SplitNCigar reads tool is not running
REQUIRED for all errors and issues:
a) GATK version used:GATK v4.4.0.0
b) Exact command used: gatk SplitNCigarReads -R SplitNCigar_Reads/human_genome.fna -I Mark_duplicates/PicardOutput/sorted_unique_reads_withRGAlignment/SRR###_Unique_reads_WithRG.bam -O SplitNCigar_Reads/output/SRR###_SplitNCigar_out.bam --sites-only-vcf-output true --tmp-dir TMP_DIR --showHidden
c) Entire program log:
Using GATK jar /DATA/RamanDeep/Tools/miniconda3/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /DATA/RamanDeep/Tools/miniconda3/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar SplitNCigarReads -R SplitNCigar_Reads/human_genome.fna -I Mark_duplicates/PicardOutput/sorted_unique_reads_withRGAlignment/SRR###_Unique_reads_WithRG.bam -O SplitNCigar_Reads/output/SRR###_SplitNCigar_out.bam --sites-only-vcf-output true --tmp-dir TMP_DIR --showHidden
11:39:16.931 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/DATA/Rami/Tools/miniconda3/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:39:16.962 INFO SplitNCigarReads - ------------------------------------------------------------
11:39:16.965 INFO SplitNCigarReads - The Genome Analysis Toolkit (GATK) v4.4.0.0
11:39:16.965 INFO SplitNCigarReads - For support and documentation go to https://software.broadinstitute.org/gatk/
11:39:16.965 INFO SplitNCigarReads - Executing as user@user on Linux v4.15.0-213-generic amd64
11:39:16.965 INFO SplitNCigarReads - Java runtime: OpenJDK 64-Bit Server VM v17.0.9-internal+0-adhoc..src
11:39:16.965 INFO SplitNCigarReads - Start Date/Time: 4 December 2023 at 11:39:16 am IST
11:39:16.965 INFO SplitNCigarReads - ------------------------------------------------------------
11:39:16.965 INFO SplitNCigarReads - ------------------------------------------------------------
11:39:16.966 INFO SplitNCigarReads - HTSJDK Version: 3.0.5
11:39:16.966 INFO SplitNCigarReads - Picard Version: 3.0.0
11:39:16.966 INFO SplitNCigarReads - Built for Spark Version: 3.3.1
11:39:16.966 INFO SplitNCigarReads - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:39:16.967 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:39:16.967 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:39:16.967 INFO SplitNCigarReads - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:39:16.967 INFO SplitNCigarReads - Deflater: IntelDeflater
11:39:16.967 INFO SplitNCigarReads - Inflater: IntelInflater
11:39:16.967 INFO SplitNCigarReads - GCS max retries/reopens: 20
11:39:16.967 INFO SplitNCigarReads - Requester pays: disabled
11:39:16.968 INFO SplitNCigarReads - Initializing engine
11:39:17.123 INFO SplitNCigarReads - Done initializing engine
11:39:17.155 INFO SplitNCigarReads - Shutting down engine
[4 December 2023 at 11:39:17 am IST] org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=285212672
htsjdk.samtools.util.RuntimeIOException: Error opening file: file:///DATA1/Niharika/NSCLC_DATA_ANALYSIS/RE_ANALYSIS_RNA_SEQ/SplitNCigar_Reads/output/SRR###_SplitNCigar_out.bam
at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:306)
at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:263)
at htsjdk.samtools.SAMFileWriterFactory.makeSAMOrBAMWriter(SAMFileWriterFactory.java:444)
at htsjdk.samtools.SAMFileWriterFactory.makeWriter(SAMFileWriterFactory.java:496)
at org.broadinstitute.hellbender.utils.read.ReadUtils.createCommonSAMWriterFromFactory(ReadUtils.java:1016)
at org.broadinstitute.hellbender.utils.read.ReadUtils.createCommonSAMWriter(ReadUtils.java:964)
at org.broadinstitute.hellbender.engine.GATKTool.createSAMWriter(GATKTool.java:847)
at org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads.onTraversalStart(SplitNCigarReads.java:175)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1096)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.nio.file.NoSuchFileException: SplitNCigar_Reads/output/SRR###_SplitNCigar_out.bam
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
at java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(FileSystemProvider.java:484)
at java.base/java.nio.file.Files.newOutputStream(Files.java:228)
at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:294)
... 14 more
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Hello Niharika.
It sounds like there is an issue in your code attempting to make the output writer
```
Caused by: java.nio.file.NoSuchFileException: SplitNCigar_Reads/output/SRR###_SplitNCigar_out.bamat java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
```
Can you check that that directory exists on your system and is writeable? Furthermore I would suggest (if it isn't censorship) removing the # signs from your paths in case those are causing problems with java io on your system.
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