxml /mnt/driveB/jdemeter/bin/msf/tmp2/interact.prot.xml
Stopping 5/12 processes (7 already finished) Processing interrupted, stopping ReportFilter
prvst
commented
5 years ago Now open a terminal, run the following:
export LC_ALL=en_US.UTF-8
And then try again.
jd690764
commented
5 years ago HI Felipe,
I get the exact same problem.
Janos
ProteinProphet [Work dir: /mnt/driveB/jdemeter/bin/msf/tmp2] /var/lib/snapd/snap/bin/philosopher proteinprophet --maxppmdiff 2000000 /mnt/driveB/jdemeter/bin/msf/tmp2/interact-Jurkat_WCL_100_Slot1-48_1_1013.pep.xml time="18:59:24" level=info msg="Executing ProteinProphet v1.0.1" terminate called after throwing an instance of 'std::runtime_error' what(): locale::facet::_S_create_c_locale name not valid ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.2.0 Flammagenitus, Build 201903151138-exported (Linux-x86_64)) 2019/06/17 18:59:24 open /tmp/f519a2e5-ca66-448e-a22e-7b2184e63fa0/interact.prot.xml: no such file or directory Process 'ProteinProphet' finished, exit code: 1
prvst
commented
5 years ago Then I'm sorry to say that I'm out of ideas on how to proceed with your issue. The message is actually coming from ProteinProphet, I advise you to contact the main developers directly via their mailing list
Describe the problem
I'm submitting a:
My MSFragger use case:
put your general problem description here I am running mzXML files (from converted Bruker .d folder output by timstof run) using FragPipe on linux. MSFragger runs fine, but I have problem with some of the downstream software. In this case it is the ProteinProphet, that is stopping with an error. I attached the log from FragPipe.
System info
You can find that printed on the Config tab.
Describe your experiment
Genral proteomics experiment description
Human wcl
...
Input data files
e.g. "fractionated HeLa, 5 samples, 3 bio replicates, 2 technical replicates" or "ten 3 hour LC gradients, full cell lysate, fruit fly" or or at least "5 mzml files 1.5Gb each"
Sequence database
Uniprot
Attach fragger.params file
You can find it in the output directory you specified for analysis.
Run log output