BaseRecalibrator on MT .bam files

Answered

Follow

Sharon Cox

• February 19, 2021 09:48
• Edited

I am using the baserecalibrator tool on my.bam files containing mitochondrial reads. I wanted to know 1) did the tool work on my data since the log shows "0reads filetered"  2 )  Why does it say "21:27:05.064 INFO  ProgressMeter -           chrM:16457", my chrM is 16569 long and both .fasta e .fai report 16859

I am providing the following:

a) GATK version used:gatk4-4.1.9.0-0
b) Exact command used:

gatk BaseRecalibrator -R chrM.fa -I sorted_nodup_prefix.bam -O 01_liver.table --known-sites MITOMAP_HMTDB_known_indels_RCRS.vcf --java-options -DGATK_STACKTRACE_ON_USER_EXCEPTION=true

c) error log:

21:26:59.277 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.9.0

21:26:59.277 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/

21:26:59.278 INFO  BaseRecalibrator - Executing as sharonnatashacox@ui03.recas.ba.infn.it on Linux v3.10.0-862.14.4.el7.x86_64 amd64

21:26:59.278 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-b11

21:26:59.278 INFO  BaseRecalibrator - Start Date/Time: February 17, 2021 9:26:58 PM CET

21:26:59.279 INFO  BaseRecalibrator - ------------------------------------------------------------

21:26:59.279 INFO  BaseRecalibrator - ------------------------------------------------------------

21:26:59.280 INFO  BaseRecalibrator - HTSJDK Version: 2.23.0

21:26:59.280 INFO  BaseRecalibrator - Picard Version: 2.23.3

21:26:59.280 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2

21:26:59.280 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

21:26:59.280 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

21:26:59.280 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

21:26:59.280 INFO  BaseRecalibrator - Deflater: IntelDeflater

21:26:59.280 INFO  BaseRecalibrator - Inflater: IntelInflater

21:26:59.281 INFO  BaseRecalibrator - GCS max retries/reopens: 20

21:26:59.281 INFO  BaseRecalibrator - Requester pays: disabled

21:26:59.281 INFO  BaseRecalibrator - Initializing engine

21:27:00.022 INFO  FeatureManager - Using codec VCFCodec to read file file:///lustrehome/sharonnatashacox/NewMToolBox/MToolBox/MToolBox/data/MITOMAP_HMTDB_known_indels_RCRS_modsha.vcf

21:27:00.042 WARN  IndexUtils - Feature file "/lustrehome/sharonnatashacox/NewMToolBox/MToolBox/MToolBox/data/MITOMAP_HMTDB_known_indels_RCRS_modsha.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file

21:27:00.048 INFO  BaseRecalibrator - Done initializing engine

21:27:00.079 INFO  BaseRecalibrationEngine - The covariates being used here:

21:27:00.079 INFO  BaseRecalibrationEngine -    ReadGroupCovariate

21:27:00.079 INFO  BaseRecalibrationEngine -    QualityScoreCovariate

21:27:00.079 INFO  BaseRecalibrationEngine -    ContextCovariate

21:27:00.079 INFO  BaseRecalibrationEngine -    CycleCovariate

21:27:00.082 INFO  ProgressMeter - Starting traversal

21:27:00.082 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute

21:27:05.063 INFO  BaseRecalibrator - 0 read(s) filtered by: MappingQualityNotZeroReadFilter

0 read(s) filtered by: MappingQualityAvailableReadFilter

0 read(s) filtered by: MappedReadFilter

0 read(s) filtered by: NotSecondaryAlignmentReadFilter

0 read(s) filtered by: NotDuplicateReadFilter

0 read(s) filtered by: PassesVendorQualityCheckReadFilter

0 read(s) filtered by: WellformedReadFilter

0 total reads filtered

21:27:05.064 INFO  ProgressMeter -           chrM:16457              0.1                 90382        1088939.8

21:27:05.064 INFO  ProgressMeter - Traversal complete. Processed 90382 total reads in 0.1 minutes.

21:27:05.224 INFO  BaseRecalibrator - Calculating quantized quality scores...

21:27:05.254 INFO  BaseRecalibrator - Writing recalibration report...

21:27:07.926 INFO  BaseRecalibrator - ...done!

21:27:07.926 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 90382 reads

21:27:07.926 INFO  BaseRecalibrator - Shutting down engine

[February 17, 2021 9:27:07 PM CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.16 minutes.

Runtime.totalMemory()=1546649600

Tool returned:

SUCCESS

.Thanks for your help

             

0

• 

  Bhanu Gandham

  • February 26, 2021 23:00

  Sharon Cox

  If you see "Tool returned: SUCCESS" at the bottom of the log and you get an output, then the tool ran just fine. The progress meter is only giving you some info on what the tool encounters while processing the data. You can ignore most of that. That info is provided for when the tool fails and we need to figure out at what point the failure happened.

  0

  Comment actions Permalink
• 

  payal banerjee

  • August 18, 2023 14:32

  Where to download the MITOMAP_HMTDB_known_indels_RCRS.vcf file from? 

  I see - https://www.mitomap.org/foswiki/bin/view/MITOMAP/Resources

  • https://mitomap.org/cgi-bin/polymorphisms.cgi?format=vcf

  Is this the same file or its a different file?

   

   

  0

  Comment actions Permalink
• 

  Sharon Natasha Cox

  • August 23, 2023 14:44

  I got it from the MToolBox data repository https://github.com/mitoNGS/MToolBox/tree/master/MToolBox/data/MITOMAP_HMTDB_known_indels_RCRS.vcf

  Sharon

  1

  Comment actions Permalink
• 

  Gökalp Çelik

  • August 28, 2023 09:46

  Thank you Sharon Natasha Cox for the response. 

  0

  Comment actions Permalink
• 

  payal banerjee

  • August 28, 2023 13:18

  Thanks Sharon Natasha Cox

  0

  Comment actions Permalink

Post is closed for comments.