GATK 4.1.7.0 VariantAnnotator Processing Speed Drop
GATK 4.1.7.0 VariantAnnotator processing speed rapidly decreases over time. Running with single-sample VCF file obtained from GenotypeGVCFs. No other tools were executed during the VariantAnnotator running. No RAM or SSD space overuse was found.
The INFO log is shown below. The exact command is at the top section of the log.
Using GATK jar /home/wgs/Tools/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx30G -Xms1G -jar /home/wgs/Tools/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar VariantAnnotator --reference /home/wgs/Genomes/hg38/bwa/hg38.fa --dbsnp /home/wgs/Tools/Supplementary/dbsnp-153-hgvs.sorted.hg38.vcf.gz --variant ./barcode.raw21-22.vcf.gz --output ../annotated_output/barcode.gatk_annotated21-22.vcf.gz -L chr21 -L chr22
18:34:24.702 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/wgs/Tools/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 07, 2020 6:34:24 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
18:34:24.814 INFO VariantAnnotator - ------------------------------------------------------------
18:34:24.815 INFO VariantAnnotator - The Genome Analysis Toolkit (GATK) v4.1.7.0
18:34:24.815 INFO VariantAnnotator - For support and documentation go to https://software.broadinstitute.org/gatk/
18:34:24.815 INFO VariantAnnotator - Executing as wgs@wgs on Linux v4.15.0-99-generic amd64
18:34:24.815 INFO VariantAnnotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_201-b09
18:34:24.815 INFO VariantAnnotator - Start Date/Time: May 7, 2020 6:34:24 PM MSK
18:34:24.815 INFO VariantAnnotator - ------------------------------------------------------------
18:34:24.815 INFO VariantAnnotator - ------------------------------------------------------------
18:34:24.815 INFO VariantAnnotator - HTSJDK Version: 2.21.2
18:34:24.815 INFO VariantAnnotator - Picard Version: 2.21.9
18:34:24.815 INFO VariantAnnotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:34:24.815 INFO VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:34:24.815 INFO VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:34:24.816 INFO VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:34:24.816 INFO VariantAnnotator - Deflater: IntelDeflater
18:34:24.816 INFO VariantAnnotator - Inflater: IntelInflater
18:34:24.816 INFO VariantAnnotator - GCS max retries/reopens: 20
18:34:24.816 INFO VariantAnnotator - Requester pays: disabled
18:34:24.816 INFO VariantAnnotator - Initializing engine
18:34:25.065 INFO FeatureManager - Using codec VCFCodec to read file file:///home/wgs/Tools/Supplementary/dbsnp-153-hgvs.sorted.hg38.vcf.gz
18:34:25.135 INFO FeatureManager - Using codec VCFCodec to read file file:///home/wgs/Analysis/barcode/gatk_gvcf_output/./barcode.raw21-22.vcf.gz
18:34:25.197 INFO IntervalArgumentCollection - Processing 97528451 bp from intervals
18:34:25.214 INFO VariantAnnotator - Done initializing engine
18:34:25.265 INFO ProgressMeter - Starting traversal
18:34:25.266 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:34:42.165 INFO ProgressMeter - chr21:5011000 0.3 5011000 17792638.2
18:34:57.943 INFO ProgressMeter - chr21:5013000 0.5 5013000 9204639.3
18:35:13.744 INFO ProgressMeter - chr21:5015000 0.8 5015000 6206939.2
18:35:28.855 INFO ProgressMeter - chr21:5017000 1.1 5017000 4733837.6
18:35:43.825 INFO ProgressMeter - chr21:5019000 1.3 5019000 3833297.3
18:35:58.909 INFO ProgressMeter - chr21:5021000 1.6 5021000 3217111.8
18:36:13.945 INFO ProgressMeter - chr21:5023000 1.8 5023000 2773120.8
18:36:28.938 INFO ProgressMeter - chr21:5025000 2.1 5025000 2437900.3
18:36:43.900 INFO ProgressMeter - chr21:5027000 2.3 5027000 2175656.8
18:36:58.880 INFO ProgressMeter - chr21:5029000 2.6 5029000 1964274.1
18:37:14.093 INFO ProgressMeter - chr21:5031000 2.8 5031000 1787994.7
18:37:29.178 INFO ProgressMeter - chr21:5033000 3.1 5033000 1641980.9
18:37:44.417 INFO ProgressMeter - chr21:5035000 3.3 5035000 1516939.4
18:37:59.497 INFO ProgressMeter - chr21:5037000 3.6 5037000 1410720.2
18:38:14.458 INFO ProgressMeter - chr21:5039000 3.8 5039000 1319156.0
18:38:29.564 INFO ProgressMeter - chr21:5041000 4.1 5041000 1238078.1
18:38:44.564 INFO ProgressMeter - chr21:5043000 4.3 5043000 1166919.9
18:38:59.513 INFO ProgressMeter - chr21:5045000 4.6 5045000 1103749.5
18:39:14.502 INFO ProgressMeter - chr21:5047000 4.8 5047000 1046965.1
18:39:29.596 INFO ProgressMeter - chr21:5049000 5.1 5049000 995432.6
18:39:44.628 INFO ProgressMeter - chr21:5051000 5.3 5051000 948954.5
18:39:59.768 INFO ProgressMeter - chr21:5053000 5.6 5053000 906362.3
18:40:14.735 INFO ProgressMeter - chr21:5055000 5.8 5055000 867888.1
18:40:29.638 INFO ProgressMeter - chr21:5057000 6.1 5057000 832720.4
18:40:44.659 INFO ProgressMeter - chr21:5059000 6.3 5059000 800069.6
18:40:59.657 INFO ProgressMeter - chr21:5061000 6.6 5061000 769946.6
18:41:14.687 INFO ProgressMeter - chr21:5063000 6.8 5063000 741974.6
18:41:29.771 INFO ProgressMeter - chr21:5065000 7.1 5065000 715892.6
18:41:44.840 INFO ProgressMeter - chr21:5067000 7.3 5067000 691624.2
18:41:59.881 INFO ProgressMeter - chr21:5069000 7.6 5069000 669005.6
18:42:14.970 INFO ProgressMeter - chr21:5071001 7.8 5071000 647769.7
18:42:30.070 INFO ProgressMeter - chr21:5073001 8.1 5073000 627841.4
18:42:45.137 INFO ProgressMeter - chr21:5075001 8.3 5075000 609157.2
18:43:00.141 INFO ProgressMeter - chr21:5077001 8.6 5077000 591638.7
18:43:15.170 INFO ProgressMeter - chr21:5079001 8.8 5079000 575085.3
18:43:30.158 INFO ProgressMeter - chr21:5081001 9.1 5081000 559487.0
18:43:45.170 INFO ProgressMeter - chr21:5083001 9.3 5083000 544700.5
18:44:00.166 INFO ProgressMeter - chr21:5085001 9.6 5085000 530701.0
18:44:15.249 INFO ProgressMeter - chr21:5087001 9.8 5087000 517336.9
18:44:30.146 INFO ProgressMeter - chr21:5089001 10.1 5089000 504795.2
18:44:45.136 INFO ProgressMeter - chr21:5091001 10.3 5091000 492780.7
18:45:00.171 INFO ProgressMeter - chr21:5093001 10.6 5093000 481300.4
18:45:15.178 INFO ProgressMeter - chr21:5095001 10.8 5095000 470371.4
18:45:30.141 INFO ProgressMeter - chr21:5097001 11.1 5097000 459966.2
18:45:45.097 INFO ProgressMeter - chr21:5099001 11.3 5099000 450023.6
18:46:00.037 INFO ProgressMeter - chr21:5101001 11.6 5101000 440519.3
18:46:14.991 INFO ProgressMeter - chr21:5103001 11.8 5103000 431406.5
18:46:29.942 INFO ProgressMeter - chr21:5105002 12.1 5105000 422671.6
18:46:44.855 INFO ProgressMeter - chr21:5107002 12.3 5107000 414311.2
18:46:59.795 INFO ProgressMeter - chr21:5109002 12.6 5109000 406266.7
18:47:14.769 INFO ProgressMeter - chr21:5111002 12.8 5111000 398517.0
18:47:29.707 INFO ProgressMeter - chr21:5113002 13.1 5113000 391081.0
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That's great! And thanks for the update Louis Bergelson
And thank you danilovkiri for bringing this to our attention!
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Hi danilovkiri
Does the process complete at all or does it run infinitely?
We think that it only seems like the tool is slowing down but it is not actually doing that. The tool skipped variants and started at locus chr21:5011000. It is using the skipped variants in the rate calculations, which is incorrect. This is causing the apparent reduction in speed. It is misleading of course but probably not a serious issue if the tool is running to completion.
We have created a ticket here to fix this issue and you can follow its progress here: https://github.com/broadinstitute/gatk/issues/6631
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Unfortunately, I can't answer the first question as I simply have been waiting for quite some time. And there is an issue here: I used to run annotation with VariantAnnotator from GATK3.8. GATK3.8 VariantAnnotator successfully annotated the same input VCF file for chromosomes 21 and 22 within 10 minutes. At the same time, GATK4.1.7.0 VariantAnnotator is somewhere at chr21:5087001 after 10 min or running. It nearly processed nothing compared to GATK3.8. Note that I did not use parallelization.
I know that GATK3.8 is not supported (but thankfully it still works), though the latest version's behaviour is really strange.
I'll run some tests again to compare performance and come back to you.
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I run the test again. I used a single-sample indexed VCF for chromosomes chr21 and chr22 to run VariantAnnotator in GATK3.8 and GATK4.1.7.0.
