error loading the cls file
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Theo
Oct 2, 2023, 11:22:32 AM10/2/23
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Hi there could you please identify what I am doing wrong here. This is the produced error and I am also attaching the cls file. Thank you:
<Error Details>
---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.IllegalStateException: ...
---- Stack Trace ----
# of exceptions: 1
------Something obviously wrong items and classes mismatched:
Template id: edu.mit.broad.genome.objects.Id@366846 name: All_comparisons.cls
Number of classes: 12
Classes:
Class: C_HOM_10
Members: K_HOM_5[0,0],K_HOM_5[1,11],K_HOM_5[2,27],K_HOM_5[3,41],K_HOM_5[4,47]
Class: C_HOM_5
Members: K_WT_10[0,1],K_WT_10[1,2],K_WT_10[2,33],K_WT_10[3,42],K_WT_10[4,53]
Class: C_WT_10
Members: C_HOM_10[0,3],C_HOM_10[1,10],C_HOM_10[2,17],C_HOM_10[3,28],C_HOM_10[4,35]
Class: C_WT_5
Members: S_WT_10[0,4],S_WT_10[1,9],S_WT_10[2,30],S_WT_10[3,45],S_WT_10[4,54]
Class: K_HOM_10
Members: K_HOM_10[0,5],K_HOM_10[1,20],K_HOM_10[2,44],K_HOM_10[3,48],K_HOM_10[4,55]
Class: K_HOM_5
Members: K_WT_5[0,6],K_WT_5[1,24],K_WT_5[2,40],K_WT_5[3,50],K_WT_5[4,52]
Class: K_WT_10
Members: C_HOM_5[0,7],C_HOM_5[1,8],C_HOM_5[2,22],C_HOM_5[3,23],C_HOM_5[4,56]
Class: K_WT_5
Members: C_WT_5[0,12],C_WT_5[1,29],C_WT_5[2,31],C_WT_5[3,49],C_WT_5[4,51]
Class: S_HOM_10
Members: C_WT_10[0,13],C_WT_10[1,19],C_WT_10[2,39],C_WT_10[3,57],C_WT_10[4,58]
Class: S_HOM_5
Members: S_WT_5[0,14],S_WT_5[1,16],S_WT_5[2,21],S_WT_5[3,36],S_WT_5[4,43]
Class: S_WT_10
Members: S_HOM_10[0,15],S_HOM_10[1,25],S_HOM_10[2,37],S_HOM_10[3,38],S_HOM_10[4,46]
Class: S_WT_5
Members: S_HOM_5[0,18],S_HOM_5[1,26],S_HOM_5[2,32],S_HOM_5[3,34],S_HOM_5[4,59]
Template is continuous: false
Template is aux: false
Class of Interest (COI) is: C_HOM_10 Index: 0
Total # of items: 60
Output as string follows:
60 12 1
# K_HOM_5 K_WT_10 C_HOM_10 S_WT_10 K_HOM_10 K_WT_5 C_HOM_5 C_WT_5 C_WT_10 S_WT_5 S_HOM_10 S_HOM_5
K_HOM_5 K_WT_10 K_WT_10 C_HOM_10 S_WT_10 K_HOM_10 K_WT_5 C_HOM_5 C_HOM_5 S_WT_10 C_HOM_10 K_HOM_5 C_WT_5 C_WT_10 S_WT_5 S_HOM_10 S_WT_5 C_HOM_10 S_HOM_5 C_WT_10 K_HOM_10 S_WT_5 C_HOM_5 C_HOM_5 K_WT_5 S_HOM_10 S_HOM_5 K_HOM_5 C_HOM_10 C_WT_5 S_WT_10 C_WT_5 S_HOM_5 K_WT_10 S_HOM_5 C_HOM_10 S_WT_5 S_HOM_10 S_HOM_10 C_WT_10 K_WT_5 K_HOM_5 K_WT_10 S_WT_5 K_HOM_10 S_WT_10 S_HOM_10 K_HOM_5 K_HOM_10 C_WT_5 K_WT_5 C_WT_5 K_WT_5 K_WT_10 S_WT_10 K_HOM_10 C_HOM_5 C_WT_10 C_WT_10 S_HOM_5
------
java.lang.IllegalStateException: Something obviously wrong items and classes mismatched:
Template id: edu.mit.broad.genome.objects.Id@366846 name: All_comparisons.cls
Number of classes: 12
Classes:
Class: C_HOM_10
Members: K_HOM_5[0,0],K_HOM_5[1,11],K_HOM_5[2,27],K_HOM_5[3,41],K_HOM_5[4,47]
