VCF file load problem

[Ruijuan li]

I have VCF files generated by cornell along with the raw GBS data they sent to us. Every time I try to load VCF files into tassel 5 on my Win 7 desktop, tassel would say "Java.Lang.NumberFormatException:for input string". Anyone here has encountered the same problem and has an idea how to fix this? 

Thanks ! 

[Veena Devi Ganeshan]

Hi Li

  I am facing the same error too when i tried to load my vcf file ! Did you find a solution to this ?

Thanks ! 

Veena

[Ruijuan li]

No, I haven't. 

[Adam Cardilini]

G'day Ruijuan and Li,

I have just run into the same problem. Did either of you find a solution to this?

Thanks,

Adam

[Zack Miller]

Hello,

We are working on better supporting VCF for the next version of tassel which will hopefully fix your problem.  

This type of error can happen in one of two places in the VCF Import code, when java attempts to convert a string of text into a number.  Looking at the code, it is likely that either you have a non-numeric or missing position number in a single VCF line, or you have an AD field which is non-numeric or missing.  It is possible that there is something else going on, but this is probably where the issue is.

If you don't mind, please run Tassel in debugging mode (https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf?rev=57f1186acbfc42c09b74d8c87317c6ee46ed3914), try to reload your file and post the output logs here.  They might help figure out exactly what is the issue.  Also it would be helpful to send me your input files.  If you are concerned about your data, you can send it directly to me.  Even a small sample dataset which replicates the issue would be helpful.

Thanks,

Zack Miller

[Martha Rose]

Hello! I am having the exact same issue trying to load a VCF file generated by stacks (from GBS raw reads) into TASSEL 5.2.16. Has there been any update on this problem? 

Many thanks,

Martha Rose

[Veena Devi Ganeshan]

Hi All,

   I figured out the solution to my problem, I could not load the vcf file (GBS data) in TASSEL 5.2.16 either it showed some sort of "java error", what i did was, load the VCF file in an older version 4.1.12 or whatever and then export the file and save it with a different name and try to load that file in TASSEL 5.2.16, IT WORKED !! good luck, hope this solves your problem ! 

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Cheers always,

Veena Devi Ganeshan Ph.D 

Dept. of Plant Pathology 

The Ohio State University 

 

------------------

 

 

 

[Martha Rose]

Hi Veena,

That's a great idea! I'll give it a go! Do you have a link for an executable version of TASSEL 4 for a windows machine? I can only find links to TASSEL 5! 

Cheers,

Martha 

[jchive...@gmail.com]

Martha,
    I am having the same problems and I found TASSEL 4 at this link for download: http://sourceforge.net/projects/tassel/files/Tassel%204.0/

Hope this helps!

[lepisorus]

Hi, All

Has this problem been solved? I am recently using Tassel 5.26, but still had this same problem. Tried to convert the file format with Tassel4, but "Could not find or load main class net.maizegenetics.pipeline.TasselPipeline". Any updates?

Thanks!

Li

在 2016年1月11日星期一 UTC-6下午4:04:03，jchive...@gmail.com写道：

[Zack Miller]

Hello,

We have made some VCF changes since Tassel 5.2.16(I am assuming that this is the version you are mentioning as we do not have a Tassel 5.26 yet) which should address this problem.  Please upgrade your version of Tassel to 5.2.23, and try again.

You should not have to use Tassel 4 to export the VCF file.  It also looks like you have a configuration problem with your Tassel 4 installation as it is not able to find the TasselPipeline class which is used to run when you use the run_pipeline script.  Is there a file called sTassel.jar in the same directory where the run_pipeline script is located?

If you are still unable to load your VCF file, please enable Debug Mode (https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf?rev=57f1186acbfc42c09b74d8c87317c6ee46ed3914) and attempt to load your file a second time.  This should give us a better idea of where Tassel is having a problem.  Please send any logs which are displayed with debug mode and also send the command used to run Tassel.

