LeftAlignIndels not recognizing input/reference/output strings
Hello. LeftAlignIndels is not reading in any of the input/reference/or output files that I have provided, and is instead only looking in my current working directory for files. What is going on here?
a) GATK version used:
$ gatk --version
The Genome Analysis Toolkit (GATK) v4.5.0.0
HTSJDK Version: 4.1.0
Picard Version: 3.1.1
b) Exact command used:
My current working directory: /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads
gatk LeftAlignIndels --reference "$bwa_ref" --input "$RGbam" --output "$LABam"
I have gatk aliased and am using variables for the files. The full command is expanded below:
/usr/lib/jvm/java-17-openjdk-17.0.10.0.7-2.el9.x86_64/bin/java -jar /home/src/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar LeftAlignIndels \
--reference /home/shared/projects/RNA-seq/references/RefSeq/bwa_indexed_genomes/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.fna.dict \
-- input /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/debug.reads_to_GCF_000001405.40_GRCh38.p14_cds_from_genomic.RG.bam \
-- output /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/debug.reads_to_GCF_000001405.40_GRCh38.p14_cds_from_genomic.LA.bam
c) Entire program log:
gatk LeftAlignIndels --reference "$bwa_ref" --input "$RGbam" --output "$LABam"
11:23:34.592 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:/home/src/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:23:34.691 INFO LeftAlignIndels - ------------------------------------------------------------
11:23:34.694 INFO LeftAlignIndels - The Genome Analysis Toolkit (GATK) v4.5.0.0
11:23:34.694 INFO LeftAlignIndels - For support and documentation go to https://software.broadinstitute.org/gatk/
11:23:34.694 INFO LeftAlignIndels - Executing as areese on Linux v5.14.0-362.13.1.el9_3.x86_64 amd64
11:23:34.694 INFO LeftAlignIndels - Java runtime: OpenJDK 64-Bit Server VM v17.0.10+7-LTS
11:23:34.694 INFO LeftAlignIndels - Start Date/Time: March 14, 2024 at 11:23:34 AM EDT
11:23:34.694 INFO LeftAlignIndels - ------------------------------------------------------------
11:23:34.694 INFO LeftAlignIndels - ------------------------------------------------------------
11:23:34.695 INFO LeftAlignIndels - HTSJDK Version: 4.1.0
11:23:34.695 INFO LeftAlignIndels - Picard Version: 3.1.1
11:23:34.695 INFO LeftAlignIndels - Built for Spark Version: 3.5.0
11:23:34.695 INFO LeftAlignIndels - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:23:34.695 INFO LeftAlignIndels - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:23:34.696 INFO LeftAlignIndels - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:23:34.696 INFO LeftAlignIndels - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:23:34.696 INFO LeftAlignIndels - Deflater: IntelDeflater
11:23:34.696 INFO LeftAlignIndels - Inflater: IntelInflater
11:23:34.696 INFO LeftAlignIndels - GCS max retries/reopens: 20
11:23:34.696 INFO LeftAlignIndels - Requester pays: disabled
11:23:34.696 INFO LeftAlignIndels - Initializing engine
11:23:34.856 INFO LeftAlignIndels - Done initializing engine
INFO 2024-03-14 11:23:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/
11:23:34.869 INFO LeftAlignIndels - Shutting down engine
[March 14, 2024 at 11:23:34 AM EDT] org.broadinstitute.hellbender.tools.LeftAlignIndels done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=285212672
htsjdk.samtools.util.RuntimeIOException: Error opening file: /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/
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.LeftAlignIndels.onTraversalStart(LeftAlignIndels.java:70)
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:166)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
at org.broadinstitute.hellbender.Main.main(Main.java:306)
Caused by: java.nio.file.FileSystemException: : Is a directory
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
I also attempted to use a separate install of gatk, directly from my conda env, with the variables defined above, and without. When using the variables with the LeftAlignIndels call the output flag is empty when being read into the command, but the variable is not empty:
/home/areese/.conda/envs/WES_dev2/bin/gatk LeftAlignIndels --input "$RGbam" --output "$LABam" --reference "$bwa_ref"
Using GATK jar /home/areese/.conda/envs/WES_dev2/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-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 /home/areese/.conda/envs/WES_dev2/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar LeftAlignIndels --input /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/debug.reads_to_GCF_000001405.40_GRCh38.p14_cds_from_genomic.RG.bam --output --reference /home/shared/projects/RNA-seq/references/RefSeq/bwa_indexed_genomes/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.fna
