OSX 10.11.5 TOPPAS V2.0.0(66a7739)OPenMS TOPPAS無法找到的Java
我是新來OpenMS和TOPPAS。我正在嘗試執行DeMIX TOPPAS工作流程: https://github.com/userbz/DeMix
我相信我的一切都正確配置。我已根據自述更改了.toppas文件,包括更改所有路徑。
該工作流使用「MSGFPlus.jar」,該文件在工作流程(.toppas)中顯示爲正確的路徑。然而,當我運行的工作流程,我得到的錯誤...
Fatal error: Java not found. Java is needed to run MS-GF+. Make sure that it can be executed by calling 'java', e.g. add the directory containing the Java binary to your PATH variable."
我相信TOPP運行我的本地用戶,但它似乎沒有,如果我作爲本地用戶或root身份運行到重要。這個錯誤表明我檢查了java是否在我的路徑中,這似乎是本地用戶和root用戶的。
Mikes-MacBook-Pro:~ mikes$ java -version
java version "1.8.0_74"
Java(TM) SE Runtime Environment (build 1.8.0_74-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.74-b02, mixed mode)
Mikes-MacBook-Pro:~ mikes$
Mikes-MacBook-Pro:~ mikes$ sudo bash
Password:
bash-3.2# java -version
java version "1.8.0_74"
Java(TM) SE Runtime Environment (build 1.8.0_74-b02)
Java HotSpot(TM) 64-Bit Server VM (build 25.74-b02, mixed mode)
bash-3.2#
編輯: 我曾嘗試使用 '打開' 命令行打開TOPPAS.app,並增加 '的/ usr/bin中/ JAVA' 到Info.plist中...的建議here,但我仍然會得到相同的錯誤。
編輯: 有問題的.jar文件並運行在命令行OK ......
Mikes-MacBook-Pro:MSGFPlus mikes$ java -jar ./MSGFPlus.jar -s /Users/.../DeMix-master/Example/20131106_Q2_SDC_120MIN_HELA1.mzML -d /Users/.../2016-21-07_uniprot_sprot.fasta
MS-GF+ Beta (v10089) (7/16/2014)
Loading database files...
Creating the suffix array indexed file... Size: 197666693
AlphabetSize: 28
Suffix creation: 0.00% complete.
Suffix creation: 5.06% complete.
(snip)
Sorting 0.00% complete.
Sorting 5.81% complete.
(snip)
Sorting 98.78% complete.
Loading database finished (elapsed time: 207.38 sec)
Reading spectra...
Ignoring spectrum controllerType=0 controllerNumber=1 scan=20845: spectrum is not centroided.
(snip)
Ignoring spectrum controllerType=0 controllerNumber=1 scan=21339: spectrum is not centroided.
Ignoring 421 profile spectra.
Ignoring 0 spectra having less than 10 peaks.