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compomics / compomics-utilities

Open source Java library for computational proteomics
http://compomics.github.io/projects/compomics-utilities.html
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Error accessing PeptideMapper #37

Closed CarlaCristinaUranga closed 3 years ago

CarlaCristinaUranga commented 4 years ago

Hi I am trying to install and use Peptide Mapper but get the following error:

wget http://genesis.ugent.be/maven2/com/compomics/utilities/4.10.0/utilities-4.10.0.zip --2020-05-13 13:27:20-- http://genesis.ugent.be/maven2/com/compomics/utilities/4.10.0/utilities-4.10.0.zip Resolving genesis.ugent.be... 157.193.160.40 Connecting to genesis.ugent.be|157.193.160.40|:80... connected. HTTP request sent, awaiting response... 404 Resource does not exist 2020-05-13 13:27:20 ERROR 404: Resource does not exist.

dominik-kopczynski commented 4 years ago

Hi Carla, thank you for your message. For utilities 4.10.0, there is no zip file, just the compiled jar file. However, I would recommend to you to use the most recent version of utilities, that is 4.12.16. You can choose between:

wget http://genesis.ugent.be/maven2/com/compomics/utilities/4.10.0/utilities-4.10.0.jar

or

wget http://genesis.ugent.be/maven2/com/compomics/utilities/4.12.16/utilities-4.12.16.zip

If you still have trouble to download utilities or later on issues with PeptideMapper, please don't hesitate to reopen the thread again.

Cheers, Dominik

CarlaCristinaUranga commented 4 years ago

Awesome, thank you! One question, can we only use Uniprot databases right now or can we adapt a custom database? If so is there a header syntax you might be able to provide?

Best wishes, Carla

On Wed, May 13, 2020 at 10:22 PM dominik-kopczynski < notifications@github.com> wrote:

Hi Carla, thank you for your message. For utilities 4.10.0, there is no zip file, just the compiled jar file. However, I would recommend to you to use the most recent version of utilities, that is 4.12.16. You can choose between:

wget http://genesis.ugent.be/maven2/com/compomics/utilities/4.10.0/utilities-4.10.0.jar

or

wget http://genesis.ugent.be/maven2/com/compomics/utilities/4.12.16/utilities-4.12.16.zip

Cheers, Dominik

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/37#issuecomment-628393839, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HC6WBKRMI6EOKQCHFRTRRN5X7ANCNFSM4M766USQ .

CarlaCristinaUranga commented 4 years ago

Sorry I saw that you also accept generic FASTA files. I have a FASTA file that works with PeptideShaker, but for some reason PeptideMapper reports an error, stating it cannot open the FASTA file.

Best, Carla

On Thu, May 14, 2020 at 8:19 AM Carla Uranga urangacarla@gmail.com wrote:

Awesome, thank you! One question, can we only use Uniprot databases right now or can we adapt a custom database? If so is there a header syntax you might be able to provide?

Best wishes, Carla

On Wed, May 13, 2020 at 10:22 PM dominik-kopczynski < notifications@github.com> wrote:

Hi Carla, thank you for your message. For utilities 4.10.0, there is no zip file, just the compiled jar file. However, I would recommend to you to use the most recent version of utilities, that is 4.12.16. You can choose between:

wget http://genesis.ugent.be/maven2/com/compomics/utilities/4.10.0/utilities-4.10.0.jar

or

wget http://genesis.ugent.be/maven2/com/compomics/utilities/4.12.16/utilities-4.12.16.zip

Cheers, Dominik

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/37#issuecomment-628393839, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HC6WBKRMI6EOKQCHFRTRRN5X7ANCNFSM4M766USQ .

dominik-kopczynski commented 4 years ago

Hi Carla, thank you for the report. Is it possible to get the exact error message? The best would even be, if I could get the actual fasta file you are trying to load. So I can quickly reproduce the error and try to fix it asap.

