search

Nesvilab / philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
https://philosopher.nesvilab.org
GNU General Public License v3.0
111 stars 19 forks source link

Fatal Error: workspace not found. #23

Closed ot0tot closed 6 years ago

ot0tot commented 6 years ago

Describe the problem

Fatal Error: workspace not found. Run 'philosopher workspace --init' to create one or execute the command inside a workspace directory" Using the MSFragger/FragPipe issue reporting template as I'm getting the error while running MSFragger-GUI, but I get the same error when I run philosopher from the command line. Tested on both an Ubuntu and Windows machine with the same error. Running philosopher workspace --init immediately followed by $> /home/xxx/xxx/philosopher_linux_amd64 filter --sequential --mapmods --tag rev_ --pepxml /home/xxx/xxx/run1/result --protxml /home/xxx/xxx/run1/result/interact.prot.xml in the working directory results in the same error. Some information redacted with "xxx".

System info

You can find that printed on the Config tab.

Describe your experiment

Genral proteomics experiment description

Rabbit polyclonal antibodies digested with trypsin

Input data files

1 mzML file ~150 Mb in size

Sequence database

Custom rabbit V region sequence database and decoys
3 Mb

Run log output

System info:
System OS: Linux, Architecture: amd64
Java Info: 10.0.1, Java HotSpot(TM) 64-Bit Server VM, "Oracle Corporation"

Version info:
MSFragger-GUI version 6.0
MSFragger version 20180223-RC1
Philosopher version Philosopher 20180530

Will execute 9 commands:
java -jar /home/xxx/xxx/msfragger-20180223-RC1.one-jar.jar /home/xxx/xxx/run1/result/fragger.params /home/xxx/xxx/run1/QExxxxx-LUMOS.mzML 

java -cp /home/xxx/xxx/run1/MSFragger-GUI.jar umich.msfragger.util.FileMove /home/xxx/xxx/run1/QExxxxx-LUMOS.pepXML /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 

/home/xxx/xxx/philosopher_linux_amd64 workspace --clean 

/home/xxx/xxx/philosopher_linux_amd64 workspace --init 

/home/xxx/xxx/philosopher_linux_amd64 peptideprophet --decoy rev_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database /home/xxx/xxx/run1/AVH.fas /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 

/home/xxx/xxx/philosopher_linux_amd64 proteinprophet --output interact --maxppmdiff 20 interact-QExxxxx-LUMOS.pep.xml 

/home/xxx/xxx/philosopher_linux_amd64 database --annotate /home/xxx/xxx/run1/AVH.fas --prefix rev_ 

/home/xxx/xxx/philosopher_linux_amd64 filter --sequential --mapmods --tag rev_ --pepxml /home/xxx/xxx/run1/result --protxml /home/xxx/xxx/run1/result/interact.prot.xml 

