Renaming rpt dir on error

[WANG Zifeng]

Hi authors,

   Thanks for your great software. I run 3 groups analysis using the commond: 

awk '{print "gsea-cli.sh  GSEA -res 002_GSEA/"$7"_all.TMP.GeneName.gct   -cls 2v2.cls#Treat_versus_Ctrl   -gmx h.all.v7.4.symbols.gmt   -out  002_GSEA -rpt_label  "$7".hallmark    -collapse No_Collapse -permute gene_set -mode Max_probe -norm meandiv -nperm 1000  -rnd_type no_balance -scoring_scheme weighted  -metric Signal2Noise -sort real -order descending -create_gcts false -create_svgs false -include_only_symbols true -make_sets true -median false -num 100 -plot_top_x 50 -rnd_seed timestamp -save_rnd_lists false -set_max 500 -set_min 15 -zip_report false"}' Sample.info.2Rep | uniq | xargs -iCMD -P0 bash -c CMD

Two groups finished successfully, but one field. I confirm there is no mistake on input data format. 

/data/software/biosoftware/003_gsea/GSEA_Linux_4.1.0/gsea-cli.sh  GSEA -res 002_GSEA/Eca109_oep38_PFD400mM24h_vs_Eca109_Vec_Vehicle_all.TMP.GeneName.gct   -cls /data/home/000_index/024_GSEA_GeneSet/2v2.cls#Treat_versus_Ctrl   -gmx /data/home/000_index/024_GSEA_GeneSet/010_Homo_GeneSets_Broad_v20210420/h.all.v7.4.symbols.gmt   -out  002_GSEA -rpt_label  Eca109_oep38_PFD400mM24h_vs_Eca109_Vec_Vehicle.hallmark    -collapse No_Collapse -permute gene_set -mode Max_probe -norm meandiv -nperm 1000  -rnd_type no_balance -scoring_scheme weighted  -metric Signal2Noise -sort real -order descending -create_gcts false -create_svgs false -include_only_symbols true -make_sets true -median false -num 100 -plot_top_x 50 -rnd_seed timestamp -save_rnd_lists false -set_max 500 -set_min 5 -zip_report false

echo Using bundled JDK.

WARNING: package com.apple.laf not in java.desktop

WARNING: package com.sun.java.swing.plaf.windows not in java.desktop

WARNING: package sun.awt.windows not in java.desktop

720      [INFO  ] - Parameters passed to GSEA tool:

722      [INFO  ] - gmx /data/home/000_index/024_GSEA_GeneSet/010_Homo_GeneSets_Broad_v20210420/h.all.v7.4.symbols.gmt

722      [INFO  ] - res 002_GSEA/Eca109_oep38_PFD400mM24h_vs_Eca109_Vec_Vehicle_all.TMP.GeneName.gct

722      [INFO  ] - cls /data/home/000_index/024_GSEA_GeneSet/2v2.cls#Treat_versus_Ctrl

722      [INFO  ] - rpt_label Eca109_oep38_PFD400mM24h_vs_Eca109_Vec_Vehicle.hallmark

722      [INFO  ] - collapse No_Collapse

722      [INFO  ] - zip_report false

722      [INFO  ] - gui false

722      [INFO  ] - out 002_GSEA

722      [INFO  ] - mode Max_probe

722      [INFO  ] - norm meandiv

722      [INFO  ] - nperm 1000

723      [INFO  ] - permute gene_set

723      [INFO  ] - rnd_type no_balance

723      [INFO  ] - scoring_scheme weighted

723      [INFO  ] - metric Signal2Noise

723      [INFO  ] - sort real

723      [INFO  ] - order descending

723      [INFO  ] - include_only_symbols true

723      [INFO  ] - make_sets true

723      [INFO  ] - median false

723      [INFO  ] - num 100

723      [INFO  ] - plot_top_x 50

723      [INFO  ] - rnd_seed timestamp

723      [INFO  ] - save_rnd_lists false

724      [INFO  ] - create_svgs false

724      [INFO  ] - create_gcts false

724      [INFO  ] - set_max 500

724      [INFO  ] - set_min 5

792      [INFO  ] - Begun importing: Dataset from: Eca109_oep38_PFD400mM24h_vs_Eca109_Vec_Vehicle_all.TMP.GeneName.gct

>Eca109_Vec_Vehicle_Rep1<

java.lang.NumberFormatException: For input string: "Eca109_Vec_Vehicle_Rep1"

at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source)

at java.base/jdk.internal.math.FloatingDecimal.parseFloat(Unknown Source)

at java.base/java.lang.Float.parseFloat(Unknown Source)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser._parseHasDesc(GctParser.java:215)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser._parse(GctParser.java:167)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser.parse(GctParser.java:117)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:159)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:129)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:746)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:799)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:787)

at org.gsea_msigdb.gsea/xtools.api.param.PobParam.getPob(PobParam.java:79)

at org.gsea_msigdb.gsea/xtools.api.param.DatasetReqdParam.getDataset(DatasetReqdParam.java:29)

at org.gsea_msigdb.gsea/xtools.gsea.Gsea.createHeader(Gsea.java:195)

at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:115)

at org.gsea_msigdb.gsea/xtools.api.AbstractTool.module_main(AbstractTool.java:417)

at org.gsea_msigdb.gsea/org.genepattern.modules.GseaWrapper.main(GseaWrapper.java:287)

at org.gsea_msigdb.gsea/xapps.gsea.CLI.main(CLI.java:29)

# of elements = 1

/data/home/000_index/024_GSEA_GeneSet/2v2.cls#Treat_versus_Ctrl 

2014     [INFO  ] - Begun importing: Dataset from: Eca109_oep38_PFD400mM24h_vs_Eca109_Vec_Vehicle_all.TMP.GeneName.gct