Class: C_HOM_5
Members: K_WT_10[0,1],K_WT_10[1,2],K_WT_10[2,33],K_WT_10[3,42],K_WT_10[4,53]
Class: C_WT_10
Members: C_HOM_10[0,3],C_HOM_10[1,10],C_HOM_10[2,17],C_HOM_10[3,28],C_HOM_10[4,35]
Class: C_WT_5
Members: S_WT_10[0,4],S_WT_10[1,9],S_WT_10[2,30],S_WT_10[3,45],S_WT_10[4,54]
Class: K_HOM_10
Members: K_HOM_10[0,5],K_HOM_10[1,20],K_HOM_10[2,44],K_HOM_10[3,48],K_HOM_10[4,55]
Class: K_HOM_5
Members: K_WT_5[0,6],K_WT_5[1,24],K_WT_5[2,40],K_WT_5[3,50],K_WT_5[4,52]
Class: K_WT_10
Members: C_HOM_5[0,7],C_HOM_5[1,8],C_HOM_5[2,22],C_HOM_5[3,23],C_HOM_5[4,56]
Class: K_WT_5
Members: C_WT_5[0,12],C_WT_5[1,29],C_WT_5[2,31],C_WT_5[3,49],C_WT_5[4,51]
Class: S_HOM_10
Members: C_WT_10[0,13],C_WT_10[1,19],C_WT_10[2,39],C_WT_10[3,57],C_WT_10[4,58]
Class: S_HOM_5
Members: S_WT_5[0,14],S_WT_5[1,16],S_WT_5[2,21],S_WT_5[3,36],S_WT_5[4,43]
Class: S_WT_10
Members: S_HOM_10[0,15],S_HOM_10[1,25],S_HOM_10[2,37],S_HOM_10[3,38],S_HOM_10[4,46]
Class: S_WT_5
Members: S_HOM_5[0,18],S_HOM_5[1,26],S_HOM_5[2,32],S_HOM_5[3,34],S_HOM_5[4,59]
Template is continuous: false
Template is aux: false
Class of Interest (COI) is: C_HOM_10 Index: 0
Total # of items: 60
Output as string follows:
60 12 1
# K_HOM_5 K_WT_10 C_HOM_10 S_WT_10 K_HOM_10 K_WT_5 C_HOM_5 C_WT_5 C_WT_10 S_WT_5 S_HOM_10 S_HOM_5
K_HOM_5 K_WT_10 K_WT_10 C_HOM_10 S_WT_10 K_HOM_10 K_WT_5 C_HOM_5 C_HOM_5 S_WT_10 C_HOM_10 K_HOM_5 C_WT_5 C_WT_10 S_WT_5 S_HOM_10 S_WT_5 C_HOM_10 S_HOM_5 C_WT_10 K_HOM_10 S_WT_5 C_HOM_5 C_HOM_5 K_WT_5 S_HOM_10 S_HOM_5 K_HOM_5 C_HOM_10 C_WT_5 S_WT_10 C_WT_5 S_HOM_5 K_WT_10 S_HOM_5 C_HOM_10 S_WT_5 S_HOM_10 S_HOM_10 C_WT_10 K_WT_5 K_HOM_5 K_WT_10 S_WT_5 K_HOM_10 S_WT_10 S_HOM_10 K_HOM_5 K_HOM_10 C_WT_5 K_WT_5 C_WT_5 K_WT_5 K_WT_10 S_WT_10 K_HOM_10 C_HOM_5 C_WT_10 C_WT_10 S_HOM_5
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.runChecksPost(TemplateImpl.java:354)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.assignItems2ClassInOrder(TemplateImpl.java:392)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate_ordered_assign(TemplateFactory.java:211)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate(TemplateFactory.java:104)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser._parse_genecluster_style_categorical(ClsParser.java:249)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser.parse(ClsParser.java:225)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory._readTemplates(ParserFactory.java:340)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:291)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:765)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:735)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
<Error Details>
---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
java.lang.IllegalStateException: ...
