Holiday Notice:
The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!

Bad PED line 1: wrong number of fields in PED files in PhaseByTransmission

Hello,

when using the PhaseByTransmission I always get this error:

ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/pub/yuanjian/software_script/GATK-3.8/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO 02:32:46,897 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 02:32:46,897 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 02:32:46,898 GenomeAnalysisEngine - Strictness is SILENT
INFO 02:32:46,989 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 02:32:47,058 PedReader - Reading PED file output.vcf2plink.ped with missing fields: []

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.8-0-ge9d806836):
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 https://software.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: File associated with name [email protected] is malformed: Bad PED line 1: wrong number of fields
ERROR ------------------------------------------------------------------------------------------

my command is:
java -jar /pub/yuanjian/software_script/GATK-3.8/GenomeAnalysisTK.jar -T PhaseByTransmission -R /pub/yuanjian/reference/human_g1k_v37.fasta -V output.vcf -ped output.vcf2plink.ped -o file.vcf

I use plink to convert a vcf file to a ped file,and my ped file is:

GENOTYPE.437 GENOTYPE.437 0 0 0 0 0 0 0 0 A A 0 0 C C G G C C A A 0 0 0 0 C T 0 0 0 0
GENOTYPE.430 GENOTYPE.430 0 0 0 0 0 0 0 0 A A C T C C G G C C A A 0 0 G A T T C G A
GENOTYPE.450 GENOTYPE.450 0 0 0 0 G G G G A A 0 0 C C G G C C A A C G 0 0 0 0 0 0 0 0

So what's wrong with my ped file?

Answers

Sign In or Register to comment.