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ylab-hi / ScanExitron

A computational workflow for exitron splicing identification
MIT License
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Detailed workflow of cptac.py in the application folder #7

Closed ptnaimelmm closed 7 months ago

ptnaimelmm commented 3 years ago

Hi there,

Could you please provide a detailed workflow for cptac.py identifying exitron-derived polypeptides? Thanks in advance.

ptnaimelmm commented 3 years ago

Hi, IDMerger could not be found when running cptac.py. Besides, I wonder where .exitron file was used in cptac.py. Thanks.

dolittle007 commented 3 years ago

IDMerger is part of OpenMS(https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IDMerger.html). Another command such as MSGFPlusAdapter is also part of OpenMS. If you have installed OpenMS successfully, you will see them.

ptnaimelmm commented 3 years ago

Thanks. Unfortunately, I failed to build OpenMS in my system.

ptnaimelmm commented 3 years ago

Hi, I successfully installed OpenMS in my system. However, I got an error as attached. What do you think the problem is and can you give me any suggestions? Thanks. cptac_error

dolittle007 commented 3 years ago

The error message clearly showed that the error happened at 'MSGFPlusAdapter'. the parameter file version did not match. The database contains letter of 'U', which does not correspond to an amino acid. You may need to read the error message carefully and locate the problem.

ptnaimelmm commented 3 years ago

Hi Carlos,

Thanks for your reply. Actually, I noticed it and removed Us in the database sequence, but I still got the error message on java invocation as follows. @./Scanexitron_env) @.@compute0194 exitron_NeurolinC]$ ~/Scanexitron_env/bin/MSGFPlusAdapter -ini ~/privatemodules/ScanExitron/Applications/config/config.ini -in Masspec/testTof/Tutorial_TOFCalibration_raw.mzML -out Testtof.idXML -database hspro.fasta -executable ~/Scanexitron_env/share/msgf_plus-2017.07.21-1/MSGFPlus.jar -java_memory 20000 -threads 16 Warning: Parameters file version (2.4.0-HEAD-2018-10-26) does not match the version of this tool (2.5.0-HEAD-HASH-NOTFOUND-HEAD-HASH-NOTFOUND). Your current parameters are still valid, but there might be new valid values or even new parameters. Upgrading the INI might be useful. Running MSGFPlus search... Executing: @./Scanexitron_env/bin/java FATAL ERROR: External invocation of /home-3/ @./Scanexitron_env/bin/java failed. Standard output and error were: Standard output: MS-GF+ Release (v2017.07.21) (21 July 2017) Loading database files... Creating the suffix array indexed file... Size: 45394295 AlphabetSize: 28 Suffix creation: 0.00% complete. Suffix creation: 22.03% complete. Suffix creation: 44.06% complete. Suffix creation: 66.09% complete. Suffix creation: 88.12% complete. Sorting 0.00% complete. Sorting 5.81% complete. Sorting 11.62% complete. Sorting 17.43% complete. Sorting 23.24% complete. Sorting 29.05% complete. Sorting 34.86% complete. Sorting 40.67% complete. Sorting 46.48% complete. Sorting 52.29% complete. Sorting 58.10% complete. Sorting 63.91% complete. Sorting 69.73% complete. Sorting 75.54% complete. Sorting 81.35% complete. Sorting 87.16% complete. Sorting 92.97% complete. Sorting 98.78% complete. Loading database finished (elapsed time: 42.02 sec) Reading spectra...

Standard error: Exception in thread "main" java.lang.ExceptionInInitializerError at uk.ac.ebi.jmzml.xml.Constants.(Constants.java:56) at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory$MzMlIndexerImpl.(MzMLIndexerFactory.java:82) at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory$MzMlIndexerImpl.(MzMLIndexerFactory.java:52) at uk.ac.ebi.jmzml.xml.xxindex.MzMLIndexerFactory.buildIndex(MzMLIndexerFactory.java:49) at uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller.(MzMLUnmarshaller.java:121) at uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller.(MzMLUnmarshaller.java:100) at edu.ucsd.msjava.mzml.MzMLAdapter.(MzMLAdapter.java:27) at edu.ucsd.msjava.msutil.SpectraAccessor.getSpecMap(SpectraAccessor.java:38) at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:217) at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:105) at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:56) Caused by: javax.xml.bind.DataBindingException: javax.xml.bind.JAXBException

Exit code: 1

On Sat, Oct 30, 2021 at 2:58 PM Carlos D. Wang @.***> wrote:

The error message clearly showed that the error happened at 'MSGFPlusAdapter'. the parameter file version did not match. The database contains letter of 'U', which does not correspond to an amino acid. You may need to read the error message carefully and locate the problem.

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dolittle007 commented 2 years ago

There is something wrong with the JAVA you installed. (https://mkyong.com/java/java-lang-classnotfoundexception-com-sun-xml-bind-v2-contextfactory/) You may need to install an older version of JAVA. (Maybe Java 8)

ptnaimelmm commented 2 years ago

I tried Java8 previously, but got quite similar error notes. Maybe I can try other versions of JAVA. Thanks.

dolittle007 commented 2 years ago

Dealing with software dependency is a daunting task. You can use anaconda (https://www.anaconda.com/) to install all OpenMS and java. To make it work, you may need to create a new Conda environment, then install all the necessary packages, including msgf_plus, openms.

Hope it helps.