String index out of range: 2

[Alexander Berry]

Hi,

I am trying to load a VCF file into Tassel 5 and I am getting a String index out of range: 2 error. I've been successfully using this software but this file just isn't loading and I cannot figure out why. Any insight here would be greatly appreciated. 

Thanks,

Alex

Here is the debug info:

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.29  Date: August 4, 2016

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 3641 MB

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X

[AWT-EventQueue-0] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 4

[Thread-7] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: /Users/alex/Desktop/cruzi_data/Organized/First_60/HaplotypeCaller/test_haploid_1_DP20_remove_ast_excel.vcf time: Aug 13, 2016 12:23:39

Err Site Number:0

Err Site Number:0

Err Site Number:Position Chr:KB222878.1 Pos:486638 Name:SKB222878.1_486638 Variants:A/G MAF:NaN Ref:A

Err:KB222878.1 486638 . A G 6685.2 . AC=4;AF=1.00;AN=4;DP=178;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=41.76;QD=32.20;SOR=0.716 GT:AD:DP:GQ:PL 1:0,38:38:99:1370,0 1:0,47:47:99:1781,0 1:0,50:50:99:1879,0 1:0,43:43:99:1682,0

Err Site Number:0

Err Site Number:Position Chr:KB222880.1 Pos:241058 Name:SKB222880.1_241058 Variants:A/G MAF:NaN Ref:A

Err:KB222880.1 241058 . A G 365.42 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.38;ClippingRankSum=1.76;DP=177;FS=8.112;MLEAC=2;MLEAF=0.500;MQ=41.98;MQRankSum=0.263;QD=3.62;ReadPosRankSum=1.42;SOR=1.450 GT:AD:DP:GQ:PL 1:20,25:45:99:195,0 1:25,31:56:99:205,0 0:42,0:42:99:0,294 0:34,0:34:99:0,155

Err Site Number:Position Chr:KB222877.1 Pos:1258 Name:SKB222877.1_1258 Variants:G/A MAF:NaN Ref:G

Err:KB222877.1 1258 . G A 7332.2 . AC=4;AF=1.00;AN=4;DP=190;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=42.00;QD=26.02;SOR=0.693 GT:AD:DP:GQ:PL 1:0,50:50:99:1912,0 1:0,35:35:99:1369,0 1:0,53:53:99:2015,0 1:0,52:52:99:2063,0

Err Site Number:0

Err Site Number:Position Chr:KB222882.1 Pos:148739 Name:SKB222882.1_148739 Variants:C/G MAF:NaN Ref:C

Err:KB222882.1 148739 . C G 6369.2 . AC=4;AF=1.00;AN=4;DP=170;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=41.75;QD=29.02;SOR=1.106 GT:AD:DP:GQ:PL 1:0,38:38:99:1453,0 1:0,45:45:99:1616,0 1:0,41:41:99:1553,0 1:0,46:46:99:1774,0

Err Site Number:0

Err Site Number:Position Chr:KB222885.1 Pos:20487 Name:SKB222885.1_20487 Variants:G/A MAF:NaN Ref:G

Err:KB222885.1 20487 . G A 4129.2 . AC=4;AF=1.00;AN=4;DP=115;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=29.61;QD=25.50;SOR=1.219 GT:AD:DP:GQ:PL 1:0,30:30:99:1067,0 1:0,31:31:99:1101,0 1:0,30:30:99:1089,0 1:0,24:24:99:899,0

Err Site Number:0

Err Site Number:Position Chr:KB222887.1 Pos:220351 Name:SKB222887.1_220351 Variants:T/C MAF:NaN Ref:T

Err:KB222887.1 220351 . T C 6602.2 . AC=4;AF=1.00;AN=4;DP=188;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=37.54;QD=25.99;SOR=0.759 GT:AD:DP:GQ:PL 1:0,53:53:99:1920,0 1:0,28:28:99:993,0 1:0,47:47:99:1706,0 1:0,58:58:99:2010,0