The command to run GATK3.8 is shown below:
java -jar -Djava.io.tmpdir=/mnt/disk2/TMP -Xmx30G /home/wgs/Tools/GATK_3.8/GenomeAnalysisTK.jar \
-T VariantAnnotator -R /home/wgs/Genomes/hg38/bwa/hg38.fa --variant ./barcode.raw21-22.vcf.gz \
--dbsnp /home/wgs/Tools/Supplementary/dbsnp-153-hgvs-atlasids.sorted.split.hg38.vcf.gz -nt 1 \
--out ./barcode.annotated.raw21-22.vcf.gz -L chr21 -L chr22The command to run GATK4.1.7.0 is as follows:
/home/wgs/Tools/gatk-4.1.7.0/gatk --java-options "-Xmx30G -Xms1G" \
VariantAnnotator --reference /home/wgs/Genomes/hg38/bwa/hg38.fa \
--dbsnp /home/wgs/Tools/Supplementary/dbsnp-153-hgvs-atlasids.sorted.split.hg38.vcf.gz \
--variant ./barcode.raw21-22.vcf.gz --output ./barcode.annotated_gatk4.raw21-22.vcf.gz \
-L chr21 -LGATK3.8 VariantAnnotator successfully completed annotation within 10 min. The log is shown below:
INFO 19:27:32,846 HelpFormatter - ------------------------------------------------------------------------------------
INFO 19:27:32,847 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50
INFO 19:27:32,847 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 19:27:32,847 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 19:27:32,847 HelpFormatter - [Tue Jun 02 19:27:32 MSK 2020] Executing on Linux 4.15.0-99-generic amd64
INFO 19:27:32,847 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_201-b09
INFO 19:27:32,849 HelpFormatter - Program Args: -T VariantAnnotator -R /home/wgs/Genomes/hg38/bwa/hg38.fa --variant ./barcode.raw21-22.vcf.gz --dbsnp /home/wgs/Tools/Supplementary/dbsnp-153-hgvs-atlasids.sorted.split.hg38.vcf.gz -nt 1 --out ./barcode.annotated.raw21-22.vcf.gz -L chr21 -L chr22
INFO 19:27:32,850 HelpFormatter - Executing as wgs@wgs on Linux 4.15.0-99-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_201-b09.
INFO 19:27:32,851 HelpFormatter - Date/Time: 2020/06/02 19:27:32
INFO 19:27:32,851 HelpFormatter - ------------------------------------------------------------------------------------
INFO 19:27:32,851 HelpFormatter - ------------------------------------------------------------------------------------
INFO 19:27:32,863 NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/wgs/Tools/GATK_3.8/GenomeAnalysisTK.jar!/com/intel/gkl/native/libgkl_compression.so
INFO 19:27:32,871 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 19:27:32,871 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 19:27:32,871 GenomeAnalysisEngine - Strictness is SILENT
INFO 19:27:33,679 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
INFO 19:27:34,389 IntervalUtils - Processing 97528451 bp from intervals
WARN 19:27:34,390 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
WARN 19:27:34,390 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
INFO 19:27:34,419 GenomeAnalysisEngine - Preparing for traversal
INFO 19:27:34,420 GenomeAnalysisEngine - Done preparing for traversal
INFO 19:27:34,420 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 19:27:34,420 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 19:27:34,420 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 19:28:04,421 ProgressMeter - chr21:9028901 9000000.0 30.0 s 3.0 s 9.3% 5.4 m 4.9 m
INFO 19:28:34,422 ProgressMeter - chr21:14765701 1.4E7 60.0 s 4.0 s 15.1% 6.6 m 5.6 m
INFO 19:29:14,423 ProgressMeter - chr21:20002201 2.0E7 100.0 s 5.0 s 20.5% 8.1 m 6.5 m
INFO 19:29:54,423 ProgressMeter - chr21:25356201 2.5E7 2.3 m 5.0 s 26.0% 9.0 m 6.6 m
INFO 19:30:24,424 ProgressMeter - chr21:29303601 2.9E7 2.8 m 5.0 s 30.0% 9.4 m 6.6 m
INFO 19:31:04,424 ProgressMeter - chr21:34687201 3.4E7 3.5 m 6.0 s 35.6% 9.8 m 6.3 m
INFO 19:31:34,425 ProgressMeter - chr21:38644201 3.8E7 4.0 m 6.0 s 39.6% 10.1 m 6.1 m
INFO 19:32:14,426 ProgressMeter - chr21:43986501 4.3E7 4.7 m 6.0 s 45.1% 10.3 m 5.7 m
INFO 19:32:54,426 ProgressMeter - chr22:10108401 5.6709983E7 5.3 m 5.0 s 58.3% 9.2 m 3.8 m
INFO 19:33:24,427 ProgressMeter - chr22:16711701 6.2709983E7 5.8 m 5.0 s 65.0% 9.0 m 3.1 m
INFO 19:34:04,427 ProgressMeter - chr22:22250201 6.8709983E7 6.5 m 5.0 s 70.7% 9.2 m 2.7 m
INFO 19:34:34,428 ProgressMeter - chr22:26324601 7.2709983E7 7.0 m 5.0 s 74.9% 9.3 m 2.3 m
INFO 19:35:14,428 ProgressMeter - chr22:31496901 7.7709983E7 7.7 m 5.0 s 80.2% 9.6 m 113.0 s
INFO 19:35:44,430 ProgressMeter - chr22:35375301 8.1709983E7 8.2 m 5.0 s 84.2% 9.7 m 92.0 s
INFO 19:36:14,431 ProgressMeter - chr22:39382301 8.5709983E7 8.7 m 6.0 s 88.3% 9.8 m 69.0 s
INFO 19:36:54,431 ProgressMeter - chr22:44578501 9.0709983E7 9.3 m 6.0 s 93.6% 10.0 m 38.0 s
INFO 19:37:24,432 ProgressMeter - chr22:48423901 9.4709983E7 9.8 m 6.0 s 97.5% 10.1 m 14.0 s
INFO 19:37:43,505 VariantAnnotator - Processed 97525111 loci.
INFO 19:37:43,521 ProgressMeter - done 9.7528451E7 10.2 m 6.0 s 100.0% 10.2 m 0.0 s
INFO 19:37:43,522 ProgressMeter - Total runtime 609.10 secs, 10.15 min, 0.17 hours
------------------------------------------------------------------------------------------
Done. There were 2 WARN messages, the first 2 are repeated below.
WARN 19:27:34,390 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
WARN 19:27:34,390 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validationGATK4.1.7.0 did not complete annotation within 295 min. I did not decide to wait as it seemed like it was going to take an eternity of CPU time which I was not going to pay for. The available log is shown below:
Using GATK jar /home/wgs/Tools/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx30G -Xms1G -jar /home/wgs/Tools/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar VariantAnnotator --reference /home/wgs/Genomes/hg38/bwa/hg38.fa --dbsnp /home/wgs/Tools/Supplementary/dbsnp-153-hgvs-atlasids.sorted.split.hg38.vcf.gz --variant ./barcode.raw21-22.vcf.gz --output ./barcode.annotated_gatk4.raw21-22.vcf.gz -L chr21 -L chr22
19:57:35.768 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/wgs/Tools/gatk-4.1.7.0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jun 02, 2020 7:57:35 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
19:57:35.893 INFO VariantAnnotator - ------------------------------------------------------------
19:57:35.893 INFO VariantAnnotator - The Genome Analysis Toolkit (GATK) v4.1.7.0
19:57:35.893 INFO VariantAnnotator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:57:35.893 INFO VariantAnnotator - Executing as wgs@wgs on Linux v4.15.0-99-generic amd64
19:57:35.893 INFO VariantAnnotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_201-b09
19:57:35.893 INFO VariantAnnotator - Start Date/Time: June 2, 2020 7:57:35 PM MSK
19:57:35.893 INFO VariantAnnotator - ------------------------------------------------------------
19:57:35.893 INFO VariantAnnotator - ------------------------------------------------------------
19:57:35.894 INFO VariantAnnotator - HTSJDK Version: 2.21.2
19:57:35.894 INFO VariantAnnotator - Picard Version: 2.21.9
19:57:35.894 INFO VariantAnnotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:57:35.894 INFO VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:57:35.894 INFO VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:57:35.894 INFO VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:57:35.894 INFO VariantAnnotator - Deflater: IntelDeflater
19:57:35.894 INFO VariantAnnotator - Inflater: IntelInflater
19:57:35.894 INFO VariantAnnotator - GCS max retries/reopens: 20
19:57:35.894 INFO VariantAnnotator - Requester pays: disabled
19:57:35.894 INFO VariantAnnotator - Initializing engine
19:57:36.143 INFO FeatureManager - Using codec VCFCodec to read file file:///home/wgs/Tools/Supplementary/dbsnp-153-hgvs-atlasids.sorted.split.hg38.vcf.gz
19:57:36.213 INFO FeatureManager - Using codec VCFCodec to read file file:///home/wgs/Miscellaneous/gatk_varann_bug_report/./barcode.raw21-22.vcf.gz
