The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

RealignerTargetCreator error with -o

rossinrossin BroadMember Posts: 1

Hi,

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/1373342599.1240274.shell: 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

Answers

Sign In or Register to comment.