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PrintRead -BQSR gets stuck on a contig

Hi GATK team!

I am analysing WGS data following GATK best practices. I am using GATK version 3.8-1-0, java version 1.8.0_191 and human genome version GRCh38 from ensembl.

I downloaded from GATK bundle Mills_and_1000G_gold_standard.indels.hg38.vcf.gz and dbsnp_138.hg38.vcf.gz files and I used them as KnownSites to generate covariates tables with BaseRecalibrator tool. Then I am using PrintReads tool with -BQSR option to generate bam file with recalibrated bases using the next command:
java -jar GenomeAnalysisTK.jar -T PrintReads -R Homo_sapiens.GRCh38.dna.primary_assembly.fa H_bwa_sort_dup.bam -BQSR H_post_recal_data.table -o H_bwa_sort_dup_recal.bam -nct 20

As I show with the std output I paste below, PrintRead tool gets too slow once reaches contig KI270394.1, and stays there for hours (even saying that process was 100% complete) till it finishes. I guess that is not a normal behaviour and I would like to know if I did something wrong or how to solve the problem.

Thank you!

INFO 14:37:58,968 HelpFormatter - ------------------------------------------------------------------------------------
INFO 14:37:58,970 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-1-0-gf15c1c3ef, Compiled 2018/02/19 05:43:50
INFO 14:37:58,970 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 14:37:58,971 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 14:37:58,971 HelpFormatter - [Wed Dec 11 14:37:58 CET 2019] Executing on Linux 3.10.0-862.14.4.el7.x86_64 amd64
INFO 14:37:58,971 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_191-b12
INFO 14:37:58,973 HelpFormatter - Program Args: -T PrintReads -R Homo_sapiens.GRCh38.dna.primary_assembly.fa -I H_bwa_sort_dup.bam -BQSR H_post_recal_data.table -o H_bwa_sort_dup_recal.bam -nct 20
INFO 14:37:58,979 HelpFormatter - Executing as [email protected] on Linux 3.10.0-862.14.4.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_191-b12.
INFO 14:37:58,979 HelpFormatter - Date/Time: 2019/12/11 14:37:58
INFO 14:37:58,979 HelpFormatter - ------------------------------------------------------------------------------------
INFO 14:37:58,980 HelpFormatter - ------------------------------------------------------------------------------------
INFO 14:37:59,034 NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/root/software/GenomeAnalysisTK-3.8-1-0/GenomeAnalysisTK.jar!/com/intel/gkl/native/libgkl_compression.so
INFO 14:37:59,057 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 14:37:59,057 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 14:37:59,058 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:37:59,773 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 14:37:59,828 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 14:37:59,840 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
WARNING: BAM index file /lustre/heritagen_scratch/larrasa/H/secundario/H_bwa_sort_dup.bai is older than BAM /lustre/heritagen_scratch/larrasa/H/secundario/H_bwa_sort_dup.bam
INFO 14:37:59,925 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
INFO 14:38:00,005 MicroScheduler - Running the GATK in parallel mode with 20 total threads, 20 CPU thread(s) for each of 1 data thread(s), of 24 processors available on this machine
INFO 14:38:00,091 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 14:38:00,095 GenomeAnalysisEngine - Done preparing for traversal
INFO 14:38:00,096 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 14:38:00,096 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 14:38:00,096 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 14:38:00,105 ReadShardBalancer$1 - Loading BAM index data
