error in step 7 with GenomeAnalysisTKLite.jar

[yeroslaviz]

When running seqMule with mouse genome, I get he following error in step 7

----------NOTICE----------
[ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at Tue Mar 10 11:00:43 CET 2020, Time Elapsed: 1 hr 27 min 0 s]
[ => SeqMule Execution Status: step 6 is finished at Tue Mar 10 11:00:43 CET 2020, Filter BAM file by mapping quality]

INFO  11:00:46,450 ArgumentTypeDescriptor - Dynamically determined type of /local/Assa/projects/Guru/WES_b2m/SeqMule/S0276129_Covered.bed to be BED
INFO  11:00:46,471 HelpFormatter - --------------------------------------------------------------------------------
INFO  11:00:46,471 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2013/01/11 20:03:13
INFO  11:00:46,471 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  11:00:46,471 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  11:00:46,474 HelpFormatter - Program Args: -T RealignerTargetCreator -I Sample1_result/Sample1.0_bwamem.sort.rmdup.readfiltered.bam -R /home/yeroslaviz/software/SeqMule/database/bwa/Mmu.GrCm38.fa -o /tmp/15584.9712444046.tmp.intervals -L /local/Assa/projects/Guru/WES_b2m/SeqMule/S0276129_Covered.bed
INFO  11:00:46,474 HelpFormatter - Date/Time: 2020/03/10 11:00:46
INFO  11:00:46,474 HelpFormatter - --------------------------------------------------------------------------------
INFO  11:00:46,475 HelpFormatter - --------------------------------------------------------------------------------
INFO  11:00:46,480 GenomeAnalysisEngine - Strictness is SILENT
INFO  11:00:46,581 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000, Using the new downsampling implementation
INFO  11:00:46,589 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO  11:00:46,605 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO  11:00:48,871 GenomeAnalysisEngine - Processing 49388818 bp from intervals
INFO  11:00:48,902 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  11:00:48,903 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
WARN  11:01:08,015 RestStorageService - Error Response: PUT '/GATK_Run_Reports/1Cf79xsY0eGOUAg8GJNRJjvLO4w4ZTUR.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 916, Content-MD5: qL2zdd2S3r3mOCE1gv5pSA==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: a8bdb375dd92debde638213582fe6948, Date: Tue, 10 Mar 2020 10:01:07 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:U5pT8WTf0Hdl3rnXrhFrTOorelg=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-72-generic; amd64; en; JVM 1.7.0_67), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 03898E3E59EE6002, x-amz-id-2: 3hg25dxyfiJ7DCDMKlg7aoz+KlbiRdoPJbl+TXXuhJIi2rOVoROkruqa8jds6lurNAQmdK0C5Rk=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Tue, 10 Mar 2020 10:07:32 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: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 195471971 is less than start 196469947 in contig 1
##### ERROR ------------------------------------------------------------------------------------------


----------ERROR----------
[ => SeqMule Execution Status: step 7 FAILED at Tue Mar 10 11:01:09 CET 2020, gatklite realn]
ERROR: command failed
/local/Assa/software/SeqMule/bin/secondary/../../bin/secondary/worker /home/yeroslaviz/projects/Guru/WES_b2m/SeqMule/seqmule.03102020.20785.logs 7 "/local/Assa/software/SeqMule/bin/secondary/../../bin/secondary/runGATKLITEREALN -advanced Sample1.config -n 6 -ref /home/yeroslaviz/software/SeqMule/database/bwa/Mmu.GrCm38.fa -java java -jmem 1750m -gatk /local/Assa/software/SeqMule/exe/gatklite/GenomeAnalysisTKLite.jar -threads 10 -gatk-nt 8 -tmpdir /tmp  -bed /local/Assa/projects/Guru/WES_b2m/SeqMule/S0276129_Covered.bed -goldindel /home/yeroslaviz/software/SeqMule/database/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz  -dbsnp /home/yeroslaviz/software/SeqMule/database/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.md5  -samtools /local/Assa/software/SeqMule/exe/samtools/samtools  -pl ILLUMINA  -bam Sample1_result/Sample1.0_bwamem.sort.rmdup.readfiltered.bam -out Sample1_result/Sample1.0_bwamem.sort.rmdup.readfiltered.realn.bam "
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd /home/yeroslaviz/projects/Guru/WES_b2m/SeqMule' and 'seqmule run Sample1.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Is there any explanation for that?

Is there a way to run seqmule without the gatk-steps? Can I just delete it from the Sample1.script?

thanks

[yunfeiguo]

Hi @yeroslaviz GATK complains

 MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 195471971 is less than start 196469947 in contig 1

Can you check relevant lines in your /local/Assa/projects/Guru/WES_b2m/SeqMule/S0276129_Covered.bed?

It's possible to turn off GATK, need to set all GATK callers to 0, e.g. 8p_gatklite_variant=0 in the config file. See https://github.com/WGLab/SeqMule/blob/7a46f27930d2cdc17665963df04f76043d8b4750/doc/Tutorials/Analysis.md#change-pipeline-change-advanced_config for more details.