>Eca109_Vec_Vehicle_Rep1<

java.lang.NumberFormatException: For input string: "Eca109_Vec_Vehicle_Rep1"

at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source)

at java.base/jdk.internal.math.FloatingDecimal.parseFloat(Unknown Source)

at java.base/java.lang.Float.parseFloat(Unknown Source)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser._parseHasDesc(GctParser.java:215)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser._parse(GctParser.java:167)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.GctParser.parse(GctParser.java:117)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:159)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetGct(ParserFactory.java:129)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:746)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:799)

at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:787)

at org.gsea_msigdb.gsea/xtools.api.param.PobParam.getPob(PobParam.java:79)

at org.gsea_msigdb.gsea/xtools.api.param.DatasetReqdParam.getDataset(DatasetReqdParam.java:29)

at org.gsea_msigdb.gsea/xtools.api.param.DatasetReqdParam.getDataset(DatasetReqdParam.java:33)

at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:143)

at org.gsea_msigdb.gsea/xtools.api.AbstractTool.module_main(AbstractTool.java:417)

at org.gsea_msigdb.gsea/org.genepattern.modules.GseaWrapper.main(GseaWrapper.java:287)

at org.gsea_msigdb.gsea/xapps.gsea.CLI.main(CLI.java:29)

============================

I tried to change the 

 -set_max 500 -set_min 5 

 -set_max 500 -set_min 100

 -set_max 5000 -set_min 5  

 -set_max 5000 -set_min 1000

it still showed the same error.

anybody can help me to solve it? Thanks

 

[WANG Zifeng]

the error report is:

2129     [INFO  ] - Renaming rpt dir on error to: 002_GSEA/error_Eca109_oep38_PFD400mM24h_vs_Eca109_Vec_Vehicle.hallmark.Gsea.1629951360812

[Anthony Castanza]

Hello,

 

Based on the error message it appears to be an issue with the GCT parser when reading data from the Eca109_Vec_Vehicle_Rep1 sample.

Could you perhaps send us a screenshot of the GCT file open in something like Excel? Or a truncated version of the GCT plaintext file – we wouldn't need the information for all genes, just enough to debug why it's not able to parse the file for this specific condition.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[David Eby]

HI Wang,

From the error message, the problem is that the string "Eca109_Vec_Vehicle_Rep1" appears in a field that should have a numeric value.  Check the file contents against the Data Formats page in our Wiki.

It's just a guess, but Eca109_Vec_Vehicle_Rep1 appears to be some sort of sample name.  It may be that the data matrix header line (the third line of the GCT format) has been somehow duplicated or misplaced within the file.  Try searching for all occurrences of that string to see if any appear where they should not.

Regards,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

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[WANG Zifeng]

Dear Anthony and David, 

   Thanks for your reply.

    I run the R code to generate the gct files again (no change, totally the same with the previous code), and then run the GSEA again, it was successful!! too unexpected!

========

The R code to generate gct files is:

###  GSEA gct files

RNAcocktail.DEG <- read.table(paste0("001_DEG_GO-KEGG/",  pathname, "/", pathname, "_annotation.46.txt", sep=""), sep = '\t', header=F)
Description.col <- data.frame("DESCRIPTION"=c("DESCRIPTION", (rep("na",nrow(all.GeneName)-1))))
all.GeneName.gct <- cbind(all.GeneName[,1],Description.col[,1],all.GeneName[,2:ncol(all.GeneName)])
all.GeneName.gct <- as.data.frame(all.GeneName.gct)
t_all.GeneName.gct <- t(all.GeneName.gct)
t_all.GeneName.gct <- as.data.frame(t_all.GeneName.gct)

all.GeneName.gsea.gct <- subset(all.GeneName.gct, all.GeneName.gct$V1 %in% RNAcocktail.DEG$V10)

t_gsea_file <- t(all.GeneName.gsea.gct)
t_gsea_file <- as.data.frame(t_gsea_file)

t_gsea_file$'#1.2' <- c("#1.2", rep(NA,(nrow(t_gsea_file)-1)))
t_gsea_file$'geneNumber' <- c((ncol(t_gsea_file)-1), "4", rep(NA,4)) 
t_gsea_file$'geneName' <- t_all.GeneName.gct$V1  

t_gsea_file <- t_gsea_file[,c(which(colnames(t_gsea_file)=="#1.2"),which(colnames(t_gsea_file)== "geneNumber"), which(colnames(t_gsea_file)== "geneName"),1:(ncol(t_gsea_file)-3))]
test_pre <- t(t_gsea_file)

test_pre <- as.data.frame(test_pre)
write.table(test_pre, file=paste0("002_GSEA/", pathname, "_all.TMP.GeneName.gct"),quote = F, col.names = F,row.names = F, na = "", sep = "\t")

=========

The gct file format is:

22438 raws, the same with previous generated file!

I don't know what's wrong. Never the less, it is successful now.  Thanks for your replay again. 

Anthony Castanza <acas...@cloud.ucsd.edu> 于2021年8月27日周五 上午2:28写道：

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[Anthony Castanza]

Hello,

 

That is very strange. Could you perhaps send us the old and new files as well as the CLS so we can dig in to what may have gone wrong in the first run? You can send them confidentially to gsea...@broadinstitute.org if you're willing.

If not, I'll consider this resolved.

Glad you got it working!

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[WANG Zifeng]

Dear Anthony, I overwrite the old files. So I can't send it to you. I re-run the program again, it still work well😂.   It's solved, thanks for your time.

Anthony Castanza <acas...@cloud.ucsd.edu> 于2021年8月28日周六 上午1:00写道：

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