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Issue tracker for the beta release of PeptideShaker 2.0
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Problems running Comet and Andromeda in 4.0.0 beta on Linux server #50

Closed ohickl closed 4 years ago

ohickl commented 4 years ago

Hi, I'm having trouble running Comet and Andromeda on a Linux server. I am using the following command:

java -cp engines/SearchGUI-4.0.0-beta/SearchGUI-4.0.0-beta.jar eu.isas.searchgui.cmd.SearchCLI \
    -spectrum_files data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.mgf \
    -fasta_file databases/Mock_Comm_RefDB_V3_sg_fix_rev.fasta \
    -output_folder engine_test/searchgui \
    -id_params engines/SearchGUI-4.0.0-beta/configs/mock_test.par \
    -xtandem 0 \
    -msgf 0 \
    -comet 1 \
    -andromeda 1 \
    -threads 1 \
    -output_data 1 \
    -output_date 1 \
    -temp_folder engine_test/searchgui/tmp \
    -comet_temp engine_test/searchgui/tmp/comet \
    -andromeda_temp engine_test/searchgui/tmp/andromeda \
    -log engine_test/searchgui

Using either Comet or Andromea will give me different errors while e.g. X!Tandem and MS-GF+ run fine.

Comet outputs the following when I use the default tmp folder path:

Path configuration completed.
Wed Feb 12 16:11:59 CET 2020 Validating MGF file: /mnt/lscratch/users/ohickl/proteomics/data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.mgf

Wed Feb 12 16:12:01 CET 2020 Indexing spectrum files.
Wed Feb 12 16:12:01 CET 2020 Extracting search settings.

Processing: 2D_10pH_G1_2_pH8.mgf (1/1)

comet command: 
/mnt/lscratch/users/ohickl/proteomics/engines/SearchGUI-4.0.0-beta/resources/Comet/linux/comet.exe /mnt/lscratch/users/ohickl/proteomics/data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.mgf 

Wed Feb 12 16:12:01 CET 2020 Processing 2D_10pH_G1_2_pH8.mgf with Comet.

 Error - cannot read database file "databases/Mock_Comm_RefDB_V3_sg_fix_rev.fasta". 
 Check that the file exists and is readable. 

Wed Feb 12 16:12:01 CET 2020 Comet finished for 2D_10pH_G1_2_pH8.mgf (23.0 milliseconds).

Wed Feb 12 16:12:01 CET 2020 Error: Source 'data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.comet.pep.xml' does not exist
Wed Feb 12 16:12:01 CET 2020 An error occurred while running SearchGUI. Please contact the developers.
Wed Feb 12 16:12:01 CET 2020 The search or processing did not finish properly!

With log entry:

Wed Feb 12 16:11:59 CET 2020: SearchGUI version 4.0.0-beta.
Memory given to the Java virtual machine: 31136546816.
Total amount of memory in the Java virtual machine: 2041446400.
Free memory: 2018920328.
Java version: 1.8.0_162.
java.io.FileNotFoundException: Source 'data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.comet.pep.xml' does not exist
        at org.apache.commons.io.FileUtils.moveFile(FileUtils.java:1805)
        at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2157)
        at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at javax.swing.SwingWorker.run(SwingWorker.java:334)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)

With custom temp and comet_temp folder I get:

Path configuration completed.
Wed Feb 12 16:15:20 CET 2020 Validating MGF file: /mnt/lscratch/users/ohickl/proteomics/data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.mgf

Wed Feb 12 16:15:22 CET 2020 Indexing spectrum files.
Wed Feb 12 16:15:22 CET 2020 Extracting search settings.

Processing: 2D_10pH_G1_2_pH8.mgf (1/1)

comet command: 
/mnt/lscratch/users/ohickl/proteomics/engines/SearchGUI-4.0.0-beta/resources/Comet/linux/comet.exe -Pengine_test/searchgui/tmp/comet/comet.params /mnt/lscratch/users/ohickl/proteomics/data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.mgf 

Wed Feb 12 16:15:22 CET 2020 Processing 2D_10pH_G1_2_pH8.mgf with Comet.

 Comet version 2019.01 rev. 3 
 Error - cannot open parameter file "engine_test/searchgui/tmp/comet/comet.params". 

Wed Feb 12 16:15:22 CET 2020 Comet finished for 2D_10pH_G1_2_pH8.mgf (41.0 milliseconds).

Wed Feb 12 16:15:22 CET 2020 Error: Source 'data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.comet.pep.xml' does not exist
Wed Feb 12 16:15:22 CET 2020 An error occurred while running SearchGUI. Please contact the developers.
Wed Feb 12 16:15:22 CET 2020 The search or processing did not finish properly!