INFO 14:38:00,105 ReadShardBalancer$1 - Done loading BAM index data
INFO 14:38:30,107 ProgressMeter - chr1:2541028 300005.0 30.0 s 100.0 s 0.1% 10.2 h 10.2 h
INFO 14:39:00,192 ProgressMeter - chr1:5183218 800102.0 60.0 s 75.0 s 0.2% 10.0 h 10.0 h
INFO 14:39:30,194 ProgressMeter - chr1:8053402 1200123.0 90.0 s 75.0 s 0.3% 9.6 h 9.6 h
INFO 14:40:00,196 ProgressMeter - chr1:11028363 1600376.0 120.0 s 75.0 s 0.4% 9.4 h 9.3 h
INFO 14:40:30,198 ProgressMeter - chr1:14257429 2100382.0 2.5 m 71.0 s 0.5% 9.1 h 9.0 h
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INFO 23:25:00,628 ProgressMeter - KI270730.1:33152 4.52655195E8 8.8 h 69.0 s 99.9% 8.8 h 24.0 s
INFO 23:25:30,629 ProgressMeter - KI270438.1:110590 4.53001263E8 8.8 h 69.0 s 99.9% 8.8 h 22.0 s
INFO 23:26:00,630 ProgressMeter - KI270735.1:41022 4.53493045E8 8.8 h 69.0 s 100.0% 8.8 h 10.0 s
INFO 23:26:30,631 ProgressMeter - KI270465.1:1434 4.5395899E8 8.8 h 69.0 s 100.0% 8.8 h 0.0 s
INFO 23:27:00,688 ProgressMeter - KI270394.1:86 4.54059433E8 8.8 h 69.0 s 100.0% 8.8 h 0.0 s
INFO 23:27:30,689 ProgressMeter - KI270394.1:86 4.54059433E8 8.8 h 69.0 s 100.0% 8.8 h 0.0 s
INFO 23:28:00,690 ProgressMeter - KI270394.1:86 4.54059433E8 8.8 h 70.0 s 100.0% 8.8 h 0.0 s
INFO 23:28:30,691 ProgressMeter - KI270394.1:86 4.54059433E8 8.8 h 70.0 s 100.0% 8.8 h 0.0 s
INFO 23:29:00,692 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:29:30,694 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:30:00,695 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:30:30,696 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:31:00,697 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:31:30,699 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:32:00,700 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:32:30,701 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:33:00,702 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:33:30,703 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:34:00,704 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:34:30,705 ProgressMeter - KI270394.1:86 4.54059433E8 8.9 h 70.0 s 100.0% 8.9 h 0.0 s
INFO 23:35:00,706 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 70.0 s 100.0% 9.0 h 0.0 s
INFO 23:35:30,707 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:36:00,708 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:36:30,709 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:37:00,710 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:37:30,711 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:38:00,712 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:38:30,713 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:39:00,715 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:39:30,716 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
INFO 23:40:00,717 ProgressMeter - KI270394.1:86 4.54059433E8 9.0 h 71.0 s 100.0% 9.0 h 0.0 s
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INFO 10:45:46,810 ProgressMeter - KI270394.1:86 4.54059433E8 20.1 h 2.7 m 100.0% 20.1 h 0.0 s
INFO 10:46:46,811 ProgressMeter - KI270394.1:86 4.54059433E8 20.1 h 2.7 m 100.0% 20.1 h 0.0 s
INFO 10:47:46,812 ProgressMeter - KI270394.1:86 4.54059433E8 20.2 h 2.7 m 100.0% 20.2 h 0.0 s
INFO 10:48:46,813 ProgressMeter - KI270394.1:86 4.54059433E8 20.2 h 2.7 m 100.0% 20.2 h 0.0 s
INFO 10:49:46,814 ProgressMeter - KI270394.1:86 4.54059433E8 20.2 h 2.7 m 100.0% 20.2 h 0.0 s
INFO 10:50:46,844 ProgressMeter - KI270394.1:86 4.54059433E8 20.2 h 2.7 m 100.0% 20.2 h 0.0 s
INFO 10:51:46,845 ProgressMeter - KI270394.1:86 4.54059433E8 20.2 h 2.7 m 100.0% 20.2 h 0.0 s
INFO 10:52:46,870 ProgressMeter - KI270394.1:86 4.54059433E8 20.2 h 2.7 m 100.0% 20.2 h 0.0 s

Answers

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