Entering edit mode
2.5 years ago
Phoebe Magdy
•
0
I'm trying to make base recalibration using GATK for bam files and here is the command I used:
!gatk --java-options "-Xmx2G" BaseRecalibrator \
-R hg19.fa -I 001_S001_L001_001_sorted.markdup.bam --known-sites Tar_known_variants.vcf.gz \
-O 001_S001_L001_001_sorted.report
but the expected output file never showed up :(
Any help in interpreting why is that will be highly appreciated
Here is the whole msg that appeared while the command is running:
Using GATK jar /home/phoebemagdy/miniconda3/envs/ngs1/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-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 -Xmx2G -jar /home/phoebemagdy/miniconda3/envs/ngs1/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-local.jar BaseRecalibrator -R hg19.fa -I 001_S001_L001_001_sorted.markdup.bam --known-sites Tar_known_variants.vcf.gz -O 001_S001_L001_001_sorted.report
22:47:47.900 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/phoebemagdy/miniconda3/envs/ngs1/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jun 14, 2022 10:47:58 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
22:47:58.124 INFO BaseRecalibrator - ------------------------------------------------------------
22:47:58.125 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.9.0
22:47:58.125 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
22:47:58.125 INFO BaseRecalibrator - Executing as phoebemagdy@phoebemagdy on Linux v5.13.0-48-generic amd64
22:47:58.125 INFO BaseRecalibrator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_77-b03
22:47:58.125 INFO BaseRecalibrator - Start Date/Time: June 14, 2022 10:47:47 PM EET
22:47:58.125 INFO BaseRecalibrator - ------------------------------------------------------------
22:47:58.125 INFO BaseRecalibrator - ------------------------------------------------------------
22:47:58.126 INFO BaseRecalibrator - HTSJDK Version: 2.23.0
22:47:58.126 INFO BaseRecalibrator - Picard Version: 2.23.3
22:47:58.126 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:47:58.126 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:47:58.126 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:47:58.126 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:47:58.126 INFO BaseRecalibrator - Deflater: IntelDeflater
22:47:58.126 INFO BaseRecalibrator - Inflater: IntelInflater
22:47:58.126 INFO BaseRecalibrator - GCS max retries/reopens: 20
22:47:58.126 INFO BaseRecalibrator - Requester pays: disabled
22:47:58.127 INFO BaseRecalibrator - Initializing engine
22:47:58.412 INFO FeatureManager - Using codec VCFCodec to read file file:///home/phoebemagdy/workdir/PhD/Trial_Code/Ecto_Data/BWA_alignment/MarkedDuplicates_bam/Reports/Tar_known_variants.vcf.gz
22:47:58.451 INFO BaseRecalibrator - Done initializing engine
22:47:58.455 INFO BaseRecalibrationEngine - The covariates being used here:
22:47:58.455 INFO BaseRecalibrationEngine - ReadGroupCovariate
22:47:58.455 INFO BaseRecalibrationEngine - QualityScoreCovariate
22:47:58.455 INFO BaseRecalibrationEngine - ContextCovariate
22:47:58.455 INFO BaseRecalibrationEngine - CycleCovariate
22:47:58.459 INFO ProgressMeter - Starting traversal
22:47:58.460 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
22:47:58.663 INFO BaseRecalibrator - Shutting down engine
[June 14, 2022 10:47:58 PM EET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.18 minutes.
Runtime.totalMemory()=2068840448
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:548)
at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:382)
at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:427)
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:159)
at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:133)
at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:567)
at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:536)
at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:352)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:125)
at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:263)
at org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.apply(BaseRecalibrator.java:191)
at org.broadinstitute.hellbender.engine.ReadWalker.lambda$traverse$0(ReadWalker.java:96)
at org.broadinstitute.hellbender.engine.ReadWalker$$Lambda$93/1935994577.accept(Unknown Source)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
Thanks, i found my answer in the link that you supplied