Realigntargetcreator
Posted in Ask the GATK team | Last updated on 2013-12-03 18:03:12


Comments (9)

Dear all can anybody help me with this error while running Realigntargetcreator the run failed to pass through many filters any suggestion why

Run summary

INFO 12:07:39,628 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 12:07:39,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29 
INFO 12:07:39,631 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO 12:07:39,631 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO 12:07:39,635 HelpFormatter - Program Args: -T RealignerTargetCreator -R /home/sab/ref/human_hg19.fa -I /home/sab/pipeline/A_sorted.bam -o /home/sab/pipeline/A_sorted.IndelRealigner.intervals 
INFO 12:07:39,636 HelpFormatter - Date/Time: 2013/12/03 12:07:39 
INFO 12:07:39,636 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 12:07:39,636 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 12:07:39,697 GenomeAnalysisEngine - Strictness is SILENT 
INFO 12:07:39,789 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO 12:07:39,798 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO 12:07:39,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 
INFO 12:07:39,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO 12:07:40,400 GenomeAnalysisEngine - Done preparing for traversal 
INFO 12:07:40,400 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO 12:07:40,401 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining 
INFO 12:08:10,406 ProgressMeter - chr1:85262337 8.53e+07 30.0 s 0.0 s 2.8% 18.2 m 17.7 m 
INFO 12:08:40,407 ProgressMeter - chr1:180404225 1.80e+08 60.0 s 0.0 s 5.8% 17.2 m 16.2 m 
INFO 12:09:10,409 ProgressMeter - chr2:26489345 2.76e+08 90.0 s 0.0 s 8.9% 16.8 m 15.3 m 
INFO 12:09:40,413 ProgressMeter - chr2:126159101 3.75e+08 120.0 s 0.0 s 12.1% 16.5 m 14.5 m 
INFO 12:10:10,415 ProgressMeter - chr2:226503317 4.76e+08 2.5 m 0.0 s 15.4% 16.3 m 13.8 m 
INFO 12:10:40,417 ProgressMeter - chr3:79985305 5.72e+08 3.0 m 0.0 s 18.5% 16.2 m 13.2 m 
INFO 12:11:10,418 ProgressMeter - chr3:178616501 6.71e+08 3.5 m 0.0 s 21.7% 16.1 m 12.6 m 
INFO 12:11:40,424 ProgressMeter - chr4:82438805 7.73e+08 4.0 m 0.0 s 25.0% 16.0 m 12.0 m 
INFO 12:12:10,426 ProgressMeter - chr4:190799281 8.81e+08 4.5 m 0.0 s 28.5% 15.8 m 11.3 m 
INFO 12:12:40,427 ProgressMeter - chr5:95948005 9.78e+08 5.0 m 0.0 s 31.6% 15.8 m 10.8 m 
INFO 12:13:10,429 ProgressMeter - chr6:6479181 1.07e+09 5.5 m 0.0 s 34.5% 15.9 m 10.4 m 
INFO 12:13:40,430 ProgressMeter - chr6:92259205 1.15e+09 6.0 m 0.0 s 37.3% 16.1 m 10.1 m 
INFO 12:14:10,432 ProgressMeter - chr7:12978229 1.25e+09 6.5 m 0.0 s 40.3% 16.1 m 9.6 m 
INFO 12:14:40,433 ProgressMeter - chr7:102060237 1.34e+09 7.0 m 0.0 s 43.1% 16.2 m 9.2 m 
INFO 12:15:10,435 ProgressMeter - chr8:37320269 1.43e+09 7.5 m 0.0 s 46.2% 16.2 m 8.7 m 
INFO 12:15:40,436 ProgressMeter - chr8:134665297 1.53e+09 8.0 m 0.0 s 49.3% 16.2 m 8.2 m 
INFO 12:16:10,437 ProgressMeter - chr9:94340989 1.63e+09 8.5 m 0.0 s 52.8% 16.1 m 7.6 m 
INFO 12:16:40,439 ProgressMeter - chr10:51925797 1.73e+09 9.0 m 0.0 s 56.0% 16.1 m 7.1 m 
INFO 12:17:10,440 ProgressMeter - chr11:10504845 1.83e+09 9.5 m 0.0 s 59.0% 16.1 m 6.6 m 
INFO 12:17:40,442 ProgressMeter - chr11:102575141 1.92e+09 10.0 m 0.0 s 62.0% 16.1 m 6.1 m 
INFO 12:18:10,443 ProgressMeter - chr12:60381241 2.01e+09 10.5 m 0.0 s 65.0% 16.2 m 5.7 m 
INFO 12:18:40,445 ProgressMeter - chr13:27611641 2.11e+09 11.0 m 0.0 s 68.2% 16.1 m 5.1 m 
INFO 12:19:10,446 ProgressMeter - chr14:15346101 2.20e+09 11.5 m 0.0 s 71.6% 16.1 m 4.6 m 
INFO 12:19:40,456 ProgressMeter - chr15:9565601 2.31e+09 12.0 m 0.0 s 74.8% 16.0 m 4.0 m 
INFO 12:20:10,457 ProgressMeter - chr16:5380553 2.42e+09 12.5 m 0.0 s 78.0% 16.0 m 3.5 m 
INFO 12:20:40,459 ProgressMeter - chr17:7484705 2.51e+09 13.0 m 0.0 s 81.0% 16.0 m 3.0 m 
INFO 12:21:10,460 ProgressMeter - chr18:12533677 2.59e+09 13.5 m 0.0 s 83.8% 16.1 m 2.6 m 
INFO 12:21:40,462 ProgressMeter - chr19:34306113 2.69e+09 14.0 m 0.0 s 87.0% 16.1 m 2.1 m 
INFO 12:22:10,463 ProgressMeter - chr20:55319685 2.77e+09 14.5 m 0.0 s 89.6% 16.2 m 100.0 s 
INFO 12:22:40,465 ProgressMeter - chr22:41605677 2.87e+09 15.0 m 0.0 s 92.8% 16.2 m 70.0 s 
INFO 12:23:10,466 ProgressMeter - chrX:84912589 2.97e+09 15.5 m 0.0 s 95.8% 16.2 m 40.0 s 
INFO 12:23:40,468 ProgressMeter - chrY:30850957 3.07e+09 16.0 m 0.0 s 99.1% 16.1 m 8.0 s 
INFO 12:23:47,504 ProgressMeter - done 3.10e+09 16.1 m 0.0 s 100.0% 16.1 m 0.0 s 
INFO 12:23:47,505 ProgressMeter - Total runtime 967.10 secs, 16.12 min, 0.27 hours 
INFO 12:23:47,591 MicroScheduler - 1390162 reads were filtered out during the traversal out of approximately 5682566 total reads (24.46%) 
INFO 12:23:47,591 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter 
INFO 12:23:47,592 MicroScheduler - -> 51548 reads (0.91% of total) failing BadMateFilter 
INFO 12:23:47,592 MicroScheduler - -> 352814 reads (6.21% of total) failing DuplicateReadFilter 
INFO 12:23:47,592 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter 
INFO 12:23:47,592 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO 12:23:47,592 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter 
INFO 12:23:47,592 MicroScheduler - -> 985800 reads (17.35% of total) failing MappingQualityZeroFilter 
INFO 12:23:47,593 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter 
INFO 12:23:47,593 MicroScheduler - -> 0 reads (0.00% of total) failing Platform454Filter 
INFO 12:23:47,593 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter 
INFO 12:23:49,381 GATKRunReport - Uploaded run statistics report to AWS S3

Regards


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