19:57:36.272 INFO IntervalArgumentCollection - Processing 97528451 bp from intervals
19:57:36.288 INFO VariantAnnotator - Done initializing engine
19:57:36.337 INFO ProgressMeter - Starting traversal
19:57:36.337 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:57:53.125 INFO ProgressMeter - chr21:5011000 0.3 5011000 17910287.7
19:58:08.400 INFO ProgressMeter - chr21:5013000 0.5 5013000 9380906.3
19:58:23.621 INFO ProgressMeter - chr21:5015000 0.8 5015000 6363674.8
19:58:38.749 INFO ProgressMeter - chr21:5017000 1.0 5017000 4823110.9
19:58:53.813 INFO ProgressMeter - chr21:5019000 1.3 5019000 3886931.3
19:59:08.872 INFO ProgressMeter - chr21:5021000 1.5 5021000 3255633.0
19:59:24.138 INFO ProgressMeter - chr21:5023000 1.8 5023000 2795706.9
19:59:39.010 INFO ProgressMeter - chr21:5025000 2.0 5025000 2457753.5
19:59:54.037 INFO ProgressMeter - chr21:5027000 2.3 5027000 2190429.9
20:00:09.082 INFO ProgressMeter - chr21:5029000 2.5 5029000 1975449.3
20:00:24.173 INFO ProgressMeter - chr21:5031000 2.8 5031000 1798552.1
20:00:39.274 INFO ProgressMeter - chr21:5033000 3.0 5033000 1650732.2
20:00:54.478 INFO ProgressMeter - chr21:5035000 3.3 5035000 1524671.8
20:01:09.551 INFO ProgressMeter - chr21:5037000 3.6 5037000 1417449.1
20:01:24.606 INFO ProgressMeter - chr21:5039000 3.8 5039000 1324495.8
20:01:39.722 INFO ProgressMeter - chr21:5041000 4.1 5041000 1242722.4
20:01:54.788 INFO ProgressMeter - chr21:5043000 4.3 5043000 1170744.2
20:02:09.836 INFO ProgressMeter - chr21:5045000 4.6 5045000 1106768.2
20:02:24.871 INFO ProgressMeter - chr21:5047000 4.8 5047000 1049512.4
20:02:39.892 INFO ProgressMeter - chr21:5049000 5.1 5049000 997974.0
20:02:54.936 INFO ProgressMeter - chr21:5051000 5.3 5051000 951227.1
20:03:09.993 INFO ProgressMeter - chr21:5053000 5.6 5053000 908660.4
20:03:25.023 INFO ProgressMeter - chr21:5055000 5.8 5055000 869837.0
20:03:40.066 INFO ProgressMeter - chr21:5057000 6.1 5057000 834192.5
20:03:55.089 INFO ProgressMeter - chr21:5059000 6.3 5059000 801421.5
20:04:10.146 INFO ProgressMeter - chr21:5061000 6.6 5061000 771084.5
20:04:25.165 INFO ProgressMeter - chr21:5063000 6.8 5063000 743050.9
20:04:40.216 INFO ProgressMeter - chr21:5065000 7.1 5065000 716949.9
20:04:55.216 INFO ProgressMeter - chr21:5067000 7.3 5067000 692719.4
20:05:10.268 INFO ProgressMeter - chr21:5069000 7.6 5069000 670013.7
20:05:25.371 INFO ProgressMeter - chr21:5071001 7.8 5071000 648695.0
20:05:40.340 INFO ProgressMeter - chr21:5073001 8.1 5073000 628880.4
20:05:55.393 INFO ProgressMeter - chr21:5075001 8.3 5075000 610152.0
20:06:10.446 INFO ProgressMeter - chr21:5077001 8.6 5077000 592520.3
20:06:25.520 INFO ProgressMeter - chr21:5079001 8.8 5079000 575868.8
20:06:40.574 INFO ProgressMeter - chr21:5081001 9.1 5081000 560160.4
20:06:55.635 INFO ProgressMeter - chr21:5083001 9.3 5083000 545290.7
20:07:10.679 INFO ProgressMeter - chr21:5085001 9.6 5085000 531216.6
20:07:25.755 INFO ProgressMeter - chr21:5087001 9.8 5087000 517832.8
20:07:40.835 INFO ProgressMeter - chr21:5089001 10.1 5089000 505114.2
20:07:55.922 INFO ProgressMeter - chr21:5091001 10.3 5091000 493007.4
20:08:10.987 INFO ProgressMeter - chr21:5093001 10.6 5093000 481493.7
20:08:26.072 INFO ProgressMeter - chr21:5095001 10.8 5095000 470499.5
20:08:41.144 INFO ProgressMeter - chr21:5097001 11.1 5097000 460013.2
20:08:56.257 INFO ProgressMeter - chr21:5099001 11.3 5099000 449964.7
20:09:11.414 INFO ProgressMeter - chr21:5101001 11.6 5101000 440325.3
20:09:26.441 INFO ProgressMeter - chr21:5103001 11.8 5103000 431176.3
20:09:41.454 INFO ProgressMeter - chr21:5105002 12.1 5105000 422414.6
20:09:56.452 INFO ProgressMeter - chr21:5107002 12.3 5107000 414016.7
20:10:11.690 INFO ProgressMeter - chr21:5109002 12.6 5109000 405823.5
20:10:26.902 INFO ProgressMeter - chr21:5111002 12.8 5111000 397967.7
20:10:42.087 INFO ProgressMeter - chr21:5113002 13.1 5113000 390429.5
20:10:57.173 INFO ProgressMeter - chr21:5115002 13.3 5115000 383224.5
20:11:12.352 INFO ProgressMeter - chr21:5117002 13.6 5117000 376243.1
20:11:27.473 INFO ProgressMeter - chr21:5119002 13.9 5119000 369542.4
20:11:42.537 INFO ProgressMeter - chr21:5121002 14.1 5121000 363105.6
20:11:57.599 INFO ProgressMeter - chr21:5123002 14.4 5123000 356894.9
20:12:12.687 INFO ProgressMeter - chr21:5125002 14.6 5125000 350887.2
20:12:27.581 INFO ProgressMeter - chr21:5127002 14.9 5127000 345158.0
20:12:42.378 INFO ProgressMeter - chr21:5129002 15.1 5129000 339653.5
20:12:57.438 INFO ProgressMeter - chr21:5131002 15.4 5131000 334230.4
20:13:12.573 INFO ProgressMeter - chr21:5133002 15.6 5133000 328955.5
20:13:27.846 INFO ProgressMeter - chr21:5135002 15.9 5135000 323801.5
20:13:42.879 INFO ProgressMeter - chr21:5137002 16.1 5137000 318889.4
20:13:57.936 INFO ProgressMeter - chr21:5139002 16.4 5139000 314120.1
20:14:13.005 INFO ProgressMeter - chr21:5141002 16.6 5141000 309491.2
20:14:28.086 INFO ProgressMeter - chr21:5143002 16.9 5143000 304996.6
20:14:43.129 INFO ProgressMeter - chr21:5145002 17.1 5145000 300645.1
20:14:58.196 INFO ProgressMeter - chr21:5147002 17.4 5147000 296412.5
20:15:13.245 INFO ProgressMeter - chr21:5149002 17.6 5149000 292305.8
20:15:28.339 INFO ProgressMeter - chr21:5151002 17.9 5151000 288301.7
20:15:43.434 INFO ProgressMeter - chr21:5153002 18.1 5153000 284408.8
20:15:58.501 INFO ProgressMeter - chr21:5155002 18.4 5155000 280629.7
20:16:13.597 INFO ProgressMeter - chr21:5157002 18.6 5157000 276945.4
20:16:28.704 INFO ProgressMeter - chr21:5159002 18.9 5159000 273356.8
20:16:43.775 INFO ProgressMeter - chr21:5161002 19.1 5161000 269871.0
20:16:58.777 INFO ProgressMeter - chr21:5163002 19.4 5163000 266491.2
20:17:13.839 INFO ProgressMeter - chr21:5165002 19.6 5165000 263184.3
20:17:29.080 INFO ProgressMeter - chr21:5217002 19.9 5217000 262437.1
20:17:44.128 INFO ProgressMeter - chr21:5219003 20.1 5219000 259266.7
20:17:59.150 INFO ProgressMeter - chr21:5221004 20.4 5221000 256179.8
20:18:14.220 INFO ProgressMeter - chr21:5223004 20.6 5223000 253158.0
20:18:29.287 INFO ProgressMeter - chr21:5225004 20.9 5225000 250209.5
20:18:44.357 INFO ProgressMeter - chr21:5227004 21.1 5227000 247330.5
20:18:59.465 INFO ProgressMeter - chr21:5229005 21.4 5229000 244511.8
20:19:14.539 INFO ProgressMeter - chr21:5231008 21.6 5231000 241765.1
20:19:29.570 INFO ProgressMeter - chr21:5233009 21.9 5233000 239089.3
20:19:44.649 INFO ProgressMeter - chr21:5235010 22.1 5235000 236465.5
20:19:59.737 INFO ProgressMeter - chr21:5237010 22.4 5237000 233899.1
20:20:14.822 INFO ProgressMeter - chr21:5239010 22.6 5239000 231390.1
20:20:29.872 INFO ProgressMeter - chr21:5241010 22.9 5241000 228942.1
20:20:44.937 INFO ProgressMeter - chr21:5243012 23.1 5243000 226544.7
20:20:59.933 INFO ProgressMeter - chr21:5245012 23.4 5245000 224209.8
20:21:14.876 INFO ProgressMeter - chr21:5247012 23.6 5247000 221932.6
20:21:29.928 INFO ProgressMeter - chr21:5249014 23.9 5249000 219686.1
20:21:44.963 INFO ProgressMeter - chr21:5251015 24.1 5251000 217488.8
20:22:00.037 INFO ProgressMeter - chr21:5253016 24.4 5253000 215331.0
20:22:15.115 INFO ProgressMeter - chr21:5255016 24.6 5255000 213216.6
20:22:30.200 INFO ProgressMeter - chr21:5257016 24.9 5257000 211144.0
20:22:45.290 INFO ProgressMeter - chr21:5259016 25.1 5259000 209112.0
20:23:00.349 INFO ProgressMeter - chr21:5261016 25.4 5261000 207124.4
20:23:15.480 INFO ProgressMeter - chr21:5263016 25.7 5263000 205166.1
20:23:30.497 INFO ProgressMeter - chr21:5265020 25.9 5265000 203260.9
20:23:45.598 INFO ProgressMeter - chr21:5267020 26.2 5267000 201381.4
20:24:00.668 INFO ProgressMeter - chr21:5269020 26.4 5269000 199541.6
20:24:15.841 INFO ProgressMeter - chr21:5271020 26.7 5271000 197723.8
20:24:30.785 INFO ProgressMeter - chr21:5273021 26.9 5273000 195967.9
20:24:45.749 INFO ProgressMeter - chr21:5275021 27.2 5275000 194241.8
