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Interval File Errors
I'm been having a lot of trouble with the format for the interval file input to GATK. I've gotten 3 different errors from different versions of interval files that I've tried. It would be really helpful to get some pointers for where I might be going wrong.
Error 1. Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: @HD VN:1.0 SO:coordinate
The file that I was using for this is hg19.list.txt (when I run the tool, the file extension is .list, but the forum wouldn't let me upload it). MuTect has been fine running with an example file that I pulled off of the ftp site (hg19examplelist.txt), but when I compare both files, I don't see a major difference in the format. To create hg19.list.txt I followed the directions from the FAQ and pulled the header information from my reference dict file and added my intervals. MuTect returns Error 1 with hg19examplelist.txt, but not hg19list.txt.
Error 2. INFO 15:33:54,965 GenomeAnalysisEngine - Processing 0 bp from intervals
WARN 15:33:54,967 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process.
INFO 15:33:54,981 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:33:54,982 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 15:33:55,032 Walker - [REDUCE RESULT] Traversal result is: 0
INFO 15:33:55,034 ProgressMeter - done 0.00e+00 0.1 s 14.3 h 0.0% Infinity w Infinity w
INFO 15:33:55,034 ProgressMeter - Total runtime 0.05 secs, 0.00 min, 0.00 hours
INFO 15:33:56,851 GATKRunReport - Uploaded run statistics report to AWS S3
I've mostly gotten this error when I tried to run the intervals information in bed format. After seeing this, I'm thinking that I might be misunderstanding what the interval file is for, even after looking at both FAQs. Are these the intervals that MuTect will be looking at or something generated from the sequencing process? If it helps any, I did not create these bam files, they are from someone else in my lab.
- Comparison method violates its general contract!
I'm running java 1.7 (this error does not always show up). It would be helpful to know why this might occur with some .list files and not others.
Thank you for any help that you can provide!