Failed to find GenomeAnalysisTKLite.jar file

Question

[bioinformatics98]

Hi everyone,

I am trying to run the seqmule pipeline without GATKLite (I want the pipeline to use the full GATK instead) -- I have already removed any command asking for gatklite in the advanced config file of seqmule, however I keep getting this error:

[ => SeqMule Execution Status: Running 33 of 37 steps: Generate alignment and coverage stat, at Mon Feb 17 11:38:07 CST 2020, Time Elapsed: 0 hr 0 min 3 s]
Current version: 1.2.6
Check for upgrade ...
NOTICE: This is the latest version!
NOTICE: normalzing VCF with Vt...
NOTICE: Calculating coverage for Sample_result/Sample_bwamem.merge.bam. This takes a while
NOTICE: checking contig(chromosome) name consistency in /home/CLSR/user2/softwares/SeqMule/database/hg19/hg19_Exon.bed and Sample_result/Sample_bwamem.merge.bam.
ERROR: Failed to find GenomeAnalysisTKLite.jar.

I do not understand why it keeps asking for the GenomeAnalysisTKLite.jar file -- any help will be much appreciated! Thanks!

[ATpoint]

I want the pipeline to use the full GATK instead

Ok, but how do you tell the pipeline to do that? If that GenomeAnalysisTKLite.jar is hardcoded inside that pipeline somewhere in the source code then of course the pipeline keeps asking for it. is this documented what you do, so an official way of modifying the pipeline or are you doing custom things? Also please add relevant code / command lines.