20:25:00.685 INFO ProgressMeter - chr21:5277021 27.4 5277000 192550.5
20:25:15.615 INFO ProgressMeter - chr21:5279022 27.7 5279000 190890.3
20:25:30.568 INFO ProgressMeter - chr21:5281022 27.9 5281000 189257.2
20:25:45.547 INFO ProgressMeter - chr21:5283024 28.2 5283000 187649.8
20:26:00.505 INFO ProgressMeter - chr21:5285024 28.4 5285000 186073.2
20:26:15.524 INFO ProgressMeter - chr21:5287024 28.7 5287000 184517.4
20:26:30.499 INFO ProgressMeter - chr21:5289024 28.9 5289000 182993.4
20:26:45.543 INFO ProgressMeter - chr21:5291026 29.2 5291000 181488.1
20:27:00.528 INFO ProgressMeter - chr21:5293026 29.4 5293000 180014.5
20:27:15.509 INFO ProgressMeter - chr21:5295026 29.7 5295000 178566.2
20:27:30.467 INFO ProgressMeter - chr21:5297026 29.9 5297000 177144.4
20:27:45.419 INFO ProgressMeter - chr21:5299027 30.2 5299000 175746.6
20:28:00.352 INFO ProgressMeter - chr21:5301027 30.4 5301000 174373.6
20:28:15.276 INFO ProgressMeter - chr21:5303031 30.6 5303000 173023.7
20:28:30.221 INFO ProgressMeter - chr21:5305032 30.9 5305000 171693.6
20:28:45.169 INFO ProgressMeter - chr21:5307033 31.1 5307000 170384.5
20:29:00.094 INFO ProgressMeter - chr21:5309033 31.4 5309000 169098.2
20:29:15.042 INFO ProgressMeter - chr21:5311033 31.6 5311000 167830.2
20:29:29.989 INFO ProgressMeter - chr21:5313033 31.9 5313000 166582.0
20:29:44.995 INFO ProgressMeter - chr21:5315035 32.1 5315000 165348.1
20:30:00.147 INFO ProgressMeter - chr21:5317035 32.4 5317000 164121.0
20:30:15.321 INFO ProgressMeter - chr21:5319037 32.6 5319000 162911.1
20:30:30.378 INFO ProgressMeter - chr21:5321039 32.9 5321000 161729.2
20:30:45.452 INFO ProgressMeter - chr21:5323039 33.2 5323000 160563.9
20:31:00.505 INFO ProgressMeter - chr21:5325044 33.4 5325000 159417.8
20:31:15.466 INFO ProgressMeter - chr21:5327044 33.7 5327000 158296.0
20:31:30.557 INFO ProgressMeter - chr21:5329044 33.9 5329000 157180.6
20:31:45.702 INFO ProgressMeter - chr21:5331044 34.2 5331000 156077.6
20:32:00.880 INFO ProgressMeter - chr21:5333044 34.4 5333000 154988.3
20:32:15.972 INFO ProgressMeter - chr21:5335044 34.7 5335000 153921.2
20:32:30.933 INFO ProgressMeter - chr21:5337044 34.9 5337000 152879.1
20:32:45.906 INFO ProgressMeter - chr21:5339044 35.2 5339000 151850.9
20:33:00.955 INFO ProgressMeter - chr21:5341044 35.4 5341000 150831.9
20:33:15.997 INFO ProgressMeter - chr21:5343046 35.7 5343000 149827.5
20:33:31.131 INFO ProgressMeter - chr21:5345046 35.9 5345000 148830.9
20:33:46.193 INFO ProgressMeter - chr21:5347046 36.2 5347000 147853.1
20:34:01.242 INFO ProgressMeter - chr21:5349046 36.4 5349000 146889.7
20:34:16.117 INFO ProgressMeter - chr21:5351046 36.7 5351000 145951.0
20:34:31.099 INFO ProgressMeter - chr21:5353047 36.9 5353000 145017.8
20:34:46.200 INFO ProgressMeter - chr21:5355051 37.2 5355000 144089.6
20:35:01.325 INFO ProgressMeter - chr21:5357051 37.4 5357000 143172.3
20:35:16.424 INFO ProgressMeter - chr21:5359051 37.7 5359000 142268.9
20:35:31.466 INFO ProgressMeter - chr21:5361051 37.9 5361000 141381.0
20:35:46.418 INFO ProgressMeter - chr21:5363051 38.2 5363000 140510.3
20:36:01.481 INFO ProgressMeter - chr21:5365051 38.4 5365000 139644.2
20:36:16.529 INFO ProgressMeter - chr21:5367051 38.7 5367000 138790.2
20:36:31.608 INFO ProgressMeter - chr21:5369051 38.9 5369000 137945.4
20:36:46.665 INFO ProgressMeter - chr21:5371051 39.2 5371000 137112.8
20:37:01.735 INFO ProgressMeter - chr21:5373051 39.4 5373000 136290.0
20:37:16.788 INFO ProgressMeter - chr21:5375051 39.7 5375000 135478.5
20:37:31.840 INFO ProgressMeter - chr21:5377051 39.9 5377000 134677.4
20:37:46.918 INFO ProgressMeter - chr21:5379051 40.2 5379000 133884.7
20:38:02.161 INFO ProgressMeter - chr21:5381053 40.4 5381000 133092.9
20:38:17.250 INFO ProgressMeter - chr21:5383054 40.7 5383000 132319.3
20:38:32.292 INFO ProgressMeter - chr21:5385055 40.9 5385000 131557.8
20:38:47.339 INFO ProgressMeter - chr21:5387056 41.2 5387000 130805.2
20:39:02.394 INFO ProgressMeter - chr21:5389058 41.4 5389000 130061.4
20:39:17.596 INFO ProgressMeter - chr21:5391058 41.7 5391000 129318.9
20:39:32.656 INFO ProgressMeter - chr21:5393058 41.9 5393000 128592.6
20:39:47.735 INFO ProgressMeter - chr21:5445058 42.2 5445000 129059.1
20:40:02.806 INFO ProgressMeter - chr21:5447058 42.4 5447000 128342.4
20:40:17.579 INFO ProgressMeter - chr21:5449058 42.7 5449000 127649.0
20:40:33.068 INFO ProgressMeter - chr21:5501058 42.9 5501000 128092.5
20:40:48.095 INFO ProgressMeter - chr21:5503058 43.2 5503000 127396.2
20:41:03.112 INFO ProgressMeter - chr21:5505058 43.4 5505000 126708.3
20:41:18.229 INFO ProgressMeter - chr21:5507058 43.7 5507000 126023.5
20:41:33.266 INFO ProgressMeter - chr21:5509058 43.9 5509000 125350.4
20:41:48.372 INFO ProgressMeter - chr21:5511058 44.2 5511000 124681.6
20:42:03.581 INFO ProgressMeter - chr21:5513058 44.5 5513000 124015.7
20:42:18.687 INFO ProgressMeter - chr21:5515058 44.7 5515000 123362.0
20:42:33.779 INFO ProgressMeter - chr21:5517058 45.0 5517000 122716.3
20:42:48.802 INFO ProgressMeter - chr21:5519058 45.2 5519000 122080.8
20:43:03.737 INFO ProgressMeter - chr21:5521058 45.5 5521000 121456.3
20:43:18.682 INFO ProgressMeter - chr21:5523058 45.7 5523000 120838.2
20:43:33.667 INFO ProgressMeter - chr21:5525058 46.0 5525000 120225.0
20:43:48.610 INFO ProgressMeter - chr21:5527058 46.2 5527000 119620.3
20:44:03.549 INFO ProgressMeter - chr21:5529058 46.5 5529000 119022.2
20:44:18.514 INFO ProgressMeter - chr21:5531058 46.7 5531000 118429.3
20:44:33.628 INFO ProgressMeter - chr21:5533058 47.0 5533000 117836.6
20:44:48.700 INFO ProgressMeter - chr21:5535058 47.2 5535000 117251.9
20:45:03.798 INFO ProgressMeter - chr21:5537058 47.5 5537000 116672.4
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20:45:33.945 INFO ProgressMeter - chr21:5541058 48.0 5541000 115533.5
20:45:49.190 INFO ProgressMeter - chr21:5543058 48.2 5543000 114966.1
20:46:04.254 INFO ProgressMeter - chr21:5545058 48.5 5545000 114411.8
20:46:19.649 INFO ProgressMeter - chr21:5547058 48.7 5547000 113850.3
20:46:34.591 INFO ProgressMeter - chr21:5549058 49.0 5549000 113312.2
20:46:49.552 INFO ProgressMeter - chr21:5551058 49.2 5551000 112778.8
20:47:04.503 INFO ProgressMeter - chr21:5553058 49.5 5553000 112251.1
20:47:19.471 INFO ProgressMeter - chr21:5555058 49.7 5555000 111728.1
20:47:34.462 INFO ProgressMeter - chr21:5557058 50.0 5557000 111209.5
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20:48:04.339 INFO ProgressMeter - chr21:5561058 50.5 5561000 110191.5
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20:48:34.358 INFO ProgressMeter - chr21:5565058 51.0 5565000 109188.3
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20:49:04.489 INFO ProgressMeter - chr21:5569058 51.5 5569000 108200.6
20:49:19.536 INFO ProgressMeter - chr21:5571058 51.7 5571000 107714.7
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20:50:04.645 INFO ProgressMeter - chr21:5577058 52.5 5577000 106285.7
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20:52:04.340 INFO ProgressMeter - chr21:5593058 54.5 5593000 102686.6
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20:53:04.582 INFO ProgressMeter - chr21:5601058 55.5 5601000 100972.1
20:53:19.697 INFO ProgressMeter - chr21:5603058 55.7 5603000 100551.5
20:53:34.770 INFO ProgressMeter - chr21:5605058 56.0 5605000 100136.0
20:53:49.841 INFO ProgressMeter - chr21:5607058 56.2 5607000 99724.2
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20:54:19.962 INFO ProgressMeter - chr21:5611058 56.7 5611000 98912.2
20:54:35.040 INFO ProgressMeter - chr21:5613058 57.0 5613000 98511.0
20:54:50.042 INFO ProgressMeter - chr21:5615058 57.2 5615000 98115.6
20:55:05.081 INFO ProgressMeter - chr21:5617058 57.5 5617000 97722.5
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20:56:50.436 INFO ProgressMeter - chr21:5681058 59.2 5681000 95906.2