---- Stack Trace ----
# of exceptions: 1
------Something obviously wrong items and classes mismatched:
Template id: edu.mit.broad.genome.objects.Id@366846 name: All_comparisons.cls
Number of classes: 12
Classes:
Class: C_HOM_10
Members: K_HOM_5[0,0],K_HOM_5[1,11],K_HOM_5[2,27],K_HOM_5[3,41],K_HOM_5[4,47]
Class: C_HOM_5
Members: K_WT_10[0,1],K_WT_10[1,2],K_WT_10[2,33],K_WT_10[3,42],K_WT_10[4,53]
Class: C_WT_10
Members: C_HOM_10[0,3],C_HOM_10[1,10],C_HOM_10[2,17],C_HOM_10[3,28],C_HOM_10[4,35]
Class: C_WT_5
Members: S_WT_10[0,4],S_WT_10[1,9],S_WT_10[2,30],S_WT_10[3,45],S_WT_10[4,54]
Class: K_HOM_10
Members: K_HOM_10[0,5],K_HOM_10[1,20],K_HOM_10[2,44],K_HOM_10[3,48],K_HOM_10[4,55]
Class: K_HOM_5
Members: K_WT_5[0,6],K_WT_5[1,24],K_WT_5[2,40],K_WT_5[3,50],K_WT_5[4,52]
Class: K_WT_10
Members: C_HOM_5[0,7],C_HOM_5[1,8],C_HOM_5[2,22],C_HOM_5[3,23],C_HOM_5[4,56]
Class: K_WT_5
Members: C_WT_5[0,12],C_WT_5[1,29],C_WT_5[2,31],C_WT_5[3,49],C_WT_5[4,51]
Class: S_HOM_10
Members: C_WT_10[0,13],C_WT_10[1,19],C_WT_10[2,39],C_WT_10[3,57],C_WT_10[4,58]
Class: S_HOM_5
Members: S_WT_5[0,14],S_WT_5[1,16],S_WT_5[2,21],S_WT_5[3,36],S_WT_5[4,43]
Class: S_WT_10
Members: S_HOM_10[0,15],S_HOM_10[1,25],S_HOM_10[2,37],S_HOM_10[3,38],S_HOM_10[4,46]
Class: S_WT_5
Members: S_HOM_5[0,18],S_HOM_5[1,26],S_HOM_5[2,32],S_HOM_5[3,34],S_HOM_5[4,59]
Template is continuous: false
Template is aux: false
Class of Interest (COI) is: C_HOM_10 Index: 0
Total # of items: 60
Output as string follows:
60 12 1
# K_HOM_5 K_WT_10 C_HOM_10 S_WT_10 K_HOM_10 K_WT_5 C_HOM_5 C_WT_5 C_WT_10 S_WT_5 S_HOM_10 S_HOM_5
K_HOM_5 K_WT_10 K_WT_10 C_HOM_10 S_WT_10 K_HOM_10 K_WT_5 C_HOM_5 C_HOM_5 S_WT_10 C_HOM_10 K_HOM_5 C_WT_5 C_WT_10 S_WT_5 S_HOM_10 S_WT_5 C_HOM_10 S_HOM_5 C_WT_10 K_HOM_10 S_WT_5 C_HOM_5 C_HOM_5 K_WT_5 S_HOM_10 S_HOM_5 K_HOM_5 C_HOM_10 C_WT_5 S_WT_10 C_WT_5 S_HOM_5 K_WT_10 S_HOM_5 C_HOM_10 S_WT_5 S_HOM_10 S_HOM_10 C_WT_10 K_WT_5 K_HOM_5 K_WT_10 S_WT_5 K_HOM_10 S_WT_10 S_HOM_10 K_HOM_5 K_HOM_10 C_WT_5 K_WT_5 C_WT_5 K_WT_5 K_WT_10 S_WT_10 K_HOM_10 C_HOM_5 C_WT_10 C_WT_10 S_HOM_5
------
java.lang.IllegalStateException: Something obviously wrong items and classes mismatched:
Template id: edu.mit.broad.genome.objects.Id@366846 name: All_comparisons.cls
Number of classes: 12
Classes:
Class: C_HOM_10
Members: K_HOM_5[0,0],K_HOM_5[1,11],K_HOM_5[2,27],K_HOM_5[3,41],K_HOM_5[4,47]
Class: C_HOM_5
Members: K_WT_10[0,1],K_WT_10[1,2],K_WT_10[2,33],K_WT_10[3,42],K_WT_10[4,53]
Class: C_WT_10
Members: C_HOM_10[0,3],C_HOM_10[1,10],C_HOM_10[2,17],C_HOM_10[3,28],C_HOM_10[4,35]
Class: C_WT_5
Members: S_WT_10[0,4],S_WT_10[1,9],S_WT_10[2,30],S_WT_10[3,45],S_WT_10[4,54]
Class: K_HOM_10
Members: K_HOM_10[0,5],K_HOM_10[1,20],K_HOM_10[2,44],K_HOM_10[3,48],K_HOM_10[4,55]
Class: K_HOM_5
Members: K_WT_5[0,6],K_WT_5[1,24],K_WT_5[2,40],K_WT_5[3,50],K_WT_5[4,52]
Class: K_WT_10
Members: C_HOM_5[0,7],C_HOM_5[1,8],C_HOM_5[2,22],C_HOM_5[3,23],C_HOM_5[4,56]
Class: K_WT_5
Members: C_WT_5[0,12],C_WT_5[1,29],C_WT_5[2,31],C_WT_5[3,49],C_WT_5[4,51]
Class: S_HOM_10
Members: C_WT_10[0,13],C_WT_10[1,19],C_WT_10[2,39],C_WT_10[3,57],C_WT_10[4,58]
Class: S_HOM_5
Members: S_WT_5[0,14],S_WT_5[1,16],S_WT_5[2,21],S_WT_5[3,36],S_WT_5[4,43]
Class: S_WT_10
