Microsoft Windows [版本 10.0.17763.1817]
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C:\Users\Nano>d:
D:\>cd D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea
D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea>java -Xmx12G -jar gsea-3.0.jar
2786 [INFO ] Made Vdb dir: C:\Users\Nano\gsea_home\output\mar26
3582 [INFO ] Your current version of GSEA is 3.0. A newer version (4.1.0) is available.
To update, please download from http://gsea-msigdb.org/gsea/downloads.jsp
(build date: Thu, 30 Jul 2020 16:30:40 -0400)
3582 [INFO ] Note: GenePattern users should update through GenePattern.
2801 [INFO ] Begun importing: Template from: ls.cls
4030 [INFO ] Loaded file: D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea\ls.cls
4035 [INFO ] Loading ... 1 files
ls.cls
Files loaded successfully: 1 / 1
There were NO errors
2634 [INFO ] <html><body><b>This will remove recently used files from this list (but NOT delete the files themselves)</b></body></html>
8786 [INFO ] Loaded file: D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea\ls.cls
8795 [INFO ] Loading ... 1 files
ls.cls
Files loaded successfully: 1 / 1
There were NO errors
7482 [INFO ] Begun importing: Dataset from: ls.gct
74780 [ERROR] There were errors: ERROR(S) #:1
Parsing trouble
edu.mit.broad.genome.parsers.ParserException: Bad gct format -- expected ncols from specification on header line: 9734 but found in data: 9733
at edu.mit.broad.genome.parsers.GctParser._parse(GctParser.java:146)
at edu.mit.broad.genome.parsers.GctParser.parse(GctParser.java:118)
at edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:160)
at edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:130)
at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:747)
at edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:726)
at edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:52)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
at edu.mit.broad.xbench.core.api.AbstractWindowManager.showError(AbstractWindowManager.java:67)
7951 [INFO ] <html><body><b>This will remove recently used files from this list (but NOT delete the files themselves)</b></body></html>
5183 [INFO ] Loaded file: D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea\ls.cls
5185 [INFO ] Loading ... 1 files
ls.cls
Files loaded successfully: 1 / 1
There were NO errors
7694 [INFO ] Begun importing: Dataset from: ls.gct
0855 [INFO ] Begun importing: GeneSetMatrix from: h.all.v7.3.symbols.gmt
1215 [INFO ] Loaded file: D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea\h.all.v7.3.symbols.gmt
1216 [INFO ] Loading ... 1 files
h.all.v7.3.symbols.gmt
Files loaded successfully: 1 / 1
There were NO errors
8553 [INFO ] <html><body><b>This will remove recently used files from this list (but NOT delete the files themselves)</b></body></html>
6556 [INFO ] Begun importing: Dataset from: ls.gct
9799 [INFO ] Loaded file: D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea\ls.gct
9804 [INFO ] Loading ... 1 files
ls.gct
Files loaded successfully: 1 / 1
There were NO errors
6450 [INFO ] Loaded file: D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea\ls.cls
6451 [INFO ] Loading ... 1 files
ls.cls
Files loaded successfully: 1 / 1
There were NO errors
4628 [INFO ] Loaded file: D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea\h.all.v7.3.symbols.gmt
4633 [INFO ] Loading ... 1 files
h.all.v7.3.symbols.gmt
Files loaded successfully: 1 / 1
There were NO errors
8262 [INFO ] Loaded file: D:\桌面文件20210105\X-Human\Stimulated vs Control PBMCs20201221-X-human-1-99-0.3-3\gsea\ls.gct
8262 [INFO ] Loading ... 1 files
ls.gct
Files loaded successfully: 1 / 1
There were NO errors
6195 [INFO ] There were duplicate row identifiers in the specified dataset. One id was arbitarilly choosen. Details are below
Generally, this is OK, but if you want to avoid this automagic, edit your dataset so that all row ids are unique
# of row ids in original dataset: 18257
# of row UNIQUE ids in original dataset: 18255
# The duplicates were
1-Mar
2-Mar
3184 [INFO ] No dataset collapsing was done .. using original as is
3186 [INFO ] Got gsets: 50 now preprocessing them ... min: 15 max: 500
3201 [INFO ] Done preproc for smaller than: 15
3433 [INFO ] Extracting ds: ls.ls by template: ls.cls#LPBS_versus_LGd
4598 [INFO ] Timestamp used as random seed: 1616689393429
0139 [INFO ] Extracting ds: ls.ls by template: ls.cls#LPBS_versus_LGd
0263 [INFO ] File download started. Retrieving GENE_SYMBOL.chip from remote server...
7405 [INFO ] Download complete
8126 [INFO ] Begun importing: Chip from: ftp://gseaftp.broadinstitute.org/pub/gsea/annotations/GENE_SYMBOL.chip
8286 [INFO ] Parsed from unigene / gene symbol: 38870
5150 [INFO ] Made Vdb dir: C:\Users\Nano\gsea_home\reports_cache_April4_2006_build
4029 [INFO ] There were duplicate row identifiers in the specified dataset. One id was arbitarilly choosen. Details are below
Generally, this is OK, but if you want to avoid this automagic, edit your dataset so that all row ids are unique
# of row ids in original dataset: 18257
# of row UNIQUE ids in original dataset: 18255
# The duplicates were
1-Mar
2-Mar
0962 [INFO ] No dataset collapsing was done .. using original as is
0962 [INFO ] Got gsets: 50 now preprocessing them ... min: 15 max: 500
0969 [INFO ] Done preproc for smaller than: 15
1188 [INFO ] Extracting ds: ls.ls by template: ls.cls#LPBS_versus_LGd
1972 [INFO ] Timestamp used as random seed: 1616717571187
image.png
There were duplicate row identifiers in the specified dataset. One id was arbitarilly choosen. Details are below
Generally, this is OK, but if you want to avoid this automagic, edit your dataset so that all row ids are unique
of row ids in original dataset: 18257
of row UNIQUE ids in original dataset: 18255
The duplicates were
1-Mar
2-Mar
指定的数据集中有重复的行标识符。 一个id被任意选择。 详细信息如下
通常，这是可以的，但是如果您想避免这种自动操作，请编辑数据集，以使所有行ID都是唯一的
gene名有重复，
有几个被改成了月份
原始数据集中的行ID数：18257
原始数据集中的行唯一ID的数量：18255
＃重复的是
1月1日
3月2日
0962 [INFO ] No dataset collapsing was done .. using original as is
0962 [INFO ] Got gsets: 50 now preprocessing them ... min: 15 max: 500
0969 [INFO ] Done preproc for smaller than: 15
1188 [INFO ] Extracting ds: ls.ls by template: ls.cls#LPBS_versus_LGd
1972 [INFO ] Timestamp used as random seed: 1616717571187
0962 [INFO]未按原样使用原始数据进行数据折叠
0962 [信息]得到了gsets：现在对其进行预处理... 50：最小值：15最大值：500
0969 [INFO]完成小于以下的过程：15
1188 [信息]通过模板ls.cls＃LPBS_versus_LGd提取ds：ls.ls
1972 [INFO]时间戳用作随机种子：1616717571187
结束重做了
