"SimpleTimer " when using "HaplotypeCaller"

wubinwubin ChinaMember

"SimpleTimer " when using "HaplotypeCaller"

I'm running the "HaplotypeCaller" by each chromosome(wgs data, human). generally, it takes a couple of hours for each chromosome.however, it costed too long for some chromosomes.
in the standard error log file, we can see:
"WARN 03:28:54,316 SimpleTimer - Clock drift of -1,440,383,149,496,872,229 - -1,440,383,142,207,201,586 = 7,289,670,643 nanoseconds detected, vs. max allowable drift of 5,000,000,000. Assuming checkpoint/restart event. "

we can also see that the log file infered it would take more than 50 hours to finish. how can I solve this problem?

my Command Prompt is as follows:

java -Xmx10g -Djava.io.tmpdir=pwd/tmp \
-jar ./GATK/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-nct 5 \
-R ./hg19/ucsc.hg19.fasta \
-I ./chr14.output.recal.cleaned.bam \
--dbsnp ./Data/dbsnp_138.hg19.excluding_sites_after_129.vcf \
--emitRefConfidence GVCF \
--variant_index_type LINEAR \
--variant_index_parameter 128000 \
-o ./chr14.SNP_Indel_HaplotypeCaller.g.vcf

==========================================================================================

the log file:

INFO 22:51:19,251 ProgressMeter - chr1:29466701 16571.0 30.0 s 30.7 m 0.9% 53.2 m 52.7 m
INFO 22:52:24,821 ProgressMeter - chr1:43229721 16571.0 96.0 s 96.6 m 1.4% 116.1 m 114.5 m
INFO 22:52:55,453 ProgressMeter - chr1:68908783 16571.0 2.1 m 2.1 h 2.2% 95.6 m 93.5 m
INFO 22:53:25,999 ProgressMeter - chr1:95292401 16571.0 2.6 m 2.6 h 3.0% 86.1 m 83.5 m
INFO 22:53:56,327 ProgressMeter - chr1:115804951 16571.0 3.1 m 3.1 h 3.7% 84.4 m 81.3 m
INFO 22:54:26,570 ProgressMeter - chr1:144636753 16571.0 3.6 m 3.7 h 4.6% 78.4 m 74.8 m
INFO 22:54:57,663 ProgressMeter - chr1:157892015 16571.0 4.1 m 4.2 h 5.0% 82.1 m 78.0 m
INFO 22:55:27,690 ProgressMeter - chr1:178923101 16571.0 4.6 m 4.7 h 5.7% 81.2 m 76.6 m
INFO 22:55:58,227 ProgressMeter - chr1:201554018 16571.0 5.2 m 5.2 h 6.4% 80.2 m 75.0 m
INFO 22:56:29,745 ProgressMeter - chr1:220739801 16571.0 5.7 m 5.7 h 7.0% 80.5 m 74.9 m
INFO 22:57:00,816 ProgressMeter - chr1:238406801 16571.0 6.2 m 6.2 h 7.6% 81.6 m 75.4 m
INFO 22:57:32,256 ProgressMeter - chr2:358222 2.49267192E8 6.7 m 1.0 s 8.0% 84.4 m 77.7 m
INFO 22:58:08,580 ProgressMeter - chr2:4971401 2.49267192E8 7.3 m 1.0 s 8.1% 90.3 m 83.0 m
INFO 22:58:43,845 ProgressMeter - chr2:6290112 2.49267192E8 7.9 m 1.0 s 8.1% 97.2 m 89.3 m
INFO 22:59:18,423 ProgressMeter - chr2:8081200 2.49267192E8 8.5 m 2.0 s 8.2% 103.4 m 94.9 m
INFO 22:59:55,374 ProgressMeter - chr2:9351582 2.49267192E8 9.1 m 2.0 s 8.2% 110.4 m 101.3 m
INFO 23:00:31,578 ProgressMeter - chr2:9918701 2.49267192E8 9.7 m 2.0 s 8.3% 117.4 m 107.7 m
INFO 23:01:03,321 ProgressMeter - chr2:15790519 2.49267192E8 10.2 m 2.0 s 8.4% 2.0 h 110.9 m
INFO 23:01:33,862 ProgressMeter - chr2:37830100 2.49267192E8 10.8 m 2.0 s 9.2% 117.5 m 106.7 m
INFO 23:02:04,893 ProgressMeter - chr2:55471903 2.49267192E8 11.3 m 2.0 s 9.7% 116.0 m 104.7 m
INFO 23:02:35,001 ProgressMeter - chr2:77596236 2.49267192E8 11.8 m 2.0 s 10.4% 112.9 m 101.2 m
INFO 23:03:05,295 ProgressMeter - chr2:100354601 2.49267192E8 12.3 m 2.0 s 11.1% 110.1 m 97.8 m
INFO 23:03:36,053 ProgressMeter - chr2:126084979 2.49267192E8 12.8 m 3.0 s 12.0% 106.8 m 94.1 m
INFO 23:04:07,866 ProgressMeter - chr2:146356001 2.49267192E8 13.3 m 3.0 s 12.6% 105.6 m 92.3 m
INFO 23:04:38,385 ProgressMeter - chr2:169203470 2.49267192E8 13.8 m 3.0 s 13.3% 103.6 m 89.8 m
INFO 23:05:08,421 ProgressMeter - chr2:191521489 2.49267192E8 14.3 m 3.0 s 14.1% 101.9 m 87.6 m
INFO 23:05:38,982 ProgressMeter - chr2:216268301 2.49267192E8 14.8 m 3.0 s 14.8% 100.0 m 85.1 m
INFO 23:06:12,558 ProgressMeter - chr2:226450001 2.49267192E8 15.4 m 3.0 s 15.2% 101.4 m 86.1 m
INFO 23:06:56,831 ProgressMeter - chr3:350501 4.92466565E8 16.1 m 1.0 s 15.7% 102.7 m 86.6 m
INFO 23:07:37,499 ProgressMeter - chr3:6572630 4.92466565E8 16.8 m 2.0 s 15.9% 105.6 m 88.8 m
INFO 23:08:16,478 ProgressMeter - chr3:8537178 4.92466565E8 17.5 m 2.0 s 16.0% 109.3 m 91.8 m
INFO 23:08:59,533 ProgressMeter - chr3:9696101 4.92466565E8 18.2 m 2.0 s 16.0% 113.5 m 95.3 m
INFO 23:09:30,100 ProgressMeter - chr3:10244418 4.92466565E8 18.7 m 2.0 s 16.0% 116.6 m 97.9 m
INFO 23:10:12,033 ProgressMeter - chr3:10713701 4.92466565E8 19.4 m 2.0 s 16.0% 2.0 h 101.5 m
