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Base recalibration

I run GATK4.3 for base recalibration and I got the following result. I am not sure whether my output is right or wrong. Any help is appreciated.

The warning messages are

WARN Attempting to retrieve a sequence dictionary from the associated index file
WARN  IntelInflater - Zero Bytes Written : 0
WARN  IndexUtils - Feature file

The first and last few lines and the last part of the result are:

 Using GATK jar /export/opt/sw/gatk/4.3/gatk4_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribb                                                                le=false -Dsamjdk.compression_level=2 -jar /export/opt/sw/gatk/4.3/gatk4_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.                                                                jar BaseRecalibrator -I ../data/Afar_rD/Afar_3_dedup.bam -R ../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa --known-sites .                                                                ./GATK_reso/bos_taurus.vcf.gz --known-sites ../GATK_reso/ARS1.2PlusY_BQSR.vcf.gz -O Afar3_data.table1
16:02:11.052 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/export/opt/sw/gatk/4.3/gatk4_env/share/g                                                                atk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
16:02:11.234 INFO  BaseRecalibrator - ------------------------------------------------------------
16:02:11.235 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.3.0.0
16:02:11.235 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:02:11.235 INFO  BaseRecalibrator - Executing as wondossen@compute3.c.hgen.slu.se on Linux v3.10.0-693.21.1.el7.x86_64 amd64
16:02:11.235 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v11.0.13+7-b1751.21
16:02:11.235 INFO  BaseRecalibrator - Start Date/Time: 15 February 2023 at 16:02:11 CET
16:02:11.235 INFO  BaseRecalibrator - ------------------------------------------------------------
16:02:11.236 INFO  BaseRecalibrator - ------------------------------------------------------------
16:02:11.237 INFO  BaseRecalibrator - HTSJDK Version: 3.0.1
16:02:11.237 INFO  BaseRecalibrator - Picard Version: 2.27.5
16:02:11.237 INFO  BaseRecalibrator - Built for Spark Version: 2.4.5
16:02:11.237 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:02:11.237 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:02:11.237 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:02:11.237 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:02:11.237 INFO  BaseRecalibrator - Deflater: IntelDeflater
16:02:11.238 INFO  BaseRecalibrator - Inflater: IntelInflater
16:02:11.238 INFO  BaseRecalibrator - GCS max retries/reopens: 20
16:02:11.238 INFO  BaseRecalibrator - Requester pays: disabled
16:02:11.238 INFO  BaseRecalibrator - Initializing engine
16:02:11.822 INFO  FeatureManager - Using codec VCFCodec to read file file:///export/proj/ethiopian_cattle/NOBACKUP/../GATK_re                                                                so/bos_taurus.vcf.gz
16:02:11.979 INFO  FeatureManager - Using codec VCFCodec to read file file:///export/proj/ethiopian_cattle/NOBACKUP/../GATK_re                                                                so/ARS1.2PlusY_BQSR.vcf.gz
16:02:12.092 WARN  IndexUtils - Feature file "file:///export/proj/ethiopian_cattle/NOBACKUP/../GATK_reso/bos_taurus.vcf.gz" ap                                                                pears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
16:02:12.503 WARN  IntelInflater - Zero Bytes Written : 0
16:02:12.506 WARN  IndexUtils - Feature file "file:///export/proj/ethiopian_cattle/NOBACKUP/../GATK_reso/ARS1.2PlusY_BQSR.vcf.                                                                gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
16:02:12.584 WARN  IntelInflater - Zero Bytes Written : 0
16:02:12.610 INFO  BaseRecalibrator - Done initializing engine
16:02:12.613 INFO  BaseRecalibrationEngine - The covariates being used here:
16:02:12.613 INFO  BaseRecalibrationEngine -    ReadGroupCovariate