Members: S_HOM_10[0,15],S_HOM_10[1,25],S_HOM_10[2,37],S_HOM_10[3,38],S_HOM_10[4,46]
Class: S_WT_5
Members: S_HOM_5[0,18],S_HOM_5[1,26],S_HOM_5[2,32],S_HOM_5[3,34],S_HOM_5[4,59]
Template is continuous: false
Template is aux: false
Class of Interest (COI) is: C_HOM_10 Index: 0
Total # of items: 60
Output as string follows:
60 12 1
# K_HOM_5 K_WT_10 C_HOM_10 S_WT_10 K_HOM_10 K_WT_5 C_HOM_5 C_WT_5 C_WT_10 S_WT_5 S_HOM_10 S_HOM_5
K_HOM_5 K_WT_10 K_WT_10 C_HOM_10 S_WT_10 K_HOM_10 K_WT_5 C_HOM_5 C_HOM_5 S_WT_10 C_HOM_10 K_HOM_5 C_WT_5 C_WT_10 S_WT_5 S_HOM_10 S_WT_5 C_HOM_10 S_HOM_5 C_WT_10 K_HOM_10 S_WT_5 C_HOM_5 C_HOM_5 K_WT_5 S_HOM_10 S_HOM_5 K_HOM_5 C_HOM_10 C_WT_5 S_WT_10 C_WT_5 S_HOM_5 K_WT_10 S_HOM_5 C_HOM_10 S_WT_5 S_HOM_10 S_HOM_10 C_WT_10 K_WT_5 K_HOM_5 K_WT_10 S_WT_5 K_HOM_10 S_WT_10 S_HOM_10 K_HOM_5 K_HOM_10 C_WT_5 K_WT_5 C_WT_5 K_WT_5 K_WT_10 S_WT_10 K_HOM_10 C_HOM_5 C_WT_10 C_WT_10 S_HOM_5
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.runChecksPost(TemplateImpl.java:354)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.assignItems2ClassInOrder(TemplateImpl.java:392)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate_ordered_assign(TemplateFactory.java:211)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate(TemplateFactory.java:104)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser._parse_genecluster_style_categorical(ClsParser.java:249)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser.parse(ClsParser.java:225)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory._readTemplates(ParserFactory.java:340)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:291)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:765)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:735)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Castanza, Anthony
Oct 2, 2023, 1:46:05 PM10/2/23
to gsea...@googlegroups.com
Hi Theo,
One issue that immediately jumps out at me is that the phenotypes listed on the second line of your file need to reflect the order that they first appear on the third line of your file,
So if your first sample, as defined on the third line if your file is the “K_HOM_5” phenotype, then the second line should start
# K_HOM_5
Then the second and third both appear to be “K_WT_10”, then the fourth is C_HOM_10
so then the second line would look like
# K_HOM_5 K_WT_10 C_HOM_10
etc, for the number of samples/phenotypes that appear in your file.
After correcting this, let me know if you still have errors loading your CLS file!
-Anthony
Anthony S. Castanza, PhD
Department of Medicine
University of California, San Diego
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Theo
Oct 2, 2023, 1:49:08 PM10/2/23
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Hi Anthony,
I did not know that the appearance of the entries of the second line should be in order of appearance with the third line of the full sample list.
I will check it on Wednesday and let you know if that is the case.
Thank you.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/B87D0770-7652-4D71-BB40-BAAFAE358DD1%40hxcore.ol.
Meltem Tutar
Jan 4, 2024, 4:31:07 PM1/4/24
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I had the same error. Thanks for this thread.
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