INFO 23:10:55,293 ProgressMeter - chr3:10948301 4.92466565E8 20.1 m 2.0 s 16.0% 2.1 h 105.2 m
INFO 23:11:38,605 ProgressMeter - chr3:11065186 4.92466565E8 20.8 m 2.0 s 16.1% 2.2 h 108.9 m
INFO 23:12:22,022 ProgressMeter - chr3:11124646 4.92466565E8 21.6 m 2.0 s 16.1% 2.2 h 112.7 m
INFO 23:13:04,202 ProgressMeter - chr3:11154422 4.92466565E8 22.3 m 2.0 s 16.1% 2.3 h 116.3 m
INFO 23:13:48,357 ProgressMeter - chr3:11169249 4.92466565E8 23.0 m 2.0 s 16.1% 2.4 h 2.0 h
INFO 23:14:33,054 ProgressMeter - chr3:11176542 4.92466565E8 23.7 m 2.0 s 16.1% 2.5 h 2.1 h
INFO 23:15:03,088 ProgressMeter - chr3:11179351 4.92466565E8 24.2 m 2.0 s 16.1% 2.5 h 2.1 h
INFO 23:15:33,100 ProgressMeter - chr3:11180950 4.92466565E8 24.7 m 3.0 s 16.1% 2.6 h 2.2 h
INFO 23:16:16,236 ProgressMeter - chr3:11182601 4.92466565E8 25.5 m 3.0 s 16.1% 2.6 h 2.2 h
INFO 23:16:52,547 ProgressMeter - chr3:11182752 4.92466565E8 26.1 m 3.0 s 16.1% 2.7 h 2.3 h
INFO 23:17:22,617 ProgressMeter - chr3:11183495 4.92466565E8 26.6 m 3.0 s 16.1% 2.8 h 2.3 h
INFO 23:19:33,426 ProgressMeter - chr3:11183836 4.92466565E8 27.3 m 3.0 s 16.1% 2.8 h 2.4 h
INFO 23:52:50,878 ProgressMeter - chr3:11183839 4.92466565E8 42.2 m 5.0 s 16.1% 4.4 h 3.7 h
INFO 00:16:40,224 ProgressMeter - chr3:11183841 4.92466565E8 75.4 m 9.0 s 16.1% 7.8 h 6.6 h
INFO 00:39:55,610 ProgressMeter - chr3:11183842 4.92466565E8 94.3 m 11.0 s 16.1% 9.8 h 8.2 h
INFO 00:48:05,478 ProgressMeter - chr3:11183852 4.92466565E8 117.3 m 14.0 s 16.1% 12.2 h 10.2 h
INFO 00:50:33,583 ProgressMeter - chr3:11184232 4.92466565E8 118.4 m 14.0 s 16.1% 12.3 h 10.3 h
INFO 01:21:43,888 ProgressMeter - chr3:11184234 4.92466565E8 2.3 h 16.0 s 16.1% 14.4 h 12.1 h
INFO 01:31:17,672 ProgressMeter - chr3:11184235 4.92466565E8 2.6 h 18.0 s 16.1% 16.1 h 13.5 h
INFO 01:43:46,129 ProgressMeter - chr3:11184236 4.92466565E8 2.8 h 20.0 s 16.1% 17.2 h 14.5 h
INFO 01:52:26,774 ProgressMeter - chr3:11184237 4.92466565E8 3.0 h 21.0 s 16.1% 18.4 h 15.4 h
INFO 01:54:38,449 ProgressMeter - chr3:11184349 4.92466565E8 3.1 h 22.0 s 16.1% 19.1 h 16.0 h
INFO 02:05:18,127 ProgressMeter - chr3:11184528 4.92466565E8 3.1 h 22.0 s 16.1% 19.2 h 16.1 h
INFO 02:26:11,859 ProgressMeter - chr3:11184529 4.92466565E8 3.4 h 24.0 s 16.1% 21.2 h 17.8 h
INFO 02:37:00,901 ProgressMeter - chr3:11184531 4.92466565E8 3.6 h 26.0 s 16.1% 22.7 h 19.1 h
INFO 02:50:52,509 ProgressMeter - chr3:11184532 4.92466565E8 3.8 h 28.0 s 16.1% 23.9 h 20.1 h
INFO 03:01:21,158 ProgressMeter - chr3:11184535 4.92466565E8 4.0 h 29.0 s 16.1% 25.1 h 21.1 h
INFO 03:06:58,260 ProgressMeter - chr3:11184537 4.92466565E8 4.2 h 30.0 s 16.1% 26.4 h 22.1 h
INFO 03:07:17,407 ProgressMeter - chr3:11184572 4.92466565E8 4.3 h 31.0 s 16.1% 26.6 h 22.4 h
INFO 03:13:45,315 ProgressMeter - chr3:11184846 4.92466565E8 4.3 h 31.0 s 16.1% 26.7 h 22.5 h
WARN 03:28:54,316 SimpleTimer - Clock drift of -1,440,383,149,496,872,229 - -1,440,383,142,207,201,586 = 7,289,670,643 nanoseconds detected, vs. max allowable drift of 5,000,000,000. Assuming checkpoint/restart event.
WARN 03:37:42,748 SimpleTimer - Clock drift of -1,440,383,142,207,091,722 - -1,440,383,149,496,872,229 = 7,289,780,507 nanoseconds detected, vs. max allowable drift of 5,000,000,000. Assuming checkpoint/restart event.