CarlaCristinaUranga commented 4 years ago

Hi Dominik thank you so much I have attached a sample of the fasta, since it is 1.1 GB it would be a problem to send over. The error I get is:

(base) [curanga@dell-17 utilities-4.12.16]$ Start reading FASTA file

Error: cound not open FASTA file

Here is my command line input:

java -cp utilities-4.12.16.jar com.compomics.util.experiment.identification.protein_inference.executable.PeptideMapping -p -InputFasta /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/proteomics/PeptideMapper/FINAL5.fasta -InputList /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/proteomics/PeptideMapper/RPP1_pep.txt -OutputResultList /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/proteomics/PeptideMapper/Out -UtilitiesParameterFile /local/ifs2_projdata/0780/projects/SMU_MUC/curanga/proteomics/SearchGUI-4.0.0-beta/saliva_final.par

RPP1_pep.log &

On Thu, May 14, 2020 at 10:31 AM dominik-kopczynski < notifications@github.com> wrote:

Hi Carla, thank you for the report. Is it possible to get the exact error message? The best would even be, if I could get the actual fasta file you are trying to load. So I can quickly reproduce the error and try to fix it asap.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/37#issuecomment-628780924, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HCZOIP2VVX3Y3TMMEODRRQTGBANCNFSM4M766USQ .

dominik-kopczynski commented 4 years ago

Hi Carla, thank you for the reply. The minimalist error messages that I implemented are not really helpful for bug tracking. Would it be fine for you when I open a cloud and you would upload the file? Plan b would be to split the file. Maybe the error occurs too, when load a fasta which only has the first 100 entries of your original fasta file. This would be way smaller. For the next version of PeptideMapper, I insert a proper logging and error messaging system ;-) Cheers

CarlaCristinaUranga commented 4 years ago

Yes that would be great! Whatever it takes to get this to work. I have no trouble sharing the complete fasta with you. How do I upload it? I will also try the g drive. Thank you so much!

Carla

On Thu, May 14, 2020, 9:58 PM dominik-kopczynski notifications@github.com wrote:

Hi Carla, thank you for the reply. The minimalist error messages that I implemented are not really helpful for bug tracking. Would it be fine for you when I open a cloud and you would upload the file? Plan b would be to split the file. Maybe the error occurs too, when load a fasta which only has the first 100 entries of your original fasta file. This would be way smaller. For the next version of PeptideMapper, I insert a proper logging and error messaging system ;-) Cheers

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/37#issuecomment-629026646, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HC3PDPFYV6MA6A5PZDLRRTDV5ANCNFSM4M766USQ .

dominik-kopczynski commented 4 years ago

Hey, send you a gmail with the cloud information.

dominik-kopczynski commented 4 years ago

Hi Carla, the good news: there is nothing wrong with your fasta file. I assume that Java ran out of memory during the computation of the index. When I increased the memory size on my computer, I could ran PeptideMapper without problems. Please try to increase Javas maximum memory with: java -Xmx16G [remaining command] When this is still not solving your problem, then please clone the compomics repository, switch to "new_backend" brach, install the 5.0 beta version and try PeptideMapper with all its changes:

git clone https://github.com/compomics/compomics-utilities cd compomics-utilities git checkout new_backend mvn install cd target/utilities-5.X.X-foo/ java -Xmx16G -cp utilities-5.X.X-foo.jar com.compomics.cli.peptide_mapper.PeptideMapperCLI -p PATH/TO/FASTA_FILE.fasta PATH/TO/PEPTIDE_LIST.csv OUTPUT.csv

Cheers, Dominik

CarlaCristinaUranga commented 4 years ago

Ok that is great. I am currently trying to install apache maven. I am having a little trouble setting the path variable, but once I get this going I will let you know. Thank you!

Best wishes, Carla

On Fri, May 15, 2020 at 2:39 AM dominik-kopczynski notifications@github.com wrote:

Hi Carla, the good news: there is nothing wrong with your fasta file. I assume that Java ran out of memory during the computation of the index. When I increased the memory size on my computer, I could ran PeptideMapper without problems. Please try to increase Javas maximum memory with: java -Xmx16G [remaining command] When this is still not solving your problem, then please clone the compomics repository, switch to "new_backend" brach, install the 5.0 beta version and try PeptideMapper with all its changes:

git clone https://github.com/compomics/compomics-utilities cd compomics-utilities git checkout new_backend mvn install cd target/utilities-5.X.X-foo/ java -Xmx16G -cp utilities-5.X.X-foo.jar com.compomics.cli.peptide_mapper.PeptideMapperCLI -p PATH/TO/FASTA_FILE.fasta PATH/TO/PEPTIDE_LIST.csv OUTPUT.csv

Cheers, Dominik

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/37#issuecomment-629138636, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HCYCJJGMFC5JM4UEEETRRUEWJANCNFSM4M766USQ .