20:57:05.466 INFO ProgressMeter - chr21:5683058 59.5 5683000 95535.9
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20:59:05.820 INFO ProgressMeter - chr21:5699058 61.5 5699000 92679.7
20:59:20.977 INFO ProgressMeter - chr21:5701058 61.7 5701000 92332.9
20:59:36.178 INFO ProgressMeter - chr21:5703058 62.0 5703000 91987.8
20:59:51.290 INFO ProgressMeter - chr21:5705058 62.2 5705000 91647.7
21:00:06.344 INFO ProgressMeter - chr21:5707058 62.5 5707000 91311.8
21:00:21.442 INFO ProgressMeter - chr21:5709058 62.8 5709000 90977.5
21:00:36.500 INFO ProgressMeter - chr21:5711058 63.0 5711000 90646.9
21:00:51.549 INFO ProgressMeter - chr21:5713058 63.3 5713000 90319.1
21:01:06.593 INFO ProgressMeter - chr21:5715058 63.5 5715000 89994.0
21:01:21.657 INFO ProgressMeter - chr21:5717058 63.8 5717000 89670.9
21:01:36.706 INFO ProgressMeter - chr21:5719058 64.0 5719000 89350.8
21:01:51.745 INFO ProgressMeter - chr21:5721058 64.3 5721000 89033.4
21:02:06.793 INFO ProgressMeter - chr21:5723058 64.5 5723000 88718.2
21:02:21.837 INFO ProgressMeter - chr21:5725058 64.8 5725000 88405.6
21:02:36.860 INFO ProgressMeter - chr21:5727058 65.0 5727000 88095.9
21:02:51.881 INFO ProgressMeter - chr21:5729058 65.3 5729000 87788.6
21:03:06.908 INFO ProgressMeter - chr21:5731058 65.5 5731000 87483.5
21:03:21.948 INFO ProgressMeter - chr21:5733058 65.8 5733000 87180.4
21:03:37.028 INFO ProgressMeter - chr21:5735058 66.0 5735000 86878.8
21:03:52.084 INFO ProgressMeter - chr21:5737058 66.3 5737000 86580.0
21:04:07.263 INFO ProgressMeter - chr21:5739058 66.5 5739000 86280.7
21:04:22.483 INFO ProgressMeter - chr21:5741058 66.8 5741000 85982.9
21:04:37.380 INFO ProgressMeter - chr21:5743058 67.0 5743000 85694.2
21:04:52.314 INFO ProgressMeter - chr21:5745058 67.3 5745000 85406.8
21:05:07.277 INFO ProgressMeter - chr21:5747058 67.5 5747000 85121.0
21:05:22.327 INFO ProgressMeter - chr21:5749058 67.8 5749000 84835.4
21:05:37.369 INFO ProgressMeter - chr21:5751058 68.0 5751000 84552.1
21:05:52.465 INFO ProgressMeter - chr21:5753058 68.3 5753000 84269.8
21:06:07.542 INFO ProgressMeter - chr21:5755058 68.5 5755000 83990.0
21:06:22.580 INFO ProgressMeter - chr21:5757058 68.8 5757000 83713.0
21:06:37.644 INFO ProgressMeter - chr21:5759058 69.0 5759000 83437.4
21:06:52.677 INFO ProgressMeter - chr21:5761058 69.3 5761000 83164.5
21:07:07.906 INFO ProgressMeter - chr21:5763058 69.5 5763000 82889.7
21:07:22.961 INFO ProgressMeter - chr21:5765058 69.8 5765000 82620.3
21:07:38.153 INFO ProgressMeter - chr21:5767058 70.0 5767000 82350.1
21:07:53.221 INFO ProgressMeter - chr21:5769058 70.3 5769000 82084.3
21:08:08.337 INFO ProgressMeter - chr21:5771058 70.5 5771000 81819.5
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21:08:38.504 INFO ProgressMeter - chr21:5775058 71.0 5775000 81296.7
21:08:53.585 INFO ProgressMeter - chr21:5777058 71.3 5777000 81038.1
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21:09:39.067 INFO ProgressMeter - chr21:5783058 72.0 5783000 80268.7
21:09:54.137 INFO ProgressMeter - chr21:5785058 72.3 5785000 80017.5
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21:10:24.275 INFO ProgressMeter - chr21:5789058 72.8 5789000 79520.4
21:10:39.535 INFO ProgressMeter - chr21:5791058 73.1 5791000 79270.9
21:10:54.631 INFO ProgressMeter - chr21:5793058 73.3 5793000 79026.1
21:11:09.833 INFO ProgressMeter - chr21:5795058 73.6 5795000 78781.1
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21:11:55.449 INFO ProgressMeter - chr21:5851058 74.3 5851000 78728.7
21:12:10.964 INFO ProgressMeter - chr21:5853058 74.6 5853000 78482.5
21:12:26.530 INFO ProgressMeter - chr21:5855058 74.8 5855000 78237.2
21:12:41.557 INFO ProgressMeter - chr21:5857058 75.1 5857000 78002.9
21:12:56.590 INFO ProgressMeter - chr21:5859058 75.3 5859000 77770.0
21:13:11.668 INFO ProgressMeter - chr21:5861058 75.6 5861000 77537.9
21:13:26.729 INFO ProgressMeter - chr21:5863058 75.8 5863000 77307.6
21:13:41.744 INFO ProgressMeter - chr21:5865058 76.1 5865000 77079.7
21:13:56.854 INFO ProgressMeter - chr21:5867058 76.3 5867000 76851.6
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21:14:42.132 INFO ProgressMeter - chr21:5873058 77.1 5873000 76177.2
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21:16:42.887 INFO ProgressMeter - chr21:5889058 79.1 5889000 74441.4
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21:17:12.993 INFO ProgressMeter - chr21:5893058 79.6 5893000 74022.5
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21:19:59.687 INFO ProgressMeter - chr21:5915058 82.4 5915000 71793.4
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21:21:08.067 INFO ProgressMeter - chr21:5974058 83.5 5974000 71520.2
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21:23:09.345 INFO ProgressMeter - chr21:5990058 85.6 5990000 70017.4
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21:24:09.831 INFO ProgressMeter - chr21:5998058 86.6 5998000 69294.4
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21:24:39.955 INFO ProgressMeter - chr21:6002058 87.1 6002000 68940.7
21:24:55.073 INFO ProgressMeter - chr21:6004058 87.3 6004000 68764.7
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21:25:40.271 INFO ProgressMeter - chr21:6010058 88.1 6010000 68244.6
21:25:55.364 INFO ProgressMeter - chr21:6012058 88.3 6012000 68072.9
21:26:10.391 INFO ProgressMeter - chr21:6014058 88.6 6014000 67903.0
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21:26:40.492 INFO ProgressMeter - chr21:6018058 89.1 6018000 67565.4
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21:27:10.781 INFO ProgressMeter - chr21:6022058 89.6 6022000 67229.3
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21:27:40.935 INFO ProgressMeter - chr21:6026058 90.1 6026000 66898.6
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21:28:11.019 INFO ProgressMeter - chr21:6030058 90.6 6030000 66572.4
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21:28:41.111 INFO ProgressMeter - chr21:6034058 91.1 6034000 66249.8
21:28:56.179 INFO ProgressMeter - chr21:6036058 91.3 6036000 66089.5
21:29:11.240 INFO ProgressMeter - chr21:6038058 91.6 6038000 65930.2
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21:30:11.186 INFO ProgressMeter - chr21:6046058 92.6 6046000 65305.1
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21:30:41.228 INFO ProgressMeter - chr21:6050058 93.1 6050000 64996.8
21:30:56.249 INFO ProgressMeter - chr21:6052058 93.3 6052000 64843.9
21:31:11.292 INFO ProgressMeter - chr21:6054058 93.6 6054000 64691.5
21:31:26.355 INFO ProgressMeter - chr21:6056058 93.8 6056000 64539.8
21:31:41.431 INFO ProgressMeter - chr21:6058058 94.1 6058000 64388.7
21:31:56.491 INFO ProgressMeter - chr21:6060058 94.3 6060000 64238.5
21:32:11.542 INFO ProgressMeter - chr21:6062058 94.6 6062000 64089.3
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21:32:41.634 INFO ProgressMeter - chr21:6066058 95.1 6066000 63793.3
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21:33:11.683 INFO ProgressMeter - chr21:6070058 95.6 6070000 63501.0
21:33:26.724 INFO ProgressMeter - chr21:6072058 95.8 6072000 63355.7
21:33:41.706 INFO ProgressMeter - chr21:6074058 96.1 6074000 63211.9
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21:34:11.970 INFO ProgressMeter - chr21:6078058 96.6 6078000 62923.2
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21:34:57.147 INFO ProgressMeter - chr21:6084058 97.3 6084000 62498.2
21:35:12.223 INFO ProgressMeter - chr21:6086058 97.6 6086000 62357.8
21:35:27.266 INFO ProgressMeter - chr21:6088058 97.8 6088000 62218.4
21:35:42.343 INFO ProgressMeter - chr21:6090058 98.1 6090000 62079.5
21:35:57.376 INFO ProgressMeter - chr21:6092058 98.4 6092000 61941.6
21:36:12.539 INFO ProgressMeter - chr21:6094058 98.6 6094000 61803.2
