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RealignerTargetCreator error with -o


I am currently running GATK-2.6.4 with Java-1.7. I am trying to run RTC. It seems to get almost to the end and then I get the following error which I believe is referring to the -o argument:

INFO 06:12:01,578 ProgressMeter - done 3.10e+09 92.2 m 1.0 s 100.0% 92.2 m 0.0 s
INFO 06:12:01,578 ProgressMeter - Total runtime 5530.95 secs, 92.18 min, 1.54 hours
INFO 06:12:01,580 MicroScheduler - 40 reads were filtered out during the traversal out of approximately 112022776 total reads (0.00%)
INFO 06:12:01,581 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 06:12:01,582 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter
INFO 06:12:01,583 MicroScheduler - -> 8 reads (0.00% of total) failing DuplicateReadFilter
INFO 06:12:01,583 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 06:12:01,584 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 06:12:01,584 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 06:12:01,585 MicroScheduler - -> 32 reads (0.00% of total) failing MappingQualityZeroFilter
INFO 06:12:01,585 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 06:12:01,586 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter
INFO 06:12:01,586 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
INFO 06:12:02,411 GATKRunReport - Uploaded run statistics report to AWS S3
/local/scratch/ line 7: -o: command not found

My RTC command is as follows:

java -Xmx2g -jar GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-R human_g1k_v37.fasta \
-I aln.sorted.rg.markdup.bam
-o forIndelRealigner.intervals \
-known 1000G_phase1.indels.b37.vcf \
-known Mills_and_1000G_gold_standard.indels.b37.sites.vcf \

Is there a new way to specify an outfile in this version of GATK?

Thanks very much!

Best Answer


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