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Depth of Coverage: Only first gene summary output
I've been trying to run DOC on a sorted RefSeq Gene list downloaded from the UCSC Table Browser as described in the DOC guide doc. After sorting/formatting, only the first record in the ref seq gene list gets summarize in the foo.sample_gene_summary file. I've tried multiple one gene files and they all work individually, but when there is more than one record only the first record gets summarized. I'm using 2.2-8 (tried 2.0-25 as well) and I'm totally flabbergasted. Below is an example command line.
java -jar ./GenomeAnalysisTK-2.2-8-gec077cd/GenomeAnalysisTK.jar \ -T DepthOfCoverage \ -R human_g1k_v37_decoy.fasta \ -I in.bam \ -geneList:REFSEQ 2genes.txt \ -L 22:1615633-18714498 \ -mmq 1 \ --outputFormat table \ -o foo \ -l DEBUG
also attached is the 2genes.txt file (put it at the end as well in case there is problem with the attachment).
Below is a little bit from the logging when DEBUG is switched on (can add more if needed).
INFO 15:13:12,293 RMDTrackBuilder - Loading Tribble index from disk for file /isilon/sequencing/Kurt/Genes/2genes.txt DEBUG 15:13:12,364 DepthOfCoverage - Refseq init done. DEBUG 15:13:12,364 DepthOfCoverage - Examining 22:1615633-18714498 DEBUG 15:13:12,365 DepthOfCoverage - Annotation list is anonymous DEBUG 15:13:12,366 DepthOfCoverage - We do overlap 000 NM_001136213 22 - 16256331 16287937 16258185 16287885 11 16256331,16258184,16266928,16268136,16269872,16275206,16277747,16279194,16282144,16282477,16287253, 16256677,16258303,16267095,16268181,16269943,16275277,16277885,16279301,16282318,16282592,16287937, 0 POTEH cmpl cmpl -1,2,0,0,1,2,2,0,0,2,0, INFO 15:13:12,462 DepthOfCoverage - Printing summary info INFO 15:13:12,479 DepthOfCoverage - Printing locus summary INFO 15:13:12,772 ProgressMeter - done 1.71e+07 2.3 m 8.1 s 100.0% 2.3 m 0.0 s INFO 15:13:12,773 ProgressMeter - Total runtime 138.10 secs, 2.30 min, 0.04 hours INFO 15:13:12,928 MicroScheduler - 808 reads were filtered out during traversal out of 49775 total (1.62%) INFO 15:13:12,928 MicroScheduler - -> 607 reads (1.22% of total) failing DuplicateReadFilter INFO 15:13:12,928 MicroScheduler - -> 201 reads (0.40% of total) failing UnmappedReadFilter INFO 15:13:12,929 NSRuntimeProfile - Input time: 22.5 s (18.59%) INFO 15:13:12,929 NSRuntimeProfile - Map time: 36.2 s (29.93%) INFO 15:13:12,929 NSRuntimeProfile - Reduce time: 59.8 s (49.47%) INFO 15:13:12,929 NSRuntimeProfile - Outside time: 2.4 s ( 2.01%) DEBUG 15:13:12,931 GATKRunReport - Aggregating data for run report DEBUG 15:13:13,112 GATKRunReport - Posting report of type STANDARD 709 NM_001136213 22 - 16256331 16287937 16258185 16287885 11 16256331,16258184,16266928,16268136,16269872,16275206,16277747,16279194,16282144,16282477,16287253, 16256677,16258303,16267095,16268181,16269943, 16275277,16277885,16279301,16282318,16282592,16287937, 0 POTEH cmpl cmpl -1,2,0,0,1,2,2,0,0,2,0, 90 NM_018943 22 + 18593452 18614498 18593631 18613903 5 18593452,18604245,18606922,18609120,18613609, 18593634,18604468,18607071,18609801,18614498, 0 TUBA8 cmpl cmpl 0,0,1,0,0,
Is this just user error?