21:36:27.592 INFO ProgressMeter - chr21:6096058 98.9 6096000 61666.5
21:36:42.628 INFO ProgressMeter - chr21:6098059 99.1 6098000 61530.8
21:36:57.641 INFO ProgressMeter - chr21:6100059 99.4 6100000 61396.0
21:37:12.683 INFO ProgressMeter - chr21:6102059 99.6 6102000 61261.5
21:37:27.732 INFO ProgressMeter - chr21:6104059 99.9 6104000 61127.7
21:37:42.770 INFO ProgressMeter - chr21:6106059 100.1 6106000 60994.6
21:37:57.809 INFO ProgressMeter - chr21:6108059 100.4 6108000 60862.2
21:38:12.815 INFO ProgressMeter - chr21:6110059 100.6 6110000 60730.8
21:38:27.844 INFO ProgressMeter - chr21:6112059 100.9 6112000 60599.8
21:38:42.899 INFO ProgressMeter - chr21:6114059 101.1 6114000 60469.2
21:38:57.915 INFO ProgressMeter - chr21:6116059 101.4 6116000 60339.6
21:39:12.929 INFO ProgressMeter - chr21:6118059 101.6 6118000 60210.7
21:39:27.986 INFO ProgressMeter - chr21:6120059 101.9 6120000 60082.0
21:39:43.041 INFO ProgressMeter - chr21:6122059 102.1 6122000 59953.9
21:39:58.093 INFO ProgressMeter - chr21:6124059 102.4 6124000 59826.5
21:40:13.182 INFO ProgressMeter - chr21:6126060 102.6 6126000 59699.4
21:40:28.305 INFO ProgressMeter - chr21:6128060 102.9 6128000 59572.6
21:40:43.399 INFO ProgressMeter - chr21:6130060 103.1 6130000 59446.6
21:40:58.496 INFO ProgressMeter - chr21:6132061 103.4 6132000 59321.3
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21:41:28.705 INFO ProgressMeter - chr21:6136061 103.9 6136000 59072.2
21:41:43.814 INFO ProgressMeter - chr21:6138061 104.1 6138000 58948.6
21:41:58.885 INFO ProgressMeter - chr21:6140061 104.4 6140000 58825.9
21:42:13.941 INFO ProgressMeter - chr21:6142061 104.6 6142000 58703.9
21:42:28.973 INFO ProgressMeter - chr21:6144061 104.9 6144000 58582.8
21:42:44.015 INFO ProgressMeter - chr21:6146061 105.1 6146000 58462.1
21:42:59.002 INFO ProgressMeter - chr21:6148061 105.4 6148000 58342.5
21:43:14.021 INFO ProgressMeter - chr21:6150061 105.6 6150000 58223.2
21:43:29.214 INFO ProgressMeter - chr21:6152061 105.9 6152000 58102.8
21:43:44.448 INFO ProgressMeter - chr21:6154061 106.1 6154000 57982.7
21:43:59.562 INFO ProgressMeter - chr21:6156061 106.4 6156000 57864.2
21:44:14.669 INFO ProgressMeter - chr21:6158061 106.6 6158000 57746.3
21:44:29.685 INFO ProgressMeter - chr21:6160061 106.9 6160000 57629.8
21:44:44.704 INFO ProgressMeter - chr21:6212061 107.1 6212000 57980.5
21:44:59.628 INFO ProgressMeter - chr21:6214061 107.4 6214000 57864.8
21:45:14.567 INFO ProgressMeter - chr21:6216061 107.6 6216000 57749.6
21:45:29.538 INFO ProgressMeter - chr21:6218061 107.9 6218000 57634.5
21:45:44.572 INFO ProgressMeter - chr21:6220061 108.1 6220000 57519.5
21:45:59.696 INFO ProgressMeter - chr21:6222061 108.4 6222000 57404.2
21:46:14.817 INFO ProgressMeter - chr21:6224061 108.6 6224000 57289.4
21:46:29.810 INFO ProgressMeter - chr21:6226061 108.9 6226000 57176.3
21:46:44.837 INFO ProgressMeter - chr21:6228061 109.1 6228000 57063.4
21:46:59.854 INFO ProgressMeter - chr21:6230061 109.4 6230000 56951.2
21:47:14.903 INFO ProgressMeter - chr21:6232061 109.6 6232000 56839.1
21:47:29.949 INFO ProgressMeter - chr21:6234061 109.9 6234000 56727.6
21:47:44.997 INFO ProgressMeter - chr21:6236061 110.1 6236000 56616.6
21:48:00.025 INFO ProgressMeter - chr21:6238061 110.4 6238000 56506.3
21:48:15.053 INFO ProgressMeter - chr21:6240061 110.6 6240000 56396.4
21:48:30.019 INFO ProgressMeter - chr21:6242061 110.9 6242000 56287.6
21:48:44.997 INFO ProgressMeter - chr21:6244061 111.1 6244000 56179.2
21:48:59.865 INFO ProgressMeter - chr21:6246061 111.4 6246000 56072.2
21:49:14.784 INFO ProgressMeter - chr21:6248061 111.6 6248000 55965.2
21:49:29.873 INFO ProgressMeter - chr21:6250061 111.9 6250000 55857.3
21:49:44.927 INFO ProgressMeter - chr21:6252061 112.1 6252000 55750.2
21:50:00.065 INFO ProgressMeter - chr21:6254061 112.4 6254000 55642.8
21:50:15.148 INFO ProgressMeter - chr21:6256061 112.6 6256000 55536.4
21:50:30.379 INFO ProgressMeter - chr21:6258061 112.9 6258000 55429.2
21:50:45.338 INFO ProgressMeter - chr21:6260061 113.2 6260000 55324.8
21:51:00.369 INFO ProgressMeter - chr21:6262061 113.4 6262000 55220.2
21:51:15.413 INFO ProgressMeter - chr21:6264061 113.7 6264000 55116.0
21:51:30.475 INFO ProgressMeter - chr21:6266061 113.9 6266000 55012.1
21:51:45.513 INFO ProgressMeter - chr21:6268061 114.2 6268000 54908.8
21:52:00.568 INFO ProgressMeter - chr21:6270061 114.4 6270000 54805.8
21:52:15.688 INFO ProgressMeter - chr21:6272061 114.7 6272000 54702.8
21:52:30.798 INFO ProgressMeter - chr21:6274061 114.9 6274000 54600.4
21:52:45.901 INFO ProgressMeter - chr21:6276061 115.2 6276000 54498.4
21:53:00.912 INFO ProgressMeter - chr21:6278061 115.4 6278000 54397.6
21:53:15.976 INFO ProgressMeter - chr21:6280061 115.7 6280000 54296.8
21:53:30.998 INFO ProgressMeter - chr21:6282061 115.9 6282000 54196.7
21:53:45.959 INFO ProgressMeter - chr21:6284061 116.2 6284000 54097.6
21:54:01.021 INFO ProgressMeter - chr21:6286061 116.4 6286000 53998.1
21:54:16.100 INFO ProgressMeter - chr21:6288061 116.7 6288000 53899.0
21:54:31.123 INFO ProgressMeter - chr21:6290061 116.9 6290000 53800.6
21:54:46.158 INFO ProgressMeter - chr21:6292061 117.2 6292000 53702.6
21:55:01.176 INFO ProgressMeter - chr21:6294061 117.4 6294000 53605.2
21:55:16.207 INFO ProgressMeter - chr21:6296061 117.7 6296000 53508.1
21:55:31.266 INFO ProgressMeter - chr21:6298061 117.9 6298000 53411.1
21:55:46.452 INFO ProgressMeter - chr21:6300061 118.2 6300000 53313.7
21:56:01.613 INFO ProgressMeter - chr21:6302061 118.4 6302000 53216.8
21:56:16.659 INFO ProgressMeter - chr21:6304061 118.7 6304000 53121.2
21:56:31.792 INFO ProgressMeter - chr21:6306061 118.9 6306000 53025.4
21:56:46.802 INFO ProgressMeter - chr21:6308061 119.2 6308000 52930.8
21:57:01.820 INFO ProgressMeter - chr21:6310061 119.4 6310000 52836.6
21:57:16.780 INFO ProgressMeter - chr21:6312061 119.7 6312000 52743.3
21:57:31.763 INFO ProgressMeter - chr21:6314061 119.9 6314000 52650.1
21:57:46.803 INFO ProgressMeter - chr21:6316061 120.2 6316000 52556.9
21:58:01.845 INFO ProgressMeter - chr21:6318061 120.4 6318000 52464.1
21:58:16.906 INFO ProgressMeter - chr21:6320061 120.7 6320000 52371.6
21:58:31.971 INFO ProgressMeter - chr21:6322061 120.9 6322000 52279.4
21:58:47.029 INFO ProgressMeter - chr21:6324061 121.2 6324000 52187.6
21:59:02.076 INFO ProgressMeter - chr21:6326061 121.4 6326000 52096.3
21:59:17.184 INFO ProgressMeter - chr21:6328061 121.7 6328000 52004.9
21:59:32.247 INFO ProgressMeter - chr21:6330061 121.9 6330000 51914.3
21:59:47.298 INFO ProgressMeter - chr21:6332061 122.2 6332000 51824.0
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22:01:47.288 INFO ProgressMeter - chr21:6348061 124.2 6348000 51118.3
22:02:02.291 INFO ProgressMeter - chr21:6350061 124.4 6350000 51031.7
22:02:17.263 INFO ProgressMeter - chr21:6352061 124.7 6352000 50945.6
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22:03:32.539 INFO ProgressMeter - chr21:6362061 125.9 6362000 50517.4
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22:04:02.599 INFO ProgressMeter - chr21:6366062 126.4 6366000 50348.9
22:04:17.659 INFO ProgressMeter - chr21:6368063 126.7 6368000 50264.9
22:04:32.736 INFO ProgressMeter - chr21:6370064 126.9 6370000 50181.2
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22:05:02.852 INFO ProgressMeter - chr21:6374065 127.4 6374000 50014.9
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22:06:03.216 INFO ProgressMeter - chr21:6432066 128.4 6432000 50074.7
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22:06:48.388 INFO ProgressMeter - chr21:6438066 129.2 6438000 49829.4
22:07:03.468 INFO ProgressMeter - chr21:6440066 129.5 6440000 49748.1
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22:09:33.505 INFO ProgressMeter - chr21:6460066 132.0 6460000 48956.9