Err Site Number:0

Err Site Number:Position Chr:KB222891.1 Pos:116432 Name:SKB222891.1_116432 Variants:G/T MAF:NaN Ref:G

Err:KB222891.1 116432 . G T 332.42 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.860;ClippingRankSum=0.090;DP=184;FS=5.047;MLEAC=2;MLEAF=0.500;MQ=41.55;MQRankSum=-1.401e+00;QD=3.82;ReadPosRankSum=1.30;SOR=0.433 GT:AD:DP:GQ:PL 0:41,0:41:99:0,170 1:16,23:39:99:201,0 0:28,28:56:83:0,83 1:22,26:48:99:166,0

Err Site Number:0

Err Site Number:Position Chr:KB222895.1 Pos:264926 Name:SKB222895.1_264926 Variants:C/T MAF:NaN Ref:C

Err:KB222895.1 264926 . C T 770.18 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.837;ClippingRankSum=0.131;DP=161;FS=10.013;MLEAC=1;MLEAF=0.250;MQ=41.47;MQRankSum=0.376;QD=12.63;ReadPosRankSum=-1.483e+00;SOR=0.144 GT:AD:DP:GQ:PL 0:29,0:29:99:0,107 0:25,0:25:99:0,331 1:20,41:61:99:803,0 0:46,0:46:99:0,363

Err Site Number:0

Err Site Number:Position Chr:KB222899.1 Pos:234600 Name:SKB222899.1_234600 Variants:C/T MAF:NaN Ref:C

Err:KB222899.1 234600 . C T 8180.2 . AC=4;AF=1.00;AN=4;DP=224;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=41.91;QD=33.68;SOR=0.720 GT:AD:DP:GQ:PL 1:0,53:53:99:1936,0 1:0,55:55:99:2025,0 1:0,52:52:99:1909,0 1:0,63:63:99:2337,0

Err Site Number:0

Err Site Number:Position Chr:KB222906.1 Pos:49972 Name:SKB222906.1_49972 Variants:A/T MAF:NaN Ref:A

Err:KB222906.1 49972 . A T 5446.2 . AC=4;AF=1.00;AN=4;DP=142;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=40.03;QD=31.33;SOR=0.780 GT:AD:DP:GQ:PL 1:0,36:36:99:1436,0 1:0,31:31:99:1228,0 1:0,34:34:99:1309,0 1:0,41:41:99:1500,0

Err Site Number:0

Err Site Number:Position Chr:KB222912.1 Pos:37091 Name:SKB222912.1_37091 Variants:G/A MAF:NaN Ref:G

Err:KB222912.1 37091 . G A 7933.2 . AC=4;AF=1.00;AN=4;DP=186;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=41.33;QD=24.30;SOR=0.759 GT:AD:DP:GQ:PL 1:0,58:58:99:2510,0 1:0,45:45:99:1923,0 1:0,39:39:99:1599,0 1:0,44:44:99:1928,0

Err Site Number:0

Err Site Number:Position Chr:KB222918.1 Pos:118066 Name:SKB222918.1_118066 Variants:C/T MAF:NaN Ref:C

Err:KB222918.1 118066 . C T 1979.18 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.972;ClippingRankSum=-4.930e-01;DP=214;FS=6.127;MLEAC=3;MLEAF=0.750;MQ=41.57;MQRankSum=0.190;QD=12.22;ReadPosRankSum=0.012;SOR=0.988 GT:AD:DP:GQ:PL 1:17,39:56:99:885,0 1:21,40:61:99:699,0 0:51,0:51:99:0,513 1:17,28:45:99:428,0

Err Site Number:0

Err Site Number:Position Chr:KB222927.1 Pos:26006 Name:SKB222927.1_26006 Variants:T/C MAF:NaN Ref:T

Err:KB222927.1 26006 . T C 9435.2 . AC=4;AF=1.00;AN=4;DP=212;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=41.91;QD=35.16;SOR=1.131 GT:AD:DP:GQ:PL 1:0,52:52:99:2342,0 1:0,44:44:99:1930,0 1:0,58:58:99:2618,0 1:0,57:57:99:2572,0