Thanks,

Zack

[lepisorus]

Thanks, Zack! Using the new version 5.2.23 do solve the reading VCF problems. Thanks!

Li

在 2015年5月14日星期四 UTC-5下午1:36:09，Ruijuan li写道：

[sbhu...@teri.res.in]

I have just uploaded the vcf files to TASSEL 5 (5.2.22) and it worked well.

[Bill]

Hi Zach,

I have a VCF file that loads into TASSEL 5.2.25. However, when I make a copy of the file and make any edits, save, and reload, I get the errors below. This is true whether I use libreoffice calc with ubuntu or excel with a mac. After I make a copy of the file, it still loads, but not after I edit and save (this is true even if I insert and then delete a single space). Do you know what could be causing this? I've never had this problem with other file formats in tassel (e.g. hapmap).

Thanks!
Bill


[Thread-8] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: /home/Union_file.vcf time: Jun 10, 2016 15:58:30
Err Site Number:0
Err Site Number:0
Err Site Number:0
Err Site Number:0
[Thread-8] DEBUG net.maizegenetics.dna.snp.io.BuilderFromVCF - java.lang.ArrayIndexOutOfBoundsException
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException
    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:215)
    at net.maizegenetics.dna.snp.io.BuilderFromVCF.build(BuilderFromVCF.java:118)
    at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:110)
    at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:116)
    at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:465)
    at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
Caused by: java.lang.ArrayIndexOutOfBoundsException
[Thread-8] ERROR net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.ArrayIndexOutOfBoundsException
java.lang.IllegalStateException: java.lang.ArrayIndexOutOfBoundsException
    at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:219)
    at net.maizegenetics.dna.snp.io.BuilderFromVCF.build(BuilderFromVCF.java:118)
    at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:110)
    at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:116)
    at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:465)
    at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-8] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Nothing Loaded for File: /home/Union_file.vcf time: Jun 10, 2016 15:58:31

[Zack Miller]

Hello,

This is an odd issue, I will need to improve TASSEL's error messages.  Could you check to see if when you insert and delete a space then save that the file matches the original file(using diff on mac or linux).  I am wondering if libreoffice or excel is changing some of the characters in the file.  Can you load in the original file to a text editor(like TextEdit or TextWrangler on the mac) make the changes then save a new file and see if it throws the same error?  Could you also privately send me a small VCF file which demonstrates this behavior?  Having a file will help me figure out exactly where the problem is occurring so I can better diagnose what is happening and improve the error message in TASSEL.

Thanks,

Zack

[Bill]

Hi Zach,

Thanks for the fast reply. I realized that the issue is that libreoffice calc was adding double quotations around the ## headers at the beginning of the document. Once I removed these, it loaded fine.

Thanks,
Bill

[Alexander Berry]

Hi Zack et al.,

I've recently had the same "java.lang.ArrayIndexOutOfBoundsException: 6" error when loading a VCF file. I do have the current version. I use Tassel 5 often, usually when I use GATK's UnifiedGenotyper function and it works beautifully, however now I am using HaplotypeCaller and Tassel does not like the VCF output from that. I pasted the bottom of the debugging output below. The problem seems to be in one or several, but definitely not all SNP sites, but I cannot for the life of me figure out what is different/wrong with the "bad" lines. I've attached the full debug file.  

Note that Tassel still reads my UnifiedGenotyper-generated VCF files. It's only the HaplotypeCaller files that are giving me trouble.

Thanks!