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22:10:03.576 INFO ProgressMeter - chr21:6464066 132.5 6464000 48801.9
22:10:18.617 INFO ProgressMeter - chr21:6466066 132.7 6466000 48724.7
22:10:33.654 INFO ProgressMeter - chr21:6468066 133.0 6468000 48647.9
22:10:48.643 INFO ProgressMeter - chr21:6470066 133.2 6470000 48571.7
22:11:03.584 INFO ProgressMeter - chr21:6472066 133.5 6472000 48496.1
22:11:18.502 INFO ProgressMeter - chr21:6474066 133.7 6474000 48420.8
22:11:33.447 INFO ProgressMeter - chr21:6476066 134.0 6476000 48345.7
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22:12:03.299 INFO ProgressMeter - chr21:6480066 134.4 6480000 48196.6
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22:12:48.006 INFO ProgressMeter - chr21:6486066 135.2 6486000 47975.3
22:13:02.995 INFO ProgressMeter - chr21:6488066 135.4 6488000 47901.6
22:13:17.976 INFO ProgressMeter - chr21:6490067 135.7 6490000 47828.2
22:13:33.037 INFO ProgressMeter - chr21:6492068 135.9 6492000 47754.6
22:13:48.065 INFO ProgressMeter - chr21:6494068 136.2 6494000 47681.5
22:14:02.871 INFO ProgressMeter - chr21:6496068 136.4 6496000 47609.9
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22:14:32.789 INFO ProgressMeter - chr21:6500068 136.9 6500000 47465.7
22:14:47.899 INFO ProgressMeter - chr21:6502068 137.2 6502000 47393.2
22:15:02.998 INFO ProgressMeter - chr21:6504068 137.4 6504000 47321.0
22:15:18.089 INFO ProgressMeter - chr21:6506068 137.7 6506000 47249.1
22:15:33.129 INFO ProgressMeter - chr21:6508068 137.9 6508000 47177.7
22:15:48.110 INFO ProgressMeter - chr21:6510068 138.2 6510000 47106.9
22:16:03.157 INFO ProgressMeter - chr21:6512068 138.4 6512000 47036.0
22:16:18.196 INFO ProgressMeter - chr21:6514068 138.7 6514000 46965.5
22:16:33.256 INFO ProgressMeter - chr21:6516068 138.9 6516000 46895.0
22:16:48.356 INFO ProgressMeter - chr21:6518069 139.2 6518000 46824.6
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22:17:18.486 INFO ProgressMeter - chr21:6522069 139.7 6522000 46684.9
22:17:33.544 INFO ProgressMeter - chr21:6524069 140.0 6524000 46615.5
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22:18:03.790 INFO ProgressMeter - chr21:6528069 140.5 6528000 46476.7
22:18:18.889 INFO ProgressMeter - chr21:6530069 140.7 6530000 46407.8
22:18:33.969 INFO ProgressMeter - chr21:6532069 141.0 6532000 46339.2
22:18:49.056 INFO ProgressMeter - chr21:6534069 141.2 6534000 46270.9
22:19:04.284 INFO ProgressMeter - chr21:6536069 141.5 6536000 46202.0
22:19:19.500 INFO ProgressMeter - chr21:6538069 141.7 6538000 46133.4
22:19:34.686 INFO ProgressMeter - chr21:6540069 142.0 6540000 46065.3
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22:20:04.776 INFO ProgressMeter - chr21:6544069 142.5 6544000 45931.2
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22:20:34.906 INFO ProgressMeter - chr21:6548069 143.0 6548000 45797.8
22:20:50.109 INFO ProgressMeter - chr21:6550069 143.2 6550000 45730.8
22:21:05.181 INFO ProgressMeter - chr21:6552069 143.5 6552000 45664.7
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22:21:35.260 INFO ProgressMeter - chr21:6556069 144.0 6556000 45533.5
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22:22:05.405 INFO ProgressMeter - chr21:6560069 144.5 6560000 45402.8
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22:22:35.747 INFO ProgressMeter - chr21:6564069 145.0 6564000 45272.0
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22:23:05.839 INFO ProgressMeter - chr21:6568070 145.5 6568000 45143.5
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22:24:07.079 INFO ProgressMeter - chr21:6576070 146.5 6576000 44883.6
22:24:22.350 INFO ProgressMeter - chr21:6578070 146.8 6578000 44819.4
22:24:37.703 INFO ProgressMeter - chr21:6580070 147.0 6580000 44755.0
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22:25:53.372 INFO ProgressMeter - chr21:6640070 148.3 6640000 44779.0
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22:27:08.780 INFO ProgressMeter - chr21:6650070 149.5 6650000 44469.5
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22:32:08.944 INFO ProgressMeter - chr21:6690070 154.5 6690000 43288.8
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22:35:40.089 INFO ProgressMeter - chr21:6718070 158.1 6718000 42502.2
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22:36:10.271 INFO ProgressMeter - chr21:6722070 158.6 6722000 42392.6
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22:37:10.419 INFO ProgressMeter - chr21:6730070 159.6 6730000 42176.4
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22:39:40.970 INFO ProgressMeter - chr21:6800070 162.1 6800000 41955.3
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22:40:11.036 INFO ProgressMeter - chr21:6804070 162.6 6804000 41850.6
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22:45:57.109 INFO ProgressMeter - chr21:6850071 168.3 6850000 40690.0
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22:46:57.188 INFO ProgressMeter - chr21:6858071 169.3 6858000 40496.6
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22:47:57.286 INFO ProgressMeter - chr21:6866071 170.3 6866000 40305.5
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22:49:12.223 INFO ProgressMeter - chr21:6876071 171.6 6876000 40070.4
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22:50:12.791 INFO ProgressMeter - chr21:6884071 172.6 6884000 39882.4
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22:51:13.041 INFO ProgressMeter - chr21:6892071 173.6 6892000 39697.8
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22:52:13.434 INFO ProgressMeter - chr21:6900071 174.6 6900000 39514.8
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22:53:43.010 INFO ProgressMeter - chr21:6912071 176.1 6912000 39247.9
22:53:57.922 INFO ProgressMeter - chr21:6914071 176.4 6914000 39204.0
22:54:12.830 INFO ProgressMeter - chr21:6916071 176.6 6916000 39160.1
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22:55:12.649 INFO ProgressMeter - chr21:6924071 177.6 6924000 38985.3
22:55:27.726 INFO ProgressMeter - chr21:6926071 177.9 6926000 38941.5
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22:55:57.799 INFO ProgressMeter - chr21:6930071 178.4 6930000 38854.5
22:56:12.850 INFO ProgressMeter - chr21:6932071 178.6 6932000 38811.1
22:56:27.901 INFO ProgressMeter - chr21:6934071 178.9 6934000 38767.9
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22:56:58.173 INFO ProgressMeter - chr21:6988071 179.4 6988000 38959.9
22:57:13.221 INFO ProgressMeter - chr21:6990071 179.6 6990000 38916.6
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22:58:28.230 INFO ProgressMeter - chr21:7000071 180.9 7000000 38702.9
22:58:43.199 INFO ProgressMeter - chr21:7002071 181.1 7002000 38660.7
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22:59:28.316 INFO ProgressMeter - chr21:7008071 181.9 7008000 38533.8
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22:59:58.477 INFO ProgressMeter - chr21:7012071 182.4 7012000 38449.5
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23:13:45.823 INFO ProgressMeter - chr21:7122071 196.2 7122000 36307.4
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23:16:02.181 INFO ProgressMeter - chr21:7140071 198.4 7140000 35982.3
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23:19:10.954 INFO ProgressMeter - chr21:7215071 201.6 7215000 35792.8
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23:24:02.613 INFO ProgressMeter - chr21:7255082 206.4 7255000 35143.7
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23:24:46.095 INFO ProgressMeter - chr21:7261085 207.2 7261000 35049.8
23:25:00.561 INFO ProgressMeter - chr21:7263087 207.4 7263000 35018.7
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23:25:58.640 INFO ProgressMeter - chr21:7271087 208.4 7271000 34894.4
23:26:13.144 INFO ProgressMeter - chr21:7273087 208.6 7273000 34863.5