Err Site Number:0

Err Site Number:Position Chr:KB222937.1 Pos:23770 Name:SKB222937.1_23770 Variants:A/C MAF:NaN Ref:A

Err:KB222937.1 23770 . A C 6629.2 . AC=4;AF=1.00;AN=4;DP=175;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=41.98;QD=33.48;SOR=0.751 GT:AD:DP:GQ:PL 1:0,40:40:99:1532,0 1:0,35:35:99:1355,0 1:0,37:37:99:1425,0 1:0,63:63:99:2344,0

Err Site Number:0

Err Site Number:Position Chr:KB222946.1 Pos:104445 Name:SKB222946.1_104445 Variants:G/T MAF:NaN Ref:G

Err:KB222946.1 104445 . G T 73.18 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.09;ClippingRankSum=-5.130e-01;DP=108;FS=3.154;MLEAC=1;MLEAF=0.250;MQ=37.94;MQRankSum=2.54;QD=2.03;ReadPosRankSum=0.642;SOR=0.257 GT:AD:DP:GQ:PL 0:22,0:22:99:0,629 0:23,0:23:99:0,450 0:27,0:27:99:0,540 1:15,21:36:99:106,0

Err Site Number:0

Err Site Number:Position Chr:KB222960.1 Pos:40110 Name:SKB222960.1_40110 Variants:G/A MAF:NaN Ref:G

Err:KB222960.1 40110 . G A 6363.2 . AC=4;AF=1.00;AN=4;DP=166;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=41.84;QD=21.45;SOR=0.874 GT:AD:DP:GQ:PL 1:0,40:40:99:1537,0 1:0,45:45:99:1800,0 1:0,44:44:99:1646,0 1:0,37:37:99:1407,0

Err Site Number:0

Err Site Number:Position Chr:KB222979.1 Pos:64987 Name:SKB222979.1_64987 Variants:G/A MAF:NaN Ref:G

Err:KB222979.1 64987 . G A 504.42 . AC=2;AF=0.500;AN=4;BaseQRankSum=2.79;ClippingRankSum=0.308;DP=177;FS=4.103;MLEAC=2;MLEAF=0.500;MQ=41.91;MQRankSum=0.450;QD=5.67;ReadPosRankSum=1.82;SOR=1.201 GT:AD:DP:GQ:PL 0:47,0:47:99:0,513 0:41,0:41:99:0,915 1:19,26:45:99:329,0 1:19,25:44:99:210,0

Err Site Number:0

Err Site Number:Position Chr:KB223014.1 Pos:25714 Name:SKB223014.1_25714 Variants:T/C MAF:NaN Ref:T

Err:KB223014.1 25714 . T C 6811.2 . AC=4;AF=1.00;AN=4;DP=186;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=36.00;QD=34.56;SOR=0.759 GT:AD:DP:GQ:PL 1:0,51:51:99:2251,0 1:0,60:60:99:2043,0 1:0,27:27:99:921,0 1:0,48:48:99:1623,0

Err Site Number:0

Err Site Number:Position Chr:KB223164.1 Pos:2689 Name:SKB223164.1_2689 Variants:G/A MAF:NaN Ref:G

Err:KB223164.1 2689 . G A 2598.2 . AC=4;AF=1.00;AN=4;BaseQRankSum=-4.130e-01;ClippingRankSum=-1.734e+00;DP=103;FS=3.139;MLEAC=4;MLEAF=1.00;MQ=22.93;MQRankSum=-5.780e-01;QD=25.23;ReadPosRankSum=-1.734e+00;SOR=0.348 GT:AD:DP:GQ:PL 1:0,28:28:99:742,0 1:1,20:21:99:432,0 1:0,27:27:99:724,0 1:0,27:27:99:727,0