Alex

Err Site Number:70

Err Site Number:Position Chr:KB222878.1 Pos:320325 Name:SKB222878.1_320325 Variants:A/T/* MAF:NaN Ref:A

Err:KB222878.1 320325 . A T,* 20204.79 . AC=9,37;AF=0.173,0.712;AN=52;DP=1102;ExcessHet=0.2996;FS=0.000;InbreedingCoeff=0.3623;MLEAC=9,37;MLEAF=0.173,0.712;MQ=6.79;QD=33.50;SOR=0.552 GT:AD:DP:GQ:PL 1/2:0,0,10:19:48:398,337,319,62,0,48 2/2:0,0,19:34:58:711,711,711,58,58,0 1/2:1,0,82:126:99:3132,2770,2696,342,0,196 1/2:0,0,11:31:99:525,368,321,160,0,150 0/2:0,0,19:44:0:644,644,644,0,0,25 1/2:0,0,19:34:99:747,645,611,105,0,105 2/2:0,0,25:38:69:913,913,913,69,69,0 2/2:0,0,22:35:64:819,819,819,64,64,0 2/2:0,0,35:35:99:1298,1298,1298,105,105,0 1/2:0,0,12:35:99:753,378,317,379,0,400 1/2:0,0,14:33:99:640,482,430,152,0,135 1/2:0,0,20:36:99:818,679,638,143,0,137 2/2:0,0,13:25:32:469,469,469,32,32,0 0/0:31,0,0:31:92:0,92,1235,92,1235,1235 1/2:0,0,26:45:99:1045,886,838,165,0,156 2/2:1,0,21:40:30:715,718,751,30,63,0 0/2:4,0,14:33:50:436,448,539,0,91,50 2/2:0,0,16:37:1:545,545,546,1,1,0 2/2:1,0,26:37:44:936,939,972,44,78,0 2/2:0,0,17:32:42:622,622,622,42,42,0 2/2:0,0,17:31:41:602,602,602,41,41,0 2/2:0,0,25:46:16:886,886,886,16,16,0 0/2:1,0,15:32:6:510,513,547,0,34,6 0/2:0,0,15:33:0:502,502,502,0,1,0 2/2:0,0,23:36:22:805,805,805,22,22,0 1/2:0,0,17:32:99:794,579,533,225,0,238

[Thread-13] DEBUG net.maizegenetics.dna.snp.io.BuilderFromVCF - java.lang.ArrayIndexOutOfBoundsException

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:211)

at net.maizegenetics.dna.snp.io.BuilderFromVCF.build(BuilderFromVCF.java:114)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:110)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:116)

at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:465)

at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1645)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

Caused by: java.lang.ArrayIndexOutOfBoundsException

Err Site Number:92

Err Site Number:Position Chr:KB222877.1 Pos:27269 Name:SKB222877.1_27269 Variants:C/T/* MAF:NaN Ref:C

Err:KB222877.1 27269 . C T,* 10990.64 . AC=4,12;AF=0.077,0.231;AN=52;BaseQRankSum=0.318;ClippingRankSum=-4.710e-01;DP=1535;ExcessHet=9.0239;FS=1.835;InbreedingCoeff=-0.2622;MLEAC=4,12;MLEAF=0.077,0.231;MQ=27.14;MQRankSum=-1.404e+00;QD=17.45;ReadPosRankSum=2.47;SOR=0.885 GT:AD:DP:GQ:PGT:PID:PL 0/0:59,2,0:61:99:.:.:0,108,2155,178,2161,2231 0/2:5,0,32:37:92:.:.:975,990,1177,0,187,92 0/2:21,0,26:47:99:.:.:758,821,1562,0,742,662 0/1:39,5,0:44:33:0|1:27269_C_T:33,0,1405,150,1419,1569 0/0:53,0,0:53:41:.:.:0,41,1784,41,1784,1784 2/2:1,0,34:35:67:.:.:1447,1450,1499,67,115,0 0/1:41,6,0:47:98:0|1:27269_C_T:98,0,1616,225,1634,1859 0/0:42,2,0:44:82:0|1:27269_C_T:0,82,1675,130,1681,1729 0/2:3,0,28:31:21:.:.:852,861,966,0,104,21 0/0:66,0,0:66:80:.:.:0,80,2181,80,2181,2181 0/2:16,0,26:42:99:.:.:678,725,1248,0,523,446 0/0:36,0,0:36:99:.:.:0,111,1525,111,1525,1525 0/1:30,6,0:36:99:0|1:27269_C_T:112,0,1074,207,1092,1299 0/0:43,0,0:43:99:.:.:0,130,1739,130,1739,1739 0/2:3,0,27:30:27:.:.:892,901,1008,0,107,27 0/0:46,2,0:48:76:.:.:0,76,1846,145,1852,1921 0/0:37,3,0:40:20:0|1:27269_C_T:0,20,1397,112,1406,1498 0/2:7,0,37:44:99:.:.:1341,1362,1633,0,271,147 0/0:41,2,0:43:58:.:.:0,58,1566,124,1572,1637 0/2:7,0,32:39:99:.:.:1103,1124,1372,0,248,144 0/2:4,0,32:36:22:.:.:1013,1024,1142,0,118,22 0/2:7,0,29:36:99:.:.:962,983,1248,0,265,177 0/2:12,0,25:37:99:.:.:763,799,1230,0,431,356 0/0:50,4,0:54:38:0|1:27269_C_T:0,38,1990,177,2002,2141 0/0:49,3,0:52:38:.:.:0,38,1919,148,1928,2039 0/1:82,7,0:89:75:.:.:75,0,1772,246,1793,2039