CarlaCristinaUranga commented 4 years ago

Hi Dominik I was able to get maven working and ran maven install and got the following errors:

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 20:30 min

[INFO] Finished at: 2020-05-15T10:04:39-07:00

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:2.9.1:jar (attach-javadocs) on project utilities: MavenReportException: Error while creating archive:

[ERROR] Exit code: 1 - /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/CommandLineParser.java:73: error: attribute not supported in HTML5: name

[ERROR] This constructor requests the command-line*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:126: error: tag not supported in the generated HTML version: tt

[ERROR] The general contract of finalize is that it is invoked*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:132: error: tag not supported in the generated HTML version: tt

[ERROR] finalized. The finalize method may take any action, including*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:134: error: tag not supported in the generated HTML version: tt

[ERROR] of finalize, however, is to perform cleanup actions before*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:140: error: tag not supported in the generated HTML version: tt

[ERROR] The finalize method of class Object performs no*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:140: error: tag not supported in the generated HTML version: tt

[ERROR] The finalize method of class Object performs no*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:142: error: tag not supported in the generated HTML version: tt

[ERROR] Object may override this definition.*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:145: error: tag not supported in the generated HTML version: tt

[ERROR] invoke the finalize method for any given object. It is*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:151: error: tag not supported in the generated HTML version: tt

[ERROR] After the finalize method has been invoked for an object, no*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/general/FileLoggerImplementation.java:158: error: tag not supported in the generated HTML version: tt

[ERROR] The finalize method is never invoked more than once by a Java*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:329: error: tag not supported in the generated HTML version: tt

[ERROR] The general contract of finalize is that it is invoked*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:335: error: tag not supported in the generated HTML version: tt

[ERROR] finalized. The finalize method may take any action, including*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:337: error: tag not supported in the generated HTML version: tt

[ERROR] of finalize, however, is to perform cleanup actions before*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:343: error: tag not supported in the generated HTML version: tt

[ERROR] The finalize method of class Object performs no*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:343: error: tag not supported in the generated HTML version: tt

[ERROR] The finalize method of class Object performs no*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:345: error: tag not supported in the generated HTML version: tt

[ERROR] Object may override this definition.*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:348: error: tag not supported in the generated HTML version: tt

[ERROR] invoke the finalize method for any given object. It is*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:354: error: tag not supported in the generated HTML version: tt

[ERROR] After the finalize method has been invoked for an object, no*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/gui/JTableForDB.java:361: error: tag not supported in the generated HTML version: tt

[ERROR] The finalize method is never invoked more than once by a Java*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationImplementation.java:220: error: tag not supported in the generated HTML version: tt

[ERROR] an execution of a Java application, the hashCode method*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationImplementation.java:222: error: tag not supported in the generated HTML version: tt

[ERROR] used in equals comparisons on the object is modified.*

[ERROR] ^

[ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationImplementation.java:225: error: tag not supported in the generated HTML version: tt

[ERROR]

  • If two objects are equal according to the equals(Object)*

    [ERROR] ^

    [ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationImplementation.java:230: error: tag not supported in the generated HTML version: tt

    [ERROR] method, then calling the hashCode method on each of the*

    [ERROR] ^

    [ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationImplementation.java:237: error: tag not supported in the generated HTML version: tt

    [ERROR] class Object does return distinct integers for distinct*

    [ERROR] ^

    [ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationTemplate.java:223: error: tag not supported in the generated HTML version: tt

    [ERROR] an execution of a Java application, the hashCode method*

    [ERROR] ^

    [ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationTemplate.java:225: error: tag not supported in the generated HTML version: tt

    [ERROR] used in equals comparisons on the object is modified.*

    [ERROR] ^

    [ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationTemplate.java:228: error: tag not supported in the generated HTML version: tt

    [ERROR]

  • If two objects are equal according to the equals(Object)*

    [ERROR] ^

    [ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationTemplate.java:233: error: tag not supported in the generated HTML version: tt

    [ERROR] method, then calling the hashCode method on each of the*

    [ERROR] ^

    [ERROR] /Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/src/main/java/com/compomics/util/protein/ModificationTemplate.java:240: error: tag not supported in the generated HTML version: tt

    [ERROR] class Object does return distinct integers for distinct*

    [ERROR] ^

    [ERROR]

    [ERROR] Command line was: /Library/Java/JavaVirtualMachines/jdk-14.0.1.jdk/Contents/Home/bin/javadoc @options @packages

    [ERROR]

    [ERROR] Refer to the generated Javadoc files in '/Users/curanga/Desktop/compomics-utilities-master/compomics-utilities/docs/javadoc' dir.

    [ERROR]

    [ERROR] -> [Help 1]

    [ERROR]

    [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.

    [ERROR] Re-run Maven using the -X switch to enable full debug logging.

