seqmule gatk vcfv4.2 error

Question

[bioinformatics98]

Hi,

I am getting this error -- and help will be much appreciated! Thank you!

WARN 11:52:36,188 RestStorageService - Error Response: PUT '/GATK_Run_Reports/8Mxwpij5zPxCjkgJ3V61ne1iu4GHg824.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 837, Content-MD5: rZhKS6PEdFc2j38JlwBclw==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: ad984a4ba3c47457368f7f0997005c97, Date: Wed, 12 Feb 2020 16:52:35 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:CulSrrbUlQFgV3kMDH6nuzdLmMA=, User-Agent: JetS3t/0.8.1 (Linux/3.10.0-957.5.1.el7.x86_64; amd64; en; JVM 1.7.0_131), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 85D1808723FEFB7C, x-amz-id-2: MbhZr/Wps5nz29A2wW4MjCbbYUrNy8F7CG4HlwIVxbyAZE3pcfuGch61ktRNz3+19QgFYpYVHfw=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Wed, 12 Feb 2020 16:52:35 GMT, Connection: close, Server: AmazonS3]

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Your input file has a malformed header: VCFv4.2 is not a supported version
##### ERROR ------------------------------------------------------------------------------------------
ERROR: Failed to split VCF by sample
NOTICE: Cleaning...
NOTICE: VennDiagram not installed, now try to install it.
inferring 'repos = NULL' from 'pkgs'

[Asaf]

What was the command line? How does the input look like?

[bioinformatics98]

Here you go:

JOBID=0 PID=1863 command=/home/CSTR/user/softwares/seqmule/bin/secondary/../../bin/secondary/worker /home/CSTR/user/data/sample/seqmule.02092020.57459.logs 31 "/home/CSTR/user/softwares/seqmule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -ref /home/FCAM/CSTR/user/softwares/seqmule/bin/secondary/../../database/human_g1k_v37.fasta -jmem 1750m -jexe java -t 2 -c-vcf Sample_result/Sample_bwamem.merge.realn.recal.0_gatk_hc.extract.vcf,Sample_result/Sample_bwamem.merge.recal.0_gatk_hc.extract.vcf -p Sample_result/Sample.extract " dependency=29,30 message=Extract consensus calls nCPU_requested=1 status=error

[bioinformatics98]

The pipeline is requiring me to use GATKlite -- is there a way I can force it to use GATK instead?

[Pierre Lindenbaum]

change the pipeline......

Answer 1

[Pierre Lindenbaum]

the error is clear. The vcf version is not supported. Your gatk is far too old. New version is 4.*.*

MESSAGE: Your input file has a malformed header: VCFv4.2 is not a supported version

[Pierre Lindenbaum]

gatk 2.3.9 is ~ 8 years old....

[bioinformatics98]

Ah! Thank you so much! The pipeline is requiring me to use GATKlite (v.2.3-9) -- is there a way I can force it to use GATK instead?