[Thread-13] ERROR net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.ArrayIndexOutOfBoundsException

java.lang.IllegalStateException: java.lang.ArrayIndexOutOfBoundsException

at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:215)

at net.maizegenetics.dna.snp.io.BuilderFromVCF.build(BuilderFromVCF.java:114)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:110)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:116)

at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:465)

at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1645)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

[Thread-13] DEBUG net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.ArrayIndexOutOfBoundsException

java.lang.IllegalStateException: java.lang.ArrayIndexOutOfBoundsException

at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:215)

at net.maizegenetics.dna.snp.io.BuilderFromVCF.build(BuilderFromVCF.java:114)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:110)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:116)

at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:465)

at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1645)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

Err Site Number:32

Err Site Number:Position Chr:KB222877.1 Pos:583473 Name:SKB222877.1_583473 Variants:C/T/* MAF:NaN Ref:C

Err:KB222877.1 583473 . C T,* 10870.79 . AC=11,26;AF=0.212,0.500;AN=52;BaseQRankSum=0.198;ClippingRankSum=0.060;DP=474;ExcessHet=3.1067;FS=0.554;InbreedingCoeff=-0.0019;MLEAC=11,26;MLEAF=0.212,0.500;MQ=21.03;MQRankSum=0.135;QD=27.11;ReadPosRankSum=0.594;SOR=0.596 GT:AD:DP:GQ:PGT:PID:PL 0/1:8,3,0:11:19:.:.:19,0,154,42,163,205 0/1:9,5,0:14:81:.:.:81,0,191,108,206,314 0/1:23,28,0:51:99:.:.:526,0,486,595,569,1164 0/0:13,1,0:14:16:.:.:0,16,349,39,352,375 2/2:0,0,21:21:63:1|1:583463_TC_T:945,945,945,63,63,0 2/2:0,0,17:17:51:1|1:583463_TC_T:757,757,757,51,51,0 2/2:0,0,11:11:33:1|1:583463_TC_T:495,495,495,33,33,0 2/2:0,0,15:15:45:1|1:583463_TC_T:663,663,663,45,45,0 2/2:0,0,14:14:45:1|1:583463_TC_T:667,667,667,45,45,0 2/2:0,0,21:21:63:1|1:583463_TC_T:945,945,945,63,63,0 2/2:0,0,10:10:30:1|1:583463_TC_T:450,450,450,30,30,0 0/1:6,10,0:16:91:.:.:260,0,91,277,121,398 2/2:0,0,15:15:48:1|1:583463_TC_T:712,712,712,48,48,0 0/1:6,7,0:13:96:.:.:203,0,96,221,117,337 0/1:5,2,0:7:32:.:.:32,0,90,47,96,143 0/1:13,2,0:15:8:.:.:8,0,342,47,348,395 2/2:0,0,12:12:36:1|1:583463_TC_T:540,540,540,36,36,0 2/2:0,0,26:26:78:1|1:583463_TC_T:1138,1138,1138,78,78,0 0/1:7,7,0:14:99:.:.:149,0,204,170,225,395 2/2:0,0,17:17:51:1|1:583463_TC_T:748,748,748,51,51,0 0/1:13,3,0:16:18:.:.:18,0,302,56,310,367 2/2:0,0,15:15:45:1|1:583463_TC_T:658,658,658,45,45,0 0/1:19,2,0:21:9:0|1:583473_C_T:9,0,646,66,652,718 0/1:6,2,0:8:29:.:.:29,0,129,47,135,182 2/2:0,0,21:21:63:1|1:583463_TC_T:933,933,933,63,63,0 0/0:17,2,0:19:10:.:.:0,10,412,51,418,460

