Question: seqmule gatk vcfv4.2 error
0
gravatar for bioinformatics98
4 days ago by
bioinformatics980 wrote:

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'
seqmule vcf • 74 views
ADD COMMENTlink modified 3 days ago • written 4 days ago by bioinformatics980

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

ADD REPLYlink written 4 days ago by Asaf6.9k

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

ADD REPLYlink written 3 days ago by bioinformatics980

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

ADD REPLYlink written 3 days ago by bioinformatics980

change the pipeline......

ADD REPLYlink written 3 days ago by Pierre Lindenbaum126k
1
gravatar for Pierre Lindenbaum
4 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

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

ADD COMMENTlink modified 4 days ago • written 4 days ago by Pierre Lindenbaum126k

gatk 2.3.9 is ~ 8 years old....

ADD REPLYlink written 4 days ago by Pierre Lindenbaum126k

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?

ADD REPLYlink modified 3 days ago • written 3 days ago by bioinformatics980
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: 1154 users visited in the last hour