Extracting consensus calls and VCFv4.2 malformed headers

[ghost]

Greetings,

I have been trying to use seqmule with exome data acquired with illumina nextera rapid capture kit but i am having a problem while extracting consensus calls with gatk's vcfv4.2 support even though i disabled gatklite from the config file. Both error messages are below and config file is attached

Thanks for your time,

Barış

[advancedconfig.txt](https://github.com/WGLab/SeqMule/files/432271/advancedconfig.txt)

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: Calculating coverage ...
NOTICE: Start reading from SAMTools depth command ...
NOTICE: Generating Venn diagram...

----------ERROR----------
[ => SeqMule Execution Status: step 82 FAILED at Tue Aug 23 13:51:50 EEST 2016, Extract consensus calls]
ERROR: command failed
/home/bars/SeqMule/bin/secondary/../../bin/secondary/worker /media/bars/2tb/media/analysis_results/seqmule_results/exome_S2_L001_R1_001advancedconfig_nolite_2/seqmule.08152016.10324.logs 82 "/home/bars/SeqMule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -ref /home/bars/SeqMule/bin/secondary/../../database/human_g1k_v37.fasta -jmem 1750m -jexe java -t 2 -c-vcf exomedata_result/exomedata_bwamem.merge.0_gatk_hc.extract.vcf,exomedata_result/exomedata_bwamem.merge.0_freebayes.extract.vcf,exomedata_result/exomedata_bwamem.merge.0_samtools.extract.vcf,exomedata_result/exomedata_bwamem.merge.0_varscan.extract.vcf -p exomedata_result/exomedata.extract "
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd /media/bars/2tb/media/analysis_results/seqmule_results/exome_S2_L001_R1_001advancedconfig_nolite_2' and 'seqmule run exomedata.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

[yunfeiguo]

Hi Barış,

Unfortunately gatklite does not support VCF4.2. I will add support for VCF
manipulation using GATK (instead of GATKLite) assuming users can manually
install GATK.

Please stay tuned. Thanks.

Best,
Yunfei

On Tue, Aug 23, 2016 at 4:21 AM, barslmn [email protected] wrote:

Greetings,

I have been trying to use seqmule with exome data acquired with illumina
nextera rapid capture kit but i am having a problem while extracting
consensus calls with gatk's vcfv4.2 support even though i disabled gatklite
from the config file. Both error messages are below and config file is
attached

Thanks for your time,

Barış

advancedconfig.txt

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: Calculating coverage ...
NOTICE: Start reading from SAMTools depth command ...
NOTICE: Generating Venn diagram...

----------ERROR----------
[ => SeqMule Execution Status: step 82 FAILED at Tue Aug 23 13:51:50 EEST
2016, Extract consensus calls]
ERROR: command failed
/home/bars/SeqMule/bin/secondary/../../bin/secondary/worker
/media/bars/2tb/media/analysis_results/seqmule_results/exome_S2_L001_R1_
001advancedconfig_nolite_2/seqmule.08152016.10324.logs 82
"/home/bars/SeqMule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp
-ref /home/bars/SeqMule/bin/secondary/../../database/human_g1k_v37.fasta
-jmem 1750m -jexe java -t 2 -c-vcf exomedata_result/exomedata_
bwamem.merge.0_gatk_hc.extract.vcf,exomedata_result/
exomedata_bwamem.merge.0_freebayes.extract.vcf,exomedata_result/exomedata_
bwamem.merge.0_samtools.extract.vcf,exomedata_result/
exomedata_bwamem.merge.0_varscan.extract.vcf -p
exomedata_result/exomedata.extract "
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd /media/bars/2tb/media/
analysis_results/seqmule_results/exome_S2_L001_R1_001advancedconfig_nolite_2'
and 'seqmule run exomedata.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

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[aolai1211]

I use the GenomeAnalysisTK.jar version v3.7-0-gcfedb67, I get the similar error. How can I fix it?