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23:26:42.229 INFO ProgressMeter - chr21:7277087 209.1 7277000 34801.8
23:26:56.760 INFO ProgressMeter - chr21:7279087 209.3 7279000 34771.1
23:27:11.226 INFO ProgressMeter - chr21:7281088 209.6 7281000 34740.7
23:27:25.666 INFO ProgressMeter - chr21:7283088 209.8 7283000 34710.3
23:27:40.210 INFO ProgressMeter - chr21:7285088 210.1 7285000 34679.8
23:27:54.770 INFO ProgressMeter - chr21:7287088 210.3 7287000 34649.3
23:28:09.204 INFO ProgressMeter - chr21:7289089 210.5 7289000 34619.2
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23:29:06.949 INFO ProgressMeter - chr21:7297089 211.5 7297000 34499.5
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23:29:35.968 INFO ProgressMeter - chr21:7301089 212.0 7301000 34439.7
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00:36:04.441 INFO ProgressMeter - chr21:8101115 278.5 8101000 29091.3
00:36:18.925 INFO ProgressMeter - chr21:8103115 278.7 8103000 29073.3
00:36:33.337 INFO ProgressMeter - chr21:8105115 279.0 8105000 29055.4
00:36:47.748 INFO ProgressMeter - chr21:8107115 279.2 8107000 29037.6
00:37:02.166 INFO ProgressMeter - chr21:8109115 279.4 8109000 29019.7
00:37:16.582 INFO ProgressMeter - chr21:8111115 279.7 8111000 29002.0
00:37:30.991 INFO ProgressMeter - chr21:8113115 279.9 8113000 28984.2
00:37:45.590 INFO ProgressMeter - chr21:8115115 280.2 8115000 28966.2
00:38:00.009 INFO ProgressMeter - chr21:8117115 280.4 8117000 28948.5
00:38:14.543 INFO ProgressMeter - chr21:8119115 280.6 8119000 28930.6
00:38:29.084 INFO ProgressMeter - chr21:8121115 280.9 8121000 28912.8
00:38:43.665 INFO ProgressMeter - chr21:8123115 281.1 8123000 28894.9
00:38:58.173 INFO ProgressMeter - chr21:8125115 281.4 8125000 28877.2
00:39:12.738 INFO ProgressMeter - chr21:8127115 281.6 8127000 28859.4
00:39:27.216 INFO ProgressMeter - chr21:8129115 281.8 8129000 28841.8
00:39:41.629 INFO ProgressMeter - chr21:8131115 282.1 8131000 28824.3
00:39:56.025 INFO ProgressMeter - chr21:8133115 282.3 8133000 28806.9
00:40:10.418 INFO ProgressMeter - chr21:8135115 282.6 8135000 28789.5
00:40:24.838 INFO ProgressMeter - chr21:8137115 282.8 8137000 28772.1
00:40:39.260 INFO ProgressMeter - chr21:8139115 283.0 8139000 28754.8
00:40:53.688 INFO ProgressMeter - chr21:8141115 283.3 8141000 28737.4
00:41:08.108 INFO ProgressMeter - chr21:8143115 283.5 8143000 28720.1
00:41:22.520 INFO ProgressMeter - chr21:8145115 283.8 8145000 28702.9
00:41:36.944 INFO ProgressMeter - chr21:8147115 284.0 8147000 28685.6
00:41:51.351 INFO ProgressMeter - chr21:8149115 284.3 8149000 28668.4
00:42:05.759 INFO ProgressMeter - chr21:8151115 284.5 8151000 28651.2
00:42:20.177 INFO ProgressMeter - chr21:8153115 284.7 8153000 28634.1
00:42:34.670 INFO ProgressMeter - chr21:8155115 285.0 8155000 28616.8
00:42:49.107 INFO ProgressMeter - chr21:8157115 285.2 8157000 28599.7
00:43:03.552 INFO ProgressMeter - chr21:8159115 285.5 8159000 28582.6
00:43:17.991 INFO ProgressMeter - chr21:8161115 285.7 8161000 28565.5
00:43:32.421 INFO ProgressMeter - chr21:8163115 285.9 8163000 28548.5
00:43:46.844 INFO ProgressMeter - chr21:8165115 286.2 8165000 28531.5
00:44:01.266 INFO ProgressMeter - chr21:8167115 286.4 8167000 28514.5
00:44:15.677 INFO ProgressMeter - chr21:8169115 286.7 8169000 28497.6
00:44:30.361 INFO ProgressMeter - chr21:8171115 286.9 8171000 28480.3
00:44:44.890 INFO ProgressMeter - chr21:8173115 287.1 8173000 28463.2
00:44:59.518 INFO ProgressMeter - chr21:8175115 287.4 8175000 28446.0
00:45:14.019 INFO ProgressMeter - chr21:8177115 287.6 8177000 28429.1
00:45:28.560 INFO ProgressMeter - chr21:8179115 287.9 8179000 28412.1
00:45:43.085 INFO ProgressMeter - chr21:8181115 288.1 8181000 28395.2
00:45:57.735 INFO ProgressMeter - chr21:8183115 288.4 8183000 28378.1
00:46:12.360 INFO ProgressMeter - chr21:8185115 288.6 8185000 28361.0
00:46:26.793 INFO ProgressMeter - chr21:8187115 288.8 8187000 28344.3
00:46:41.216 INFO ProgressMeter - chr21:8189115 289.1 8189000 28327.7
00:46:55.641 INFO ProgressMeter - chr21:8191115 289.3 8191000 28311.0
00:47:10.071 INFO ProgressMeter - chr21:8193115 289.6 8193000 28294.4
00:47:24.535 INFO ProgressMeter - chr21:8195115 289.8 8195000 28277.8
00:47:39.054 INFO ProgressMeter - chr21:8197115 290.0 8197000 28261.1
00:47:53.524 INFO ProgressMeter - chr21:8199115 290.3 8199000 28244.5
00:48:07.981 INFO ProgressMeter - chr21:8201115 290.5 8201000 28228.0
00:48:22.449 INFO ProgressMeter - chr21:8203115 290.8 8203000 28211.4
00:48:36.928 INFO ProgressMeter - chr21:8205115 291.0 8205000 28194.9
00:48:51.362 INFO ProgressMeter - chr21:8207115 291.3 8207000 28178.5
00:49:05.781 INFO ProgressMeter - chr21:8209115 291.5 8209000 28162.1
00:49:20.200 INFO ProgressMeter - chr21:8211115 291.7 8211000 28145.8
00:49:34.625 INFO ProgressMeter - chr21:8213115 292.0 8213000 28129.5
00:49:49.065 INFO ProgressMeter - chr21:8215115 292.2 8215000 28113.1
00:50:03.538 INFO ProgressMeter - chr21:8217115 292.5 8217000 28096.8
00:50:18.000 INFO ProgressMeter - chr21:8219115 292.7 8219000 28080.5
00:50:32.463 INFO ProgressMeter - chr21:8221116 292.9 8221000 28064.2
00:50:46.906 INFO ProgressMeter - chr21:8223116 293.2 8223000 28048.0
00:51:01.313 INFO ProgressMeter - chr21:8225116 293.4 8225000 28031.8
00:51:15.747 INFO ProgressMeter - chr21:8227116 293.7 8227000 28015.7
00:51:30.172 INFO ProgressMeter - chr21:8229116 293.9 8229000 27999.6
00:51:44.606 INFO ProgressMeter - chr21:8231116 294.1 8231000 27983.5
00:51:59.063 INFO ProgressMeter - chr21:8233117 294.4 8233000 27967.4
00:52:13.567 INFO ProgressMeter - chr21:8235117 294.6 8235000 27951.2
00:52:28.003 INFO ProgressMeter - chr21:8237117 294.9 8237000 27935.2
00:52:42.453 INFO ProgressMeter - chr21:8239117 295.1 8239000 27919.2
00:52:56.896 INFO ProgressMeter - chr21:8241117 295.3 8241000 27903.2
00:53:11.361 INFO ProgressMeter - chr21:8243117 295.6 8243000 27887.2
00:53:25.779 INFO ProgressMeter - chr21:8245117 295.8 8245000 27871.3This is really extremely slow and is not how it is supposed to be. I can provide you with VCF file which I used upon request.
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Hi danilovkiri
I am looking into this and will get back to you shortly.
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Hi danilovkiri
Can you please provide your vcf so we can debug? Here is info on how to share data with us: https://gatk.zendesk.com/hc/en-us/articles/360035889671
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I have uploaded the archive. The name is danilovk_11Jun2020_main.tar
There is another archive there named danilovk_11Jun2020.tar, but it is truncated due to connection loss.
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Hi danilovkiri
We are looking into this and will get back to you shortly.
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Hi danilovkiri
I have created a issue ticket for this. Since we have some other tickets in the queue that we are working on, we unfortunately cannot give you a timeline by when we will be able to fix this issue. However, rest assured this is on our radar and we will get to it. You can track its progress here: https://github.com/broadinstitute/gatk/issues/6663
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Thank you for providing the test file. We used it to identify and fix a critical performance bug. In the next GATK release your command will run 3 orders of magnitude faster. (~5,000 sites per minute -> ~5,000,000). It completed the test file in about 18 minutes. This is still somewhat slower than you said it was in gatk3, but should hopefully be similar enough that it's not a problem.
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Bhanu Gandham Thank you!
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