search

MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
Other
73 stars 36 forks source link

MS-GF+ search in SearchGUI failed #77

Open AnkeTraut opened 4 years ago

AnkeTraut commented 4 years ago

Hello everybody,

I started working with SearchGUI some weeks before. Now I want to use a huge database (82 million entries) for a new project. For the first search I chose only X!Tandem and MS-GF+. After some hours I got first outputs from SearchGUI but only for X!Tandem. Here you can find output of the report: ... Search progress: 30 / 30 tasks, 100,00% 1,12 hours elapsed Writing results... java.lang.NullPointerException at edu.ucsd.msjava.mzid.MZIdentMLGen.getDBSequence(MZIdentMLGen.java:671) at edu.ucsd.msjava.mzid.MZIdentMLGen.getPeptideEvidenceList(MZIdentMLGen.java:629) at edu.ucsd.msjava.mzid.MZIdentMLGen.addSpectrumIdentificationResults(MZIdentMLGen.java:347) at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:391) at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:105) at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:56)

Fri Sep 20 13:54:59 CEST 2019 MS-GF+ finished for E:\180320_A_01.mgf (2 hours 7248.0 seconds).

Fri Sep 20 13:55:20 CEST 2019 Could not find MS-GF+ result file for 180320_A_01.mgf. ...

the developer of SearchGUI recommend to contact you directly. Have you any idea what happened? Is my database to big? Or are any other problems possible?

Thanks for helping Best regards, Anke

FarmGeek4Life commented 4 years ago

Please see issues #13 and #43. The most likely problem is that your database is too big.

alchemistmatt commented 4 years ago

FASTA files over ~250 MB in size will need to be split into separate chunks. You then will search your instrument data against each of the chunks. Following this, you can use MzidMerger to combine the .mzid files created by the searches

If your FASTA file is less than 250 MB, I would guess that MS-GF+ has not been allocated enough memory. Use the -Xmx switch when calling Java, as described at https://msgfplus.github.io/msgfplus/MSGFPlus.html For example, this reserves 12 GB of memory

java -Xmx12000M  -jar MSGFPlus.jar

Does the MS-GF+ search GUI allow you to specify the amount of memory to use?