INFO 03:53:01,717 ProgressMeter - chr3:11184939 4.92466565E8 0.0 s 0.0 s 16.1% 0.0 s 0.0 s
INFO 04:09:09,787 ProgressMeter - chr3:11184940 4.92466565E8 5.2 h 37.0 s 16.1% 32.3 h 27.1 h
INFO 04:22:05,232 ProgressMeter - chr3:11184941 4.92466565E8 5.4 h 39.0 s 16.1% 33.4 h 28.1 h
INFO 04:29:34,040 ProgressMeter - chr3:11184944 4.92466565E8 5.5 h 40.0 s 16.1% 34.6 h 29.0 h
INFO 04:33:28,232 ProgressMeter - chr3:11185000 4.92466565E8 5.7 h 41.0 s 16.1% 35.6 h 29.9 h
INFO 04:38:30,861 ProgressMeter - chr3:11185049 4.92466565E8 5.7 h 41.0 s 16.1% 35.7 h 30.0 h
INFO 05:08:35,283 ProgressMeter - chr3:11185050 4.92466565E8 6.1 h 44.0 s 16.1% 38.0 h 31.9 h
INFO 05:21:49,044 ProgressMeter - chr3:11185051 4.92466565E8 6.4 h 46.0 s 16.1% 39.8 h 33.4 h
INFO 05:35:58,587 ProgressMeter - chr3:11185055 4.92466565E8 6.6 h 48.0 s 16.1% 41.0 h 34.4 h
INFO 05:45:59,434 ProgressMeter - chr3:11185122 4.92466565E8 6.9 h 50.0 s 16.1% 43.1 h 36.2 h
INFO 06:05:38,874 ProgressMeter - chr3:11185337 4.92466565E8 6.9 h 50.0 s 16.1% 43.2 h 36.3 h
INFO 06:21:56,667 ProgressMeter - chr3:11185338 4.92466565E8 7.4 h 53.0 s 16.1% 45.9 h 38.6 h
INFO 06:33:40,417 ProgressMeter - chr3:11185340 4.92466565E8 7.5 h 55.0 s 16.1% 47.0 h 39.5 h
INFO 06:46:55,704 ProgressMeter - chr3:11185342 4.92466565E8 7.8 h 56.0 s 16.1% 48.3 h 40.6 h
INFO 06:59:14,587 ProgressMeter - chr3:11185343 4.92466565E8 8.0 h 58.0 s 16.1% 49.8 h 41.8 h
INFO 06:59:29,345 ProgressMeter - chr3:11185442 4.92466565E8 8.1 h 59.0 s 16.1% 50.7 h 42.6 h
INFO 07:18:25,396 ProgressMeter - chr3:11185727 4.92466565E8 8.2 h 59.0 s 16.1% 50.9 h 42.7 h
INFO 07:24:22,011 ProgressMeter - chr3:11185728 4.92466565E8 8.5 h 62.0 s 16.1% 52.9 h 44.4 h
INFO 07:37:20,991 ProgressMeter - chr3:11185731 4.92466565E8 8.6 h 62.0 s 16.1% 53.5 h 44.9 h
INFO 07:46:44,368 ProgressMeter - chr3:11185733 4.92466565E8 8.8 h 64.0 s 16.1% 55.1 h 46.3 h
INFO 07:58:48,457 ProgressMeter - chr3:11185738 4.92466565E8 9.0 h 65.0 s 16.1% 56.0 h 47.0 h
INFO 08:09:39,964 ProgressMeter - chr3:11185739 4.92466565E8 9.2 h 67.0 s 16.1% 57.2 h 48.0 h
INFO 08:15:25,451 ProgressMeter - chr3:11185741 4.92466565E8 9.3 h 68.0 s 16.1% 58.2 h 48.9 h
INFO 08:15:40,579 ProgressMeter - chr3:11185807 4.92466565E8 9.4 h 68.0 s 16.1% 58.6 h 49.2 h
INFO 08:34:19,047 ProgressMeter - chr3:11186072 4.92466565E8 9.4 h 68.0 s 16.1% 58.8 h 49.3 h
WARN 08:47:34,671 SimpleTimer - Clock drift of -1,440,383,148,597,424,397 - -1,440,383,142,207,402,150 = 6,390,022,247 nanoseconds detected, vs. max allowable drift of 5,000,000,000. Assuming checkpoint/restart event.
WARN 09:06:25,036 SimpleTimer - Clock drift of -1,440,383,142,206,940,487 - -1,440,383,148,597,424,397 = 6,390,483,910 nanoseconds detected, vs. max allowable drift of 5,000,000,000. Assuming checkpoint/restart event.
INFO 09:20:23,059 ProgressMeter - chr3:11186184 4.92466565E8 0.0 s 0.0 s 16.1% 0.0 s 0.0 s
INFO 09:26:52,082 ProgressMeter - chr3:11186186 4.92466565E8 10.5 h 77.0 s 16.1% 65.6 h 55.1 h
INFO 09:35:56,557 ProgressMeter - chr3:11186188 4.92466565E8 10.6 h 77.0 s 16.1% 66.2 h 55.6 h

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