AnalyzeCovariates were stopped.
Hello,
I would like to have some help to fix this issue. I am trying to run AnalyzeCovariates on GATK 4.5.0.0 and I am getting the following error message.
08:51:25.387 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/user1/Programs/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
08:51:25.875 INFO AnalyzeCovariates - ------------------------------------------------------------
08:51:25.883 INFO AnalyzeCovariates - The Genome Analysis Toolkit (GATK) v4.5.0.0
08:51:25.899 INFO AnalyzeCovariates - For support and documentation go to https://software.broadinstitute.org/gatk/
08:51:25.911 INFO AnalyzeCovariates - Executing as user1@agriserver.ca on Linux v5.4.0-150-generic amd64
08:51:25.911 INFO AnalyzeCovariates - Java runtime: OpenJDK 64-Bit Server VM v17.0.3-internal+0-adhoc..src
08:51:25.912 INFO AnalyzeCovariates - Start Date/Time: March 27, 2024 at 8:51:25 a.m. CST
08:51:25.912 INFO AnalyzeCovariates - ------------------------------------------------------------
08:51:25.912 INFO AnalyzeCovariates - ------------------------------------------------------------
08:51:25.914 INFO AnalyzeCovariates - HTSJDK Version: 4.1.0
08:51:25.914 INFO AnalyzeCovariates - Picard Version: 3.1.1
08:51:25.914 INFO AnalyzeCovariates - Built for Spark Version: 3.5.0
08:51:25.915 INFO AnalyzeCovariates - HTSJDK Defaults.COMPRESSION_LEVEL : 2
08:51:25.916 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
08:51:25.916 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
08:51:25.916 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
08:51:25.917 INFO AnalyzeCovariates - Deflater: IntelDeflater
08:51:25.917 INFO AnalyzeCovariates - Inflater: IntelInflater
08:51:25.917 INFO AnalyzeCovariates - GCS max retries/reopens: 20
08:51:25.918 INFO AnalyzeCovariates - Requester pays: disabled
08:51:25.919 INFO AnalyzeCovariates - Initializing engine
08:51:25.919 INFO AnalyzeCovariates - Done initializing engine
08:51:26.466 INFO AnalyzeCovariates - Generating csv file '/tmp/AnalyzeCovariates3787058183485354231.csv'
08:51:26.758 INFO AnalyzeCovariates - Generating plots file '/mnt/data/c04_bam/sample1.BQSRplot01.pdf'
08:51:30.429 INFO AnalyzeCovariates - Shutting down engine
[March 27, 2024 at 8:51:30 a.m. CST] org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=285212672.
My command was:
parallel -j 32 "java -XX:ParallelGCThreads=${THREADS} \
-DGATK_STACKTRACE_ON_USER_EXCEPTION=true \
-jar ${prg}/gatk-package-4.5.0.0-local.jar AnalyzeCovariates \
--bqsr-recal-file {}.recal.table \
--plots-report-file {}.BQSRplot01.pdf \
2>${log_dir}/{}.BQSRplot01.log" ::: $(ls -1 *.recal.table | sed 's/.recal.table//')
Thank you.
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Hi E Ra
We don't see any error messages in those logs. Can you elaborate more on the error message the you are receiving?
Regards.
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Hello,
Sorry for the confusion. I just noticed that I could generate a BSQRplot01.pdf file for each sample. It is actually GATK BaseRecalibration report that contains graphs. My questions would rather be where I could find info that allows me to interpret those graphs.
Thank you!
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Hi again.
We have a very brief slide for that. Basically the aim is to get recalibrated scores to align perfectly with the dotted line. If that's the case your recalibration went perfectly. If not there is still room to improve by adding more variant sites. But sometimes due to the amount of reads and covered regions you have recalibration may not work properly. In that case there is really not much to do as the whole recalibration needs as much data as possible to work.
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Hi Gökalp
That helps. Thank you very much for the answer.
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