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# VariantRecalibrator error

Hi,

I'm now at the VQSR step of the best practices and to my surprise I got the following error related to java (I think):

Error: Could not find or load main class –jar

Here is my command line:

java –jar GenomeAnalysisTK.jar –T VariantRecalibrator –R ../human_g1k_v37.fasta –input ../raw_variants.vcf -resource:hapmap,known=false,training=true,truth=true,prior=15.0 ../hapmap_3.3.b37.vcf -resource:omni,known=false,training=true,truth=false,prior=12.0 ../1000G_omni2.5.b37.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ../dbsnp_138.b37.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 ../1000G_phase1.snps.high_confidence.b37.vcf -an QD -an MQRankSum -an ReadPosRankSum -an FS --maxGaussians 4 –mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0 –recalFile raw.SNPs.recal –tranchesFile raw.SNPs.tranches -rscriptFile recal.plots.R

I don't understand what is the problem. Could someone look at it and identify if I made a mistake in my command line?

Tagged:

Nothing's jumping out at me but I would recommend re-typing your command line from scratch, at least.

Geraldine Van der Auwera, PhD

I got the same error after I having retried.
Is it possible that the VariantRecalibrator tool is just badly installed? Is there a shorter command line that I can use just to test if the tool can work?

No, you wouldn't get that error for just one tool. You can try java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -h to bring up the help message and documentation for the tool.

Geraldine Van der Auwera, PhD

I tried to recalibrate indels first with this command:

java –jar GenomeAnalysisTK.jar –T VariantRecalibrator –R ../human_g1k_v37.fasta –I ../raw_variants.vcf -resource:mills,known=true,training=true,truth=true,prior=12.0 ../Mills_and_1000G_gold_standard.indels.b37.vcf
-an QD -an MQRankSum -an ReadPosRankSum -an FS
--maxGaussians 4 –mode INDEL -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0
–recalFile ../raw.indels.recal –tranchesFile ../raw.SNPs.tranches -rscriptFile ../recal.plots.R

and got the same error. Should I reinstall java and/or GATK?

Just don't know what to do right now...

Is it also happening with other GATK tools? And are you using a version downloaded from our website, or one that you compiled yourself?

Geraldine Van der Auwera, PhD

@Geraldine_VdAuwera said:
Is it also happening with other GATK tools? And are you using a version downloaded from our website, or one that you compiled yourself?

I'll check if I could find another machine...

@Geraldine_VdAuwera said:
Hmm. You can always try downloading the package again but I can't think of why that would make a difference. Do you have access to a different machine you could test on in parallel?

I finally found what was wrong. The problem was the "-" symbol in front of "jar". The one I used (although I don't know why) was not read by the machine. The one causing problem was a little bit longer than the one it should be used...

Ack, I should have thought of that. Did you maybe compose the command line in a word processor? MS Word for example will substitute long dashes for style, but then in the shell it's interpreted as a different character.

Geraldine Van der Auwera, PhD

No. In fact if I remember well, I think I copied it from your website since the command line was pretty long...

Ah, that could cause character encoding issues. Glad it's resolved anyway.

Geraldine Van der Auwera, PhD

Now, I'm having problem to view the plot.r.pdf file. When I try to open it, I got the following message: "File type plain text document (text/plain) is not supported". When I tried to open it under windows with acrobat XI, I'm not able to open it. How can I be sure that the Variantcalibrator worked properly?

Did the run complete successfully? And have you tried opening the file on a different machine? It's a plain pdf...

Geraldine Van der Auwera, PhD

Also I've found this warning:
WARN 11:49:58,760 Utils - ********************************************************************************
WARN 11:49:58,760 Utils - * WARNING:
WARN 11:49:58,760 Utils - *
WARN 11:49:58,761 Utils - * Rscript not found in environment path. ../recal.plots.R.pdf will be
WARN 11:49:58,761 Utils - * generated but PDF plots will not.
WARN 11:49:58,761 Utils - ********************************************************************************