16:02:12.614 INFO  BaseRecalibrationEngine -    QualityScoreCovariate
16:02:12.614 INFO  BaseRecalibrationEngine -    ContextCovariate
16:02:12.614 INFO  BaseRecalibrationEngine -    CycleCovariate
16:02:12.651 INFO  ProgressMeter - Starting traversal
16:02:12.652 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
16:02:22.662 INFO  ProgressMeter -             1:393267              0.2                258000        1546762.6
16:02:32.665 INFO  ProgressMeter -            1:1606867              0.3                578000        1732960.2
16:02:42.705 INFO  ProgressMeter -            1:4309110              0.5                852000        1701051.5
16:02:52.705 INFO  ProgressMeter -            1:6825213              0.7               1143000        1712274.0
16:03:02.722 INFO  ProgressMeter -            1:9325322              0.8               1422000        1704014.4
16:03:12.722 INFO  ProgressMeter -           1:11842778              1.0               1709000        1707008.5
16:03:22.724 INFO  ProgressMeter -           1:14272945              1.2               1989000        1703105.4
16:03:32.759 INFO  ProgressMeter -           1:16686166              1.3               2268000        1698728.0
..
..
..
19:04:04.600 INFO  ProgressMeter - NKLS02001949.1:25475            181.9             288586000        1586807.4
19:04:14.617 INFO  ProgressMeter - NKLS02001029.1:14303            182.0             288865000        1586884.8
19:04:24.636 INFO  ProgressMeter - NKLS02000075.1:16243            182.2             289120000        1586830.0
19:04:34.645 INFO  ProgressMeter - NKLS02000522.1:15074            182.4             289396000        1586891.9
19:04:44.708 INFO  ProgressMeter -  NKLS02001176.1:4862            182.5             289678000        1586978.9
19:04:54.715 INFO  ProgressMeter -  NKLS02001731.1:1435            182.7             289951000        1587024.3
19:05:04.717 INFO  ProgressMeter -   NKLS02000327.1:249            182.9             290214000        1587015.8
19:05:14.722 INFO  ProgressMeter -  NKLS02001633.1:6427            183.0             290433000        1586766.6
19:05:24.750 INFO  ProgressMeter -  NKLS02001834.1:5709            183.2             290711000        1586836.3
19:05:34.762 INFO  ProgressMeter -  NKLS02001079.1:3182            183.4             290974000        1586826.7
19:05:44.781 INFO  ProgressMeter -   NKLS02000485.1:521            183.5             291289000        1587099.1
19:05:47.650 WARN  IntelInflater - Zero Bytes Written : 0
19:05:47.653 INFO  BaseRecalibrator - 40087222 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappedReadFilter
98300 read(s) filtered by: NotSecondaryAlignmentReadFilter
11495976 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: WellformedReadFilter
51681498 total reads filtered
19:05:47.654 INFO  ProgressMeter -    NKLS02001797.1:38            183.6             291356488        1587052.9
19:05:47.654 INFO  ProgressMeter - Traversal complete. Processed 291356488 total reads in 183.6 minutes.
19:05:47.887 INFO  BaseRecalibrator - Calculating quantized quality scores...
19:05:47.920 INFO  BaseRecalibrator - Writing recalibration report...
19:05:49.708 INFO  BaseRecalibrator - ...done!
19:05:49.709 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 291356488 reads
19:05:49.709 INFO  BaseRecalibrator - Shutting down engine
[15 February 2023 at 19:05:49 CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 183.6                                                                5 minutes.
Runtime.totalMemory()=2579496960

Tool returned:

SUCCESS
(base)
base-recalibration
• 1,465 views • link
updated by Ram Ram • written by wonde2000 • wonde2000

1 answer

Dear all, My be if it is helpful when I sorted dbSNP (VCF file) using picard (https://gatk.broadinstitute.org/hc/en-us/articles/360035532232-Errors-about-contigs-in-BAM-or-VCF-files-not-being-properly-ordered-or-sorted) the problem I posted here was fixed.

Thanks!

• 0 views • link
written by wonde2000 • wonde2000

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