11:40:17.465 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:/home/areese/.conda/envs/WES_dev2/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:40:18.298 INFO LeftAlignIndels - ------------------------------------------------------------
11:40:18.305 INFO LeftAlignIndels - The Genome Analysis Toolkit (GATK) v4.5.0.0
11:40:18.305 INFO LeftAlignIndels - For support and documentation go to https://software.broadinstitute.org/gatk/
11:40:18.305 INFO LeftAlignIndels - Executing as areese on Linux v5.14.0-362.13.1.el9_3.x86_64 amd64
11:40:18.305 INFO LeftAlignIndels - Java runtime: OpenJDK 64-Bit Server VM v17.0.10-internal+0-adhoc..src
11:40:18.305 INFO LeftAlignIndels - Start Date/Time: March 14, 2024 at 11:40:16 AM EDT
11:40:18.305 INFO LeftAlignIndels - ------------------------------------------------------------
11:40:18.305 INFO LeftAlignIndels - ------------------------------------------------------------
11:40:18.306 INFO LeftAlignIndels - HTSJDK Version: 4.1.0
11:40:18.306 INFO LeftAlignIndels - Picard Version: 3.1.1
11:40:18.306 INFO LeftAlignIndels - Built for Spark Version: 3.5.0
11:40:18.306 INFO LeftAlignIndels - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:40:18.307 INFO LeftAlignIndels - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:40:18.307 INFO LeftAlignIndels - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:40:18.307 INFO LeftAlignIndels - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:40:18.307 INFO LeftAlignIndels - Deflater: IntelDeflater
11:40:18.307 INFO LeftAlignIndels - Inflater: IntelInflater
11:40:18.307 INFO LeftAlignIndels - GCS max retries/reopens: 20
11:40:18.307 INFO LeftAlignIndels - Requester pays: disabled
11:40:18.308 INFO LeftAlignIndels - Initializing engine
11:40:18.579 INFO LeftAlignIndels - Done initializing engine
INFO 2024-03-14 11:40:18 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/
11:40:18.602 INFO LeftAlignIndels - Shutting down engine
[March 14, 2024 at 11:40:18 AM EDT] org.broadinstitute.hellbender.tools.LeftAlignIndels done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=285212672
htsjdk.samtools.util.RuntimeIOException: Error opening file: /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/
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.LeftAlignIndels.onTraversalStart(LeftAlignIndels.java:70)
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:166)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
at org.broadinstitute.hellbender.Main.main(Main.java:306)
Caused by: java.nio.file.FileSystemException: : Is a directory
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
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
echo "$LAbam"
/home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/debug.reads_to_GCF_000001405.40_GRCh38.p14_cds_from_genomic.LA.bam
With the full file path strings (AKA not using any variables):
/home/areese/.conda/envs/WES_dev2/bin/gatk LeftAlignIndels --reference /home/shared/projects/RNA-seq/references/RefSeq/bwa_indexed_genomes/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.fna --input /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/debug.reads_to_GCF_000001405.40_GRCh38.p14_cds_from_genomic.RG.bam
--output /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/debug.reads_to_GCF_000001405.40_GRCh38.p14_cds_from_genomic.LA.bam
Using GATK jar /net/fs001.hsf.cluster.pssclabs.com/home/areese_atcc.org/.conda/envs/WES_dev2/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-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 /net/fs001.hsf.cluster.pssclabs.com/home/areese_atcc.org/.conda/envs/WES_dev2/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar LeftAlignIndels --reference /home/shared/projects/RNA-seq/references/RefSeq/bwa_indexed_genomes/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.fna --input /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/debug.reads_to_GCF_000001405.40_GRCh38.p14_cds_from_genomic.RG.bam --output /home/shared/projects/WES/PilotStudy/ILN2_2024AE/HTB-2D-TR1/map_reads/debug.reads_to_GCF_000001405.40_GRCh38.p14_cds_from_genomic.LA.bam
USAGE: LeftAlignIndels [arguments]
Left-aligns indels from reads in a SAM/BAM/CRAM file.
Version:4.5.0.0
Required Arguments:
--input,-I <GATKPath> BAM/SAM/CRAM file containing reads This argument must be specified at least once.
Required.
--output,-O <GATKPath> Output BAM Required.
--reference,-R <GATKPath> Reference sequence file Required.
Optional Arguments:
--add-output-sam-program-record <Boolean>
If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
values: {true, false}
--add-output-vcf-command-line <Boolean>
If true, adds a command line header line to created VCF files. Default value: true.
Possible values: {true, false}
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--cloud-index-prefetch-buffer,-CIPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
cloudPrefetchBuffer if unset. Default value: -1.