[Thread-13] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Nothing Loaded for File: /Users/alex/Desktop/cruzi_data/Organized/First_60/HaplotypeCaller/test_big_HC.vcf time: Jul 25, 2016 12:18:11

[Zack Miller]

Hi Alex,

I am able to reproduce your error message, and I believe it is due to the * symbol being used in the ALT column.  Is the HaplotypeCaller doing an upstream deletion of these alleles? The lines from your VCF file seem correct, but we need to update TASSEL to handle this properly. 

Thank you for bringing this to our attention.

Zack

[Alexander Berry]

Hi Zack,

I did not notice those asterisks. Thanks for drawing them to my attention. I did a simple removal of the ",*"s, however now I receive an error that reads "Allele ID larger than number of alleles", so I'm thinking that I need to have some placeholder in that * position. There's nothing obvious in the HaplotypeCaller documentation that indicates why it adds these asterisks, but I'll dig a little deeper and see if I can't generate a file without them.

Thanks for your help,

Alex

[Marlee Labroo]

Hi Zack et al.,

I also get this error-- exported a .vcf through the command line, which loads correctly, but if I export the exact file (as a .vcf) from the GUI upon loading it back in the "java.lang.ArrayIndexOutOfBoundsException: 6" error comes up. I make no modifications to the file beyond loading it and saving it in TASSEL. Has this been resolved?

Thanks,

Marlee

[Terry Casstevens]

What version of TASSEL are you using?

Please follow these instructions to get more information.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

Best,

Terry

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[Marlee Labroo]

5.2.30. I reinstalled it in case I had missed an update. Thank you Terry.

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[Marlee Labroo]

Here is the error log:

[Thread-10] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: C:\Users\labroo2\GBS\LongiMaster_Output_Lib1to5_Outgroups\export_test time: Feb 23, 2017 16:42:44

Err Site Number:0

[Thread-10] ERROR net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.ArrayIndexOutOfBoundsException

java.lang.IllegalStateException: java.lang.ArrayIndexOutOfBoundsException

at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:215)

at net.maizegenetics.dna.snp.io.BuilderFromVCF.build(BuilderFromVCF.java:114)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:110)

at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:116)

at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:465)

at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:249)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1652)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

[Thread-10] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Nothing Loaded for File: C:\Users\labroo2\GBS\LongiMaster_Output_Lib1to5_Outgroups\export_test time: Feb 23, 2017 16:42:52

[Thread-11] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.tassel.TasselLogging: time: Feb 23, 2017 16:42:54

[Thread-11] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: Feb 23, 2017 16:42:54

On Thu, Feb 23, 2017 at 4:39 PM, Terry Casstevens <tm...@cornell.edu> wrote:

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[Zack Miller]

Hi Marlee,

It seems to me there might be a issue with your VCF file.  Is this file something you can send to me privately?  Or could you send a smaller VCF file which still throws this error?  My guess is there is a line in the VCF file that is not properly formatted.  

Thanks,

Zack

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[John Baison]