ReduceReads very Slow for MT Reads
Posted in Ask the GATK team | Last updated on 2013-02-01 13:03:47


Comments (3)

ReduceReads is very slow for MT reads. After it gets by the MT, it runs much faster (See output below)

Any ideas why and what to do to speed it up?

John

INFO 23:32:37,536 HelpFormatter - --------------------------------------------------------------------------------- INFO 23:32:37,545 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-16-g9f648cb, Compiled 2012/12/04 03:46:58 INFO 23:32:37,545 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 23:32:37,545 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 23:32:37,551 HelpFormatter - Program Args: -R /unprotected/projects/genetics_program/resources/gatk_bundle/hg19/ucsc.hg19.fasta -T ReduceReads -I bam/LP6005113-DNA_E01.recal.bam -o LP6005113- DNA_E01.reduced.bam INFO 23:32:37,551 HelpFormatter - Date/Time: 2013/01/28 23:32:37 INFO 23:32:37,551 HelpFormatter - --------------------------------------------------------------------------------- INFO 23:32:37,551 HelpFormatter - --------------------------------------------------------------------------------- INFO 23:32:37,605 GenomeAnalysisEngine - Strictness is SILENT INFO 23:32:37,984 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 23:32:37,992 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 23:32:38,073 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08 INFO 23:32:38,113 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 23:32:38,114 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 23:33:14,010 ProgressMeter - chrM:1992 4.00e+04 35.9 s 15.0 m 0.0% 93.5 w 93.5 w INFO 23:35:18,038 ProgressMeter - chrM:2879 6.00e+04 2.7 m 44.4 m 0.0% 288.2 w 288.2 w INFO 23:37:06,320 ProgressMeter - chrM:3259 7.00e+04 4.5 m 63.9 m 0.0% 427.0 w 427.0 w INFO 23:39:03,457 ProgressMeter - chrM:3662 8.00e+04 6.4 m 80.3 m 0.0% 546.0 w 546.0 w INFO 23:41:16,174 ProgressMeter - chrM:4087 9.00e+04 8.6 m 95.9 m 0.0% 657.7 w 657.7 w INFO 23:43:46,243 ProgressMeter - chrM:4550 1.00e+05 11.1 m 111.3 m 0.0% 761.8 w 761.8 w INFO 23:46:47,501 ProgressMeter - chrM:4973 1.10e+05 14.2 m 2.1 h 0.0% 886.1 w 886.1 w INFO 23:49:57,085 ProgressMeter - chrM:5379 1.20e+05 17.3 m 2.4 h 0.0% 1002.1 w 1002.1 w INFO 23:52:52,173 ProgressMeter - chrM:5823 1.30e+05 20.2 m 2.6 h 0.0% 1081.7 w 1081.7 w INFO 23:54:28,697 ProgressMeter - chrM:7492 1.70e+05 21.8 m 2.1 h 0.0% 907.5 w 907.5 w INFO 23:55:45,484 ProgressMeter - chrM:7883 1.80e+05 23.1 m 2.1 h 0.0% 913.0 w 913.0 w INFO 23:57:16,597 ProgressMeter - chrM:8305 1.90e+05 24.6 m 2.2 h 0.0% 923.5 w 923.5 w INFO 23:59:07,109 ProgressMeter - chrM:8731 2.00e+05 26.5 m 2.2 h 0.0% 944.1 w 944.1 w INFO 00:01:16,623 ProgressMeter - chrM:9124 2.10e+05 28.6 m 2.3 h 0.0% 977.1 w 977.1 w INFO 00:04:12,150 ProgressMeter - chrM:9526 2.20e+05 31.6 m 2.4 h 0.0% 1031.4 w 1031.4 w INFO 00:06:51,054 ProgressMeter - chrM:9896 2.30e+05 34.2 m 2.5 h 0.0% 1076.2 w 1076.2 w INFO 00:09:31,477 ProgressMeter - chrM:10244 2.40e+05 36.9 m 2.6 h 0.0% 1120.9 w 1120.9 w INFO 00:12:57,847 ProgressMeter - chrM:10626 2.50e+05 40.3 m 2.7 h 0.0% 1181.3 w 1181.3 w INFO 00:16:48,872 ProgressMeter - chrM:11139 2.60e+05 44.2 m 2.8 h 0.0% 1234.5 w 1234.5 w INFO 00:20:54,282 ProgressMeter - chrM:11634 2.70e+05 48.3 m 3.0 h 0.0% 1291.4 w 1291.4 w INFO 00:25:23,381 ProgressMeter - chrM:12098 2.80e+05 52.8 m 3.1 h 0.0% 1357.2 w 1357.2 w INFO 00:30:01,695 ProgressMeter - chrM:12464 2.90e+05 57.4 m 3.3 h 0.0% 1433.2 w 1433.2 w INFO 00:34:41,008 ProgressMeter - chrM:12805 3.00e+05 62.0 m 3.4 h 0.0% 1508.2 w 1508.2 w INFO 00:39:41,462 ProgressMeter - chrM:13307 3.10e+05 67.1 m 3.6 h 0.0% 1568.4 w 1568.4 w INFO 00:45:21,827 ProgressMeter - chrM:13764 3.20e+05 72.7 m 3.8 h 0.0% 1644.6 w 1644.6 w INFO 00:51:15,645 ProgressMeter - chrM:14173 3.30e+05 78.6 m 4.0 h 0.0% 1726.7 w 1726.7 w INFO 00:57:38,039 ProgressMeter - chrM:14639 3.40e+05 85.0 m 4.2 h 0.0% 1807.2 w 1807.2 w INFO 01:06:06,413 ProgressMeter - chrM:15067 3.50e+05 93.5 m 4.5 h 0.0% 1930.9 w 1930.9 w INFO 01:15:07,742 ProgressMeter - chrM:15463 3.60e+05 102.5 m 4.7 h 0.0% 2063.0 w 2063.0 w INFO 01:23:17,067 ProgressMeter - chrM:15827 3.70e+05 110.6 m 5.0 h 0.0% 2176.0 w 2176.0 w INFO 01:31:08,225 ProgressMeter - chrM:16237 3.80e+05 118.5 m 5.2 h 0.0% 2271.6 w 2271.5 w INFO 01:32:08,631 ProgressMeter - chr1:3000534 1.17e+06 119.5 m 102.5 m 0.1% 12.3 w 12.3 w INFO 01:33:09,058 ProgressMeter - chr1:5169965 1.91e+06 2.0 h 63.2 m 0.2% 7.2 w 7.2 w INFO 01:34:09,530 ProgressMeter - chr1:7090404 2.65e+06 2.0 h 45.9 m 0.2% 5.3 w 5.3 w INFO 01:35:10,334 ProgressMeter - chr1:8806475 3.32e+06 2.0 h 37.0 m 0.3% 4.3 w 4.3 w INFO 01:36:10,654 ProgressMeter - chr1:10887467 4.08e+06 2.1 h 30.3 m 0.3% 3.5 w 3.5 w INFO 01:37:10,892 ProgressMeter - chr1:12756332 4.77e+06 2.1 h 26.1 m 0.4% 3.0 w 3.0 w INFO 01:38:11,087 ProgressMeter - chr1:14746000 5.29e+06 2.1 h 23.8 m 0.5% 18.5 d 18.4 d INFO 01:39:11,327 ProgressMeter - chr1:16699493 6.02e+06 2.1 h 21.0 m 0.5% 16.5 d 16.4 d INFO 01:40:11,606 ProgressMeter - chr1:18706430 6.86e+06 2.1 h 18.6 m 0.6% 14.8 d 14.8 d


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