--cloud-prefetch-buffer,-CPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
--create-output-bam-index,-OBI <Boolean>
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
value: true. Possible values: {true, false}
--create-output-bam-md5,-OBM <Boolean>
If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
Possible values: {true, false}
--create-output-variant-index,-OVI <Boolean>
If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
true. Possible values: {true, false}
--create-output-variant-md5,-OVM <Boolean>
If true, create a a MD5 digest any VCF file created. Default value: false. Possible
values: {true, false}
--disable-bam-index-caching,-DBIC <Boolean>
If true, don't cache bam indexes, this will reduce memory requirements but may harm
performance if many intervals are specified. Caching is automatically disabled if there
are no intervals specified. Default value: false. Possible values: {true, false}
--disable-read-filter,-DF <String>
Read filters to be disabled before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {WellformedReadFilter}
--disable-sequence-dictionary-validation <Boolean>
If specified, do not check the sequence dictionaries from our inputs for compatibility.
Use at your own risk! Default value: false. Possible values: {true, false}
--exclude-intervals,-XL <String>
One or more genomic intervals to exclude from processing This argument may be specified 0
or more times. Default value: null.
--gatk-config-file <String> A configuration file to use with the GATK. Default value: null.
--gcs-max-retries,-gcs-retries <Integer>
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
connection Default value: 20.
--gcs-project-for-requester-pays <String>
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
accessed. User must have storage.buckets.get permission on the bucket being accessed.
Default value: .
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--interval-exclusion-padding,-ixp <Integer>
Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
--interval-merging-rule,-imr <IntervalMergingRule>
Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
OVERLAPPING_ONLY}
--interval-padding,-ip <Integer>
Amount of padding (in bp) to add to each interval you are including. Default value: 0.
--interval-set-rule,-isr <IntervalSetRule>
Set merging approach to use for combining interval inputs Default value: UNION. Possible
values: {UNION, INTERSECTION}
--intervals,-L <String> One or more genomic intervals over which to operate This argument may be specified 0 or
more times. Default value: null.
--lenient,-LE <Boolean> Lenient processing of VCF files Default value: false. Possible values: {true, false}
--max-variants-per-shard <Integer>
If non-zero, partitions VCF output into shards, each containing up to the given number of
records. Default value: 0.
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--read-filter,-RF <String> Read filters to be applied before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {AlignmentAgreesWithHeaderReadFilter,
AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
ExcessiveEndClippedReadFilter, FirstOfPairReadFilter,
FlowBasedTPAttributeSymetricReadFilter, FlowBasedTPAttributeValidReadFilter,
FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter,
HmerQualitySymetricReadFilter, IntervalOverlapReadFilter,
JexlExpressionReadTagValueFilter, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupHasFlowOrderReadFilter,
ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter,
ReadNameReadFilter, ReadStrandFilter, ReadTagValueFilter, SampleReadFilter,
SecondOfPairReadFilter, SeqIsStoredReadFilter, SoftClippedReadFilter,
ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedFlowBasedReadFilter,
WellformedReadFilter}
--read-index <GATKPath> Indices to use for the read inputs. If specified, an index must be provided for every read
input and in the same order as the read inputs. If this argument is not specified, the
path to the index for each input will be inferred automatically. This argument may be
specified 0 or more times. Default value: null.
--read-validation-stringency,-VS <ValidationStringency>
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default
stringency value SILENT can improve performance when processing a BAM file in which
variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default
value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
--seconds-between-progress-updates <Double>
Output traversal statistics every time this many seconds elapse Default value: 10.0.
--sequence-dictionary <GATKPath>
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
.dict file. Default value: null.
--sites-only-vcf-output <Boolean>
If true, don't emit genotype fields when writing vcf file output. Default value: false.
Possible values: {true, false}
--tmp-dir <GATKPath> Temp directory to use. Default value: null.
--use-jdk-deflater,-jdk-deflater <Boolean>
Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
Possible values: {true, false}
--use-jdk-inflater,-jdk-inflater <Boolean>
Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
Possible values: {true, false}
--verbosity <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--disable-tool-default-read-filters <Boolean>
Disable all tool default read filters (WARNING: many tools will not function correctly
without their default read filters on) Default value: false. Possible values: {true,
false}
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
Conditional Arguments for readFilter:
Valid only if "AmbiguousBaseReadFilter" is specified:
--ambig-filter-bases <Integer>Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise,
overrides threshold fraction. Default value: null. Cannot be used in conjunction with
argument(s) maxAmbiguousBaseFraction
--ambig-filter-frac <Double> Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjunction
with argument(s) maxAmbiguousBases
Valid only if "ExcessiveEndClippedReadFilter" is specified:
--max-clipped-bases <Integer> Maximum number of clipped bases on either end of a given read Default value: 1000.
Valid only if "FlowBasedTPAttributeValidReadFilter" is specified:
--read-filter-max-hmer <Integer>
maxHmer to use for testing in the filter Default value: 12.
Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length <Integer>
Maximum length of fragment (insert size) Default value: 1000000.
--min-fragment-length <Integer>
Minimum length of fragment (insert size) Default value: 0.