    [ERROR]

    [ERROR] For more information about the errors and possible solutions, please read the following articles:

    [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

    (base) curangalt-osx:compomics-utilities curanga$

    On Fri, May 15, 2020 at 2:39 AM dominik-kopczynski notifications@github.com wrote:

    Hi Carla, the good news: there is nothing wrong with your fasta file. I assume that Java ran out of memory during the computation of the index. When I increased the memory size on my computer, I could ran PeptideMapper without problems. Please try to increase Javas maximum memory with: java -Xmx16G [remaining command] When this is still not solving your problem, then please clone the compomics repository, switch to "new_backend" brach, install the 5.0 beta version and try PeptideMapper with all its changes:

    git clone https://github.com/compomics/compomics-utilities cd compomics-utilities git checkout new_backend mvn install cd target/utilities-5.X.X-foo/ java -Xmx16G -cp utilities-5.X.X-foo.jar com.compomics.cli.peptide_mapper.PeptideMapperCLI -p PATH/TO/FASTA_FILE.fasta PATH/TO/PEPTIDE_LIST.csv OUTPUT.csv

    Cheers, Dominik

    — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/37#issuecomment-629138636, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HCYCJJGMFC5JM4UEEETRRUEWJANCNFSM4M766USQ .

    • hbarsnes commented 4 years ago

    Hi Carla,

    I'm afraid that some of the JavaDoc for our old code is not compatible with the latest versions of Java. You therefore either need to downgrade your Java version or comment out the maven-javadoc-plugin section in the utilities pom file. The latter is probably the easiest. Just search for and comment out or remove the whole section labeled "Create javadoc on build".

    Best regards, Harald

    dominik-kopczynski commented 4 years ago

    Hi Carla, do I see it correctly that you are using Java 14?

    CarlaCristinaUranga commented 4 years ago

    Hi, yes I am using JDK 14. Harald's solution worked well for getting it to work with PeptideMapper. So PeptideMapper is working now. However, I see you developed MPA portable, which is specifically for metaproteomics, so I am trying to get this to work, with no success so far. I am also using SearchGUI/PeptideShaker. What would be the difference between MPA portable (I am using the CLI) and SearchGUI/Peptide Shaker?

    Best wishes, Carla

    On Sun, May 17, 2020 at 11:39 PM dominik-kopczynski < notifications@github.com> wrote:

    Hi Carla, do I see it correctly that you are using Java 14?

    — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/compomics-utilities/issues/37#issuecomment-629977435, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HCYZUIGMFJVPLRSLVETRSDJZRANCNFSM4M766USQ .

    mvaudel commented 4 years ago

    Hi,

    MPA is specifically designed for metaproteomics, the main conceptual difference is that it can aggregate results at the taxon level, while PeptideShaker only works at the peptide and protein group levels. There are also many differences in the architecture/algorithm/implementation that are required for the handling of metaproteomics results. If you want to learn more about these, feel free to contact the developers, they are much more knowledgeable than us on this :-)

    Hope it helps,

    Marc

    CarlaCristinaUranga commented 4 years ago

    Ok wonderful thank you. So can PeptideShaker handle a fasta file with 4.3 million sequences in it? I got it to work with a smaller database but now that I switched to a super database the program stops at unzipping the identification files and goes from "R" server status to Sl, and it doesn't proceed. About how long does the program take to move from Sl back to "R" status? Thanks.

    Best wishes, Carla

    On Mon, May 18, 2020 at 1:44 AM Marc Vaudel notifications@github.com wrote:

    Hi,

    MPA is specifically designed for metaproteomics, the main conceptual difference is that it can aggregate results at the taxon level, while PeptideShaker only works at the peptide and protein group levels. There are also many differences in the architecture/algorithm/implementation that are required for the handling of metaproteomics results. If you want to learn more about these, feel free to contact the developers, they are much more knowledgeable than us on this :-)

    Hope it helps,

    Marc

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    dominik-kopczynski commented 4 years ago

    Hi Carla, thank you for your message. We developed the indexing in PeptideShaker this way, that it should cope with big fasta files as long as the complete index fits into your memory. You said that you have 16G memory. Do you have the possibility to try PS on a bigger computer? What do you mean with "R" and "SI" status? Where do you see this information?

    Cheers, Dominik

    dominik-kopczynski commented 3 years ago

    After 6 months of inactivity, I am closing this thread. If you still have problems / issues, feel free to reactivate this thread or open a new issue.

    Cheers, Dominik