/home/xxx/xxx/philosopher_linux_amd64 report 

~~~~~~~~~~~~~~~~~~~~~~

Executing command:
$> java -jar /home/xxx/xxx/msfragger-20180223-RC1.one-jar.jar /home/xxx/xxx/run1/result/fragger.params /home/xxx/xxx/run1/QExxxxx-LUMOS.mzML 
Process started
MSFragger version MSFragger-20180223
(c) University of Michigan

System OS: Linux, Architecture: amd64
Java Info: 10.0.1, Java HotSpot(TM) 64-Bit Server VM, "Oracle Corporation"
JVM started with 4004MB memory

Peptide index read in 153ms
Selected fragment tolerance 0.02 Da and maximum fragment slice size of 2382.75MB
14511148 fragments to be searched in 1 slices (0.11GB total)
Operating on slice 1 of 1: 
986ms
    QExxxxx-LUMOS.mzML 
3556ms

    QExxxxx-LUMOS.mzML 3556ms [progress: 15040/21404 (70.27%) - 2991.84 spectra/s]

    QExxxxx-LUMOS.mzML 3556ms [progress: 21404/21404 (100.00%) - 1766.31 spectra/s] - completed 8770ms

Process finished, exit value: 0
Executing command:
$> java -cp /home/xxx/xxx/run1/MSFragger-GUI.jar umich.msfragger.util.FileMove /home/xxx/xxx/run1/QExxxxx-LUMOS.pepXML /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 
Process started
Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 workspace --clean 
Process started
time="21:17:15" level=info msg="Executing Workspace 20180530"

time="21:17:16" level=info msg="Removing workspace"
time="21:17:16" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 workspace --init 
Process started
time="21:17:16" level=info msg="Executing Workspace 20180530"

time="21:17:16" level=info msg="Creating workspace"

time="21:17:16" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 peptideprophet --decoy rev_ --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --database /home/xxx/xxx/run1/AVH.fas /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML 
Process started
time="21:17:17" level=info msg="Executing PeptideProphet 20180530"

 file 1: /home/xxx/xxx/run1/result/QExxxxx-LUMOS.pepXML

 processed altogether 15148 results

INFO: Results written to file: /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.pep.xml

  - /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.pep.xml

  - Building Commentz-Walter keyword tree...

  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)

init with X! Tandem trypsin 

 PeptideProphet  (TPP v5.0.1 Post-Typhoon dev, Build 201705191541-exported (Linux-x86_64)) AKeller@ISB
 read in 0 1+, 3754 2+, 8425 3+, 2490 4+, 439 5+, 40 6+, and 0 7+ spectra.
Found 3767 Decoys, and 11381 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 (7+).

model complete after 26 iterations

time="21:17:51" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 proteinprophet --output interact --maxppmdiff 20 interact-QExxxxx-LUMOS.pep.xml 
Process started
time="21:17:51" level=info msg="Executing ProteinProphet 20180530"

ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v5.0.1 Post-Typhoon dev, Build 201705221614-exported (Linux-x86_64))
 (no FPKM) (using degen pep info)
Reading in /home/xxx/xxx/run1/result/interact-QExxxxx-LUMOS.pep.xml...

...read in 0 1+, 639 2+, 432 3+, 168 4+, 51 5+, 3 6+, 0 7+ spectra with min prob 0.05

Initializing 269 peptide weights: 0%...10%...20%...30%
...40%...50%...60%...70%...80%...90%
...100%
Calculating protein lengths and molecular weights from database /home/xxx/xxx/run1/AVH.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.........:.........:.........:.........:.......  Total: 38676

Computing degenerate peptides for 27778 proteins: 0%...10%
...20%...30%
...40%
...50%...60%...70%...80%...90%
...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%...60%...80%
...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%...60%
...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%
...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%
...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%
...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%

Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%...60%...80%
...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%...40%
...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 28138 proteins.  Loop 1: 0%...20%
...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%

Computing 485 protein groups: 0%...10%
...20%
...30%
...40%
...50%
...60%
...70%
...80%
...90%
...100%
Calculating sensitivity...
and error tables...

INFO: mu=1.1061e-05, db_size=3165618

Computing MU for 28138 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%

Finished

time="21:19:52" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 database --annotate /home/xxx/xxx/run1/AVH.fas --prefix rev_ 
Process started
time="21:19:52" level=info msg="Executing Database 20180530"
time="21:19:52" level=info msg="Processing database"

time="21:19:57" level=info msg=Done

Process finished, exit value: 0
Executing command:
$> /home/xxx/xxx/philosopher_linux_amd64 filter --sequential --mapmods --tag rev_ --pepxml /home/xxx/xxx/run1/result --protxml /home/xxx/xxx/run1/result/interact.prot.xml 
Process started
time="21:19:57" level=info msg="Executing Filter 20180530"
time="21:19:57" level=info msg="Processing peptide identification files"

time="21:20:09" level=info msg="1+ Charge profile" decoy=0 target=0
time="21:20:09" level=info msg="2+ Charge profile" decoy=520 target=1941
time="21:20:09" level=info msg="3+ Charge profile" decoy=1770 target=4831
time="21:20:09" level=info msg="4+ Charge profile" decoy=123 target=1741
time="21:20:09" level=info msg="5+ Charge profile" decoy=1 target=364
time="21:20:09" level=info msg="6+ Charge profile" decoy=0 target=24
time="21:20:09" level=info msg="Database search results" ions=1938 peptides=1708 psms=11315

time="21:20:09" level=info msg="Converged to 0.00 % FDR with 0 PSMs" decoy=0 threshold=10 total=0
time="21:20:09" level=info msg="Converged to 0.00 % FDR with 0 Peptides" decoy=0 threshold=10 total=0
time="21:20:09" level=info msg="Converged to 0.00 % FDR with 0 Ions" decoy=0 threshold=10 total=0

time="21:20:21" level=info msg="Protein inference results" decoy=152 target=333
time="21:20:21" level=info msg="Converged to 9.09 % FDR with 11 Proteins" decoy=1 threshold=0.9983 total=12
time="21:20:21" level=info msg="Applying sequential FDR estimation" ions=0 peptides=0 psms=0
time="21:20:21" level=info msg="Converged to 0.00 % FDR with 0 PSMs" decoy=0 threshold=10 total=0
time="21:20:21" level=info msg="Converged to 0.00 % FDR with 0 Peptides" decoy=0 threshold=10 total=0
time="21:20:21" level=info msg="Converged to 0.00 % FDR with 0 Ions" decoy=0 threshold=10 total=0

time="21:20:21" level=info msg="Post processing identifications"

time="21:20:21" level=info msg="Mapping modifications"

time="21:20:22" level=info msg="Processing modifications"
time="21:20:22" level=info msg="Processing Protein Inference"

time="21:20:22" level=info msg="Correcting PSM to Protein mappings"
time="21:20:22" level=info msg="Mapping Ion status to PSMs"
time="21:20:22" level=info msg="Calculating Spectral Counts"
time="21:20:22" level=fatal msg="workspace not found. Run 'philosopher workspace --init' to create one or execute the command inside a workspace directory"

Process finished, exit value: 1
Previous process returned exit code [1], cancelling further processing..
Cancelled execution of: 
/home/xxx/xxx/philosopher_linux_amd64 report 
=========================
===
===        Done
===
=========================
prvst commented 6 years ago

Dear @ot0tot

Please report errors with FragPipe on the program's repository: https://github.com/chhh/FragPipe

ot0tot commented 6 years ago

I didn't think the issue was with FragPipe since the issue is reproducible when running philosopher stand-alone from the command line.

prvst commented 6 years ago

Although FragPipe uses Philosopher for its processing, the program coordinates Philosopher a little bit different from what you would do it manually, thats why we make the issues separate.

When you say its reproducible, you mean you tried with FragPipe first and then later with Philosopher itself ? Did you moved or copied the folder ? Did you renamed any folder in its path ?