[Thread-7] DEBUG net.maizegenetics.dna.snp.io.BuilderFromVCF - java.lang.StringIndexOutOfBoundsException: String index out of range: 2

java.util.concurrent.ExecutionException: java.lang.StringIndexOutOfBoundsException: String index out of range: 2

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:1652)

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

Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 2

at java.lang.String.charAt(String.java:646)

at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:606)

at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:423)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:745)

[Thread-7] ERROR net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.StringIndexOutOfBoundsException: String index out of range: 2

java.lang.IllegalStateException: java.lang.StringIndexOutOfBoundsException: String index out of range: 2

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-7] DEBUG net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.StringIndexOutOfBoundsException: String index out of range: 2

java.lang.IllegalStateException: java.lang.StringIndexOutOfBoundsException: String index out of range: 2

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-7] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Nothing Loaded for File: /Users/alex/Desktop/cruzi_data/Organized/First_60/HaplotypeCaller/test_haploid_1_DP20_remove_ast_excel.vcf time: Aug 13, 2016 12:23:46

[Zack Miller]

Hi Alex,

Your file does not have diploid genotypes.  TASSEL currently only supports loading in VCF files with diploid calls.  

For instance you have calls which look like 1:17,39:... when TASSEL is expecting 1/1:17,39:...

Thanks,

Zack

[Alexander Berry]

Ah OK thanks. I didn't realize that Tassel only dealt with diploids. 

Thanks,

Alex

[Edward S. Buckler]

Hello Alex-

What ploidy is the species that you are working with?

We deal quite well inbred?

-Ed

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[Tyr Wiesner-Hanks]

Hi Alex (or others Googling this error),

You can convert haploid to pseudo-diploid files with a sed workaround. I used the following bash code:

sed 's/\t\./\t.\/./g' haploid.vcf > diploidized.vcf 

for i in {0..9}; do 

        sed -i "s/\t$i:/\t$i\/$i:/g" diploidized.vcf 

done

The first line replaces . characters preceded by a tab (haploid missing) with ./. characters preceded by a tab (diploid missing) and pipes to a new file. The loop replaces numeric characters preceded by a tab and followed by a colon (the start of haploid genotypes) with a tab, the character, a /, and the character again (in place, consistent w/ diploids). If you have more than 10 genotypes in a given line

This works for my files, and I checked a few markers by hand back to the original haploid file. It is set up for cases where the GT field is the first entry in the VCF genotype fields, which I think is the norm. It obviously would not contain properly formatted depths or whatnot, since there was only one depth. Not sure if it will work for others.

[sarthok rahman]

Hi Tyr,

Great solution! I am also working with haploid data and I tried to implement the solution. However, it did not work for one of my vcfs. I think I have more than 10 genotypes in that file. You started writing "if you have more than 10 genotypes in a given line" ... and it was not completed so if it is possible if you please share your thoughts on it that would be very helpful! Thanks in advance! 

Sarthok

[Tyr Wiesner-Hanks]

Hmn, I'm not sure what I was going to write there. If you modify the for loop to be {0..20} or whatever, that should work. It will just get slower linearly with that number.

One important note, the above code will replace '.' fields with './.' everywhere in the file. That includes in fields 3 (ID) and 5 (filter), so it will change all your site names to './.' when read into TASSEL. Here is my workaround:

grep '#' haploid.vcf > diploidized.vcf

grep -v '#' haploid.vcf | cut -f 1-5 > tmp1

grep -v '#' haploid.vcf | cut -f 6- > tmp2

sed -i 's/\t\./\t.\/./g' tmp2 

for i in {0..20}; do 

        sed -i "s/\t$i:/\t$i\/$i:/g" tmp2 

done

paste tmp1 tmp2 >> diploidized.vcf

rm tmp1 tmp2

I think you could make this faster by using awk to skip the for loop and using csplit to not repeat the grep steps. But it's fast enough for me so I haven't tried to figure that out.

[sarthok rahman]

Thank you so much, Tyr! It worked perfectly!