I don't understand the error message I'm getting and googling it or trying different reference and input files haven't helped.
ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 0 is less than start 38566563 in contig 10
Is the error within the bam file I am trying to split reads within or the reference genome I am aligning to?
Is there any quality control or cleam up method to check if the problem lies within my bam infile? I couldn't find one but when I ran BamIndexStats on the index file of the bam I was trying to use as my infile the line about contig 10 was
10 length= 104305016 Aligned= 61 Unaligned= 3
When I look at the .fai index of my reference genome it has the line
10 104305016 4 60 61
The .dict file also has
@SQ SN:10 LN:104305016 UR:file:/home/bmoran/bin/ens70/Btau.UMD3.1.70.short.fa M5:4c1ab0477783816857a28762f7630deb
When both input and reference files are using the length 104305016 for chromosome 10 I don't understand where the start 38566563 comes from in the error.
Thank you for your help and please let me know if I should supply any more information
Emma
My command
java -Xmx3g -jar /home/bmoran/bin/gatk3.1/GenomeAnalysisTK.jar
-T SplitNCigarReads
-R /home/bmoran/bin/ens70/Btau.UMD3.1.70.short.fa
-I 526_S19_align/526_S19.sort.rmdup.rgps.bam
-o 526_S19_align/526_S19.sort.rmdup.rgps.splitN.bam
-rf ReassignMappingQuality
-DMQ 60
-U ALLOW_N_CIGAR_READS
The complete error message.
INFO 11:56:59,997 GenomeAnalysisEngine - Strictness is SILENT
INFO 11:57:00,075 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 11:57:00,087 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 11:57:00,112 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 11:57:00,192 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 11:57:00,198 GenomeAnalysisEngine - Done preparing for traversal
INFO 11:57:00,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 11:57:00,198 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining
INFO 11:57:00,227 ReadShardBalancer$1 - Loading BAM index data
INFO 11:57:00,228 ReadShardBalancer$1 - Done loading BAM index data
ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.1-1-g07a4bf8):
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 http://www.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: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 0 is less than start 38566563 in contig 10
##### ERROR ------------------------------------------------------------------------------------------