Unable to use IndelRealigner after pre-processing steps.
Coryza
EnschedeMember ✭
Hi. I'm unable to use the IndelRealigner java jar. My previous steps were;
1) Convert Bowtie2 paired-end Illumina Reads .sam to .bam
2) Use bedtools to extract pairs that fall within the Hg19 exome.
3) Convert the new .bam to .sam
4) Sort the new .sam via SortSam.jar
5) Mark duplicates via MarkDuplicates.jar
6) Use AddOrReplaceReadGroups.jar
7 ) Use ReorderSam.jar
8) Use RealignerTargetCreator
Untill this far everything went well. Now I'm trying the following command; java -jar GenomeAnalysisTK.jar -T IndelRealigner -R [.fasta] -l [ReorderedSam.bam] -targetIntervals [aligner.intervals] -o output.bam (Also when applying -known and an .vcf file Im producing the same error):
ERROR MESSAGE: Unable to match: GATK_7-PicardReorderSam.bam to a logging level, make sure it's a valid level (DEBUG, INFO, WARN, ERROR, FATAL, OFF)
I hope you can help me, because I can't find anything related on google.
Best Answers
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thibault
Broad Institute ✭✭
Make sure that the argument -I you're using is the capital letter I (Input), instead of the lowercase letter l (logging level).
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Geraldine_VdAuwera
Cambridge, MA admin
Ah, there you go -- @thibault meant you should use "I" as in capital of the letter "i", not "L".
Answers
Make sure that the argument -I you're using is the capital letter I (Input), instead of the lowercase letter l (logging level).
Omg I love you. However this throws a new error; ##### ERROR MESSAGE: Walker requires reads but none were provided.
Sounds like a typo crept in when you made the correction -- if you don't see it, post the full log output and we'll have a look.
Command:
java -jar [path to GenomeAnalysisTK.jar] -T IndelRealigner -R [path to hg19.fasta] -L GATK_7-PicardReorderSam.bam -targetIntervals G
ATK_8-GenomeAnalysisTKRealignerTargetCreator.intervals -o realigned.bam
Error:
INFO 22:00:07,009 HelpFormatter - Executing as . on Windows
7 6.1 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_55-b13.
INFO 22:00:07,009 HelpFormatter - Date/Time: 2014/04/17 22:00:06
INFO 22:00:07,010 HelpFormatter - ---------------------------------------------
-----------------------------------
INFO 22:00:07,010 HelpFormatter - ---------------------------------------------
-----------------------------------
INFO 22:00:07,405 GenomeAnalysisEngine - Strictness is SILENT
INFO 22:00:09,921 GATKRunReport - Uploaded run statistics report to AWS S3
##### 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 docum
entation guide
##### ERROR (or rerun your command with --help) to view allowable command-line a
rguments 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 real
ly tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Walker requires reads but none were provided.
##### ERROR --------------------------------------------------------------------
----------------------
Ah, there you go -- @thibault meant you should use "I" as in capital of the letter "i", not "L".
Ahw Sorry again for my mistakes... Its late in the evening here, after a hard working week.. so my apologies! Thanks a lot for the quick answers / help
Koen