With log entry:

Wed Feb 12 16:15:20 CET 2020: SearchGUI version 4.0.0-beta.
Memory given to the Java virtual machine: 31136546816.
Total amount of memory in the Java virtual machine: 2041446400.
Free memory: 2018920328.
Java version: 1.8.0_162.
java.io.FileNotFoundException: Source 'data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.comet.pep.xml' does not exist
        at org.apache.commons.io.FileUtils.moveFile(FileUtils.java:1805)
        at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2157)
        at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at javax.swing.SwingWorker.run(SwingWorker.java:334)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)

Andromeda outputs the following when I use the default tmp folder path:

Path configuration completed.
Wed Feb 12 16:19:22 CET 2020 Validating MGF file: /mnt/lscratch/users/ohickl/proteomics/data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.mgf
Wed Feb 12 16:19:24 CET 2020 Andromeda configuration.

Wed Feb 12 16:19:24 CET 2020 Error: null
Wed Feb 12 16:19:24 CET 2020 An error occurred while running SearchGUI. Please contact the developers.
Wed Feb 12 16:19:24 CET 2020 The search or processing did not finish properly!

With log entry:

Wed Feb 12 16:19:21 CET 2020: SearchGUI version 4.0.0-beta.
Memory given to the Java virtual machine: 31136546816.
Total amount of memory in the Java virtual machine: 2041446400.
Free memory: 2018920328.
Java version: 1.8.0_162.
java.lang.NullPointerException
        at eu.isas.searchgui.processbuilders.AndromedaProcessBuilder.getTempFolderPath(AndromedaProcessBuilder.java:174)
        at eu.isas.searchgui.processbuilders.AndromedaProcessBuilder.createGenericFastaFile(AndromedaProcessBuilder.java:210)
        at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:1854)
        at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at javax.swing.SwingWorker.run(SwingWorker.java:334)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)

With custom temp and andromeda_temp folder I get:

Path configuration completed.
Wed Feb 12 16:20:56 CET 2020 Validating MGF file: /mnt/lscratch/users/ohickl/proteomics/data/Project_PXD008017_mock_community/mgf/2D_10pH_G1_2_pH8.mgf
Wed Feb 12 16:20:58 CET 2020 Andromeda configuration.

Wed Feb 12 16:20:58 CET 2020 Error: conf/databases.xml (No such file or directory)
Wed Feb 12 16:20:58 CET 2020 An error occurred while running SearchGUI. Please contact the developers.
Wed Feb 12 16:20:58 CET 2020 The search or processing did not finish properly!

With log entry:

Wed Feb 12 16:20:55 CET 2020: SearchGUI version 4.0.0-beta.
Memory given to the Java virtual machine: 31136546816.
Total amount of memory in the Java virtual machine: 2041446400.
Free memory: 2018920328.
Java version: 1.8.0_162.
java.io.FileNotFoundException: conf/databases.xml (No such file or directory)
        at java.io.FileOutputStream.open0(Native Method)
        at java.io.FileOutputStream.open(FileOutputStream.java:270)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
        at java.io.FileOutputStream.<init>(FileOutputStream.java:162)
        at java.io.FileWriter.<init>(FileWriter.java:90)
        at eu.isas.searchgui.processbuilders.AndromedaProcessBuilder.createDatabaseFile(AndromedaProcessBuilder.java:237)
        at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:1856)
        at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at javax.swing.SwingWorker.run(SwingWorker.java:334)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)

Could this be a bug or might it be an error in my application of the tool? I can provide you with the .par file as well (which I created using the IdentificationParametersCLI tool), if needed.

Best

Oskar

hbarsnes commented 4 years ago

Hi Oskar,

All of the issues above should hopefully be solved by using complete paths instead of relative paths in the command line.

Best regards, Harald

hbarsnes commented 4 years ago

Hi again,

One correction. The Andromeda issues will not be solved by using complete paths, as Andromeda is only supported on Windows. :)

A version for Linux was in development, but I do not know what the status is. But we will of course update the Andromeda version in SearchGUI when/if a new version becomes available.

Best regards, Harald

ohickl commented 4 years ago

Hi Harald, using absolute paths seems to work, thanks! Regarding Andromeda, didnt they release the mono version of MaxQuant some time ago? Or does that not mean that Andromeda will now also work on Linux as a standalone?

hbarsnes commented 4 years ago

Regarding Andromeda, didnt they release the mono version of MaxQuant some time ago? Or does that not mean that Andromeda will now also work on Linux as a standalone?

They did. But the standalone version of Andromeda was never officially released as far as I know. We had access to a beta version a while back, but it had some unresolved bugs. We'll contact them again to check the status.