Valid only if "IntervalOverlapReadFilter" is specified:
--keep-intervals <String> One or more genomic intervals to keep This argument must be specified at least once.
Required.
Valid only if "JexlExpressionReadTagValueFilter" is specified:
--read-filter-expression <String>
One or more JEXL expressions used to filter This argument must be specified at least
once. Required.
Valid only if "LibraryReadFilter" is specified:
--library <String> Name of the library to keep This argument must be specified at least once. Required.
Valid only if "MappingQualityReadFilter" is specified:
--maximum-mapping-quality <Integer>
Maximum mapping quality to keep (inclusive) Default value: null.
--minimum-mapping-quality <Integer>
Minimum mapping quality to keep (inclusive) Default value: 10.
Valid only if "MateDistantReadFilter" is specified:
--mate-too-distant-length <Integer>
Minimum start location difference at which mapped mates are considered distant Default
value: 1000.
Valid only if "OverclippedReadFilter" is specified:
--dont-require-soft-clips-both-ends <Boolean>
Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
block Default value: false. Possible values: {true, false}
--filter-too-short <Integer> Minimum number of aligned bases Default value: 30.
Valid only if "PlatformReadFilter" is specified:
--platform-filter-name <String>
Platform attribute (PL) to match This argument must be specified at least once. Required.
Valid only if "PlatformUnitReadFilter" is specified:
--black-listed-lanes <String> Platform unit (PU) to filter out This argument must be specified at least once. Required.
Valid only if "ReadGroupBlackListReadFilter" is specified:
--read-group-black-list <String>
A read group filter expression in the form "attribute:value", where "attribute" is a two
character read group attribute such as "RG" or "PU". This argument must be specified at
least once. Required.
Valid only if "ReadGroupReadFilter" is specified:
--keep-read-group <String> The name of the read group to keep Required.
Valid only if "ReadLengthReadFilter" is specified:
--max-read-length <Integer> Keep only reads with length at most equal to the specified value Required.
--min-read-length <Integer> Keep only reads with length at least equal to the specified value Default value: 1.
Valid only if "ReadNameReadFilter" is specified:
--read-name <String> Keep only reads with this read name This argument must be specified at least once.
Required.
Valid only if "ReadStrandFilter" is specified:
--keep-reverse-strand-only <Boolean>
Keep only reads on the reverse strand Required. Possible values: {true, false}
Valid only if "ReadTagValueFilter" is specified:
--read-filter-tag <String> Look for this tag in read Required.
--read-filter-tag-comp <Float>Compare value in tag to this value Default value: 0.0.
--read-filter-tag-op <Operator>
Compare value in tag to value with this operator. If T is the value in the tag, OP is the
operation provided, and V is the value in read-filter-tag, then the read will pass the
filter iff T OP V is true. Default value: EQUAL. Possible values: {LESS, LESS_OR_EQUAL,
GREATER, GREATER_OR_EQUAL, EQUAL, NOT_EQUAL}
Valid only if "SampleReadFilter" is specified:
--sample <String> The name of the sample(s) to keep, filtering out all others This argument must be
specified at least once. Required.
Valid only if "SoftClippedReadFilter" is specified:
--invert-soft-clip-ratio-filter <Boolean>
Inverts the results from this filter, causing all variants that would pass to fail and
visa-versa. Default value: false. Possible values: {true, false}
--soft-clipped-leading-trailing-ratio <Double>
Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases
in read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) minimumSoftClippedRatio
--soft-clipped-ratio-threshold <Double>
Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in
read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) minimumLeadingTrailingSoftClippedRatio
***********************************************************************
A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ', { { { { { { { { { { { }' but no positional argument is defined for this tool.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
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Hi Amy Reese
Are you running GATK4 from the gatk script? Looks like parameter interpretation is lacking here. Possibly your python version could also be causing issues as well. Can you make sure that gatk script uses python3 version >= 3.6 ?
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Hi Gokalp Celik,
Yes, GATK4 ("Using GATK jar /home/areese/.conda/envs/WES_dev2/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar") and my "WES_dev2" conda env uses python 3.11.7 (see below).
(WES_dev2) [Thu Mar 14 02:24 PM] areese /home/shared/repos/RNA-seq_develop
$ which python && python --version
~/.conda/envs/WES_dev2/bin/python
Python 3.11.7Amy
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Hi again.
I tried reproducing the error that you are facing and the only time I could reproduce this error is when variables are not set properly.
Can you try running the tool without using variables for file paths? If the tool runs properly then it is definitely an issue with your exports.
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I did try that, but I'll start over and re-create the bams and the variables in case there was something that I missed along the way, and try again. I'll comment here if it still doesn't work for me after the restart. Thank you for your help.
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