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I have been trying to run the following command for Queue.jar. But its not compiling properly.

ankurc_17ankurc_17 SingaporeMember

Command:

java -jar Queue-3.4-46/Queue.jar -S call_hs_snps.scala -R human_g1k_v37_decoy.fasta -D dbsnp_138.b37.vcf -H hapmap_3.3.b37.vcf -O 1000G_omni2.5.b37.vcf -T 1000G_phase1.snps.high_confidence.b37.vcf -M Mills_and_1000G_gold_standard.indels.b37.vcf -o output_gatk/ -P pedigree.txt -E 1 -F 1 -C 1 -jobRunner ParallelShell -jobReport call_hs_snps.jobreport.txt -resMemLimit 3 -memLimit 2.00000000000000000000 --maximumNumberOfJobsToRunConcurrently 1 -I ERR1025650/alignments/splitters.bam

Error:
INFO 11:35:23,449 QScriptManager - Compiling 1 QScript
ERROR 11:35:27,463 QScriptManager - call_hs_snps.scala:147: value dbsnp is not a member of org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with pipeline.this.CommonArguments
ERROR 11:35:27,481 QScriptManager - combine.dbsnp = dbSnp
ERROR 11:35:27,483 QScriptManager - ^
ERROR 11:35:28,240 QScriptManager - two errors found

Could you please help in this issue?

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by Sheila

Issue Number
2143
State
open
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