Question: GATK's Apply Recalibration not working
0
gravatar for Hatem Elshazly
4.1 years ago by
Egypt
Hatem Elshazly60 wrote:

Hi there,

I'm having a problem using GATK's ApplyRecalibration tool using this command:

java -jar "GenomeAnalysisTK.jar" -T "ApplyRecalibration" -R human_g1k_v37.fasta -input fileContents.vcf
--ts_filter_level "99.9" --mode "SNP" --recal_file dataset_1139.dat_0.recal
--tranches_file dataset_1140.dat_0.tranches --out dataset_1142.dat_0.vcf

 

this is the error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.7-2-g6bda569): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name      FeatureType   Documentation
##### ERROR BCF2   VariantContext   (this is an external codec and is not documented within GATK)
##### ERROR  VCF   VariantContext   (this is an external codec and is not documented within GATK)
##### ERROR VCF3   VariantContext   (this is an external codec and is not documented within GATK)
##### ERROR ------------------------------------------------------------------------------------------

 

I tried to look for some solutions, I added a :NAME,VCF tag before the vcf file path, I used a different version of GATK, I tried using another vcf file and I validated the vcf file I'm using, using GATK's ValidateVariants and it was validated with no problem but this problem still presists.

 

 

Any ideas or suggestion will be appreciated.

 

Thanks in advance.

shazly

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Hatem Elshazly60
1
gravatar for Hatem Elshazly
4.1 years ago by
Egypt
Hatem Elshazly60 wrote:

Ok, Luckily I figured it out.

There is nothing wrong with the VCF file, the recal and tranches files were empty, I was mislead by the error message!

Thanks everyone.

ADD COMMENTlink written 4.1 years ago by Hatem Elshazly60

can you tell me how to solve it? I met the same question

ADD REPLYlink written 2.8 years ago by sunyanling0

In my case the recal and tranches files were empty, I was using the wrong files but this is not always the cause of this error so there may be a different reason for this error in your case but from my experience you can start with checking the validity of your input files.

ADD REPLYlink written 2.7 years ago by Hatem Elshazly60
2
gravatar for Pierre Lindenbaum
4.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:

try  '--input' instead of  '-input'

and/or

--input:myvcf,VCF fileContents.vcf

and/or

try compress and  index your vcf with bgzip+tabix

  

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Pierre Lindenbaum115k

I tried doing that and it didn't work.

Its very weird, in the log info I get this line:

INFO  14:21:11,775 ArgumentTypeDescriptor - Dynamically determined type of fileContents.vcf.gz to be VCF 

Then the error occurs.

 

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Hatem Elshazly60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1234 users visited in the last hour