VariantRecalibrator Error about Argument 'resource' was missing
I met the ERROR: Argument resource was missing: Argument 'resource' is required. I have checked the container mounted successfully on my host machine. More details are below.
a) GATK version used:4.6.0.0
b) Exact command used:gatk --java-options "-Xmx3g -Xms3g" VariantRecalibrator \
-R /mnt/sztrios/refernce/Homo_sapiens_assembly38.fasta\
-V /mnt/sztrios/20240516vcf_nonQC/B0032BD3.vcf.gz\
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 /mnt/sztrios/refernce/hapmap_3.3.hg38.vcf \
-resource:omni,known=false,training=true,truth=false,prior=12.0 /mnt/sztrios/refernce/1000G_omni2.5.hg38.vcf \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 /mnt/sztrios/refernce/1000G_phase1.snps.high_confidence.hg38.vcf\
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /mnt/sztrios/refernce/Homo_sapiens_assembly38.dbsnp138.vcf\
-an DP -an QD -an FS -an SOR -an ReadPosRankSum -an MQRankSum\
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 95.0 -tranche 90.0\
-mode SNP --max-gaussians 6 \
-O /mnt/sztrios/20240516VQSR1/B0032BD3.snps.recal\
--rscript-file /mnt/sztrios/20240516VQSR1/B0032BD3.snps.plots\
--tranches-file /mnt/sztrios/20240516VQSR1/B0032BD3.snps.tranches\
c) Entire program log:
root@6862e2ed2c33:/# gatk --java-options "-Xmx3g -Xms3g" VariantRecalibrator \
-R /mnt/sztrios/refernce/Homo_sapiens_assembly38.fasta\
-V /mnt/sztrios/20240516vcf_nonQC/B0032BD3.vcf.gz\
-resource:hapmap,known=false,training=true,truth=true,prior=15.0 /mnt/sztrios/refernce/hapmap_3.3.hg38.vcf \
-resource:omni,known=false,training=true,truth=false,prior=12.0 /mnt/sztrios/refernce/1000G_omni2.5.hg38.vcf \
-resource:1000G,known=false,training=true,truth=false,prior=10.0 /mnt/sztrios/refernce/1000G_phase1.snps.high_confidence.hg38.vcf\
-resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /mnt/sztrios/refernce/Homo_sapiens_assembly38.dbsnp138.vcf\
-an DP -an QD -an FS -an SOR -an ReadPosRankSum -an MQRankSum\
-tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 95.0 -tranche 90.0\
-mode SNP --max-gaussians 6 \
-O /mnt/sztrios/20240516VQSR1/B0032BD3.snps.recal\
--rscript-file /mnt/sztrios/20240516VQSR1/B0032BD3.snps.plots\
--tranches-file /mnt/sztrios/20240516VQSR1/B0032BD3.snps.tranches\
Using GATK jar /gatk/gatk-package-4.6.0.0-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 -Xmx3g -Xms3g -jar /gatk/gatk-package-4.6.0.0-local.jar VariantRecalibrator -R /mnt/sztrios/refernce/Homo_sapiens_assembly38.fasta -V /mnt/sztrios/20240516vcf_nonQC/B0032BD3.vcf.gz
USAGE: VariantRecalibrator [arguments]
Build a recalibration model to score variant quality for filtering purposes
Version:4.6.0.0
Required Arguments:
--output,-O <GATKPath> The output recal file used by ApplyVQSR Required.
--resource <FeatureInput> A list of sites for which to apply a prior probability of being correct but which aren't
used by the algorithm (training and truth sets are required to run) This argument must be
specified at least once. Required.
--tranches-file <File> The output tranches file used by ApplyVQSR Required.
--use-annotation,-an <String> The names of the annotations which should used for calculations This argument must be
specified at least once. Required.
--variant,-V <GATKPath> One or more VCF files containing variants This argument must be specified at least once.
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}
--aggregate <FeatureInput> This argument is DEPRECATED (This argument is not tested or used in any pipeline).
Additional raw input variants to be used in building the model This argument may be
specified 0 or more times. Default value: null.
--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}
--ignore-all-filters <Boolean>If specified, the variant recalibrator will ignore all input filters. Useful to rerun the
VQSR from a filtered output file. Default value: false. Possible values: {true, false}
--ignore-filter <String> If specified, the variant recalibrator will also use variants marked as filtered by the
specified filter name in the input VCF file This argument may be specified 0 or more
times. Default value: null.
--input,-I <GATKPath> BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times.
Default value: null.
--input-model <GATKPath> If specified, the variant recalibrator will read the VQSR model from this file path.
Default value: null.
--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.
--inverted-read-filter,-XRF <String>
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis
(after regular read filters). 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.
--mode <Mode> Recalibration mode to employ Default value: SNP. Possible values: {SNP, INDEL, BOTH}
--output-model <GATKPath> If specified, the variant recalibrator will output the VQSR model to this file path.
Default value: null.
--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}
--reference,-R <GATKPath> Reference sequence Default value: null.
--rscript-file <File> The output rscript file generated by the VQSR to aid in visualization of the input data
and learned model Default value: null.
--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}
--target-titv,-titv <Double> The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on the
optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED
FOR PLOTTING PURPOSES! Default value: 2.15.
--tmp-dir <GATKPath> Temp directory to use. Default value: null.
--truth-sensitivity-tranche,-tranche <Double>
The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1
percent) This argument may be specified 0 or more times. Default value: [100.0, 99.9,
99.0, 90.0].
--use-allele-specific-annotations,-AS <Boolean>
If specified, the variant recalibrator will attempt to use the allele-specific versions of
the specified annotations. Default value: false. Possible values: {true, false}
--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:
--bad-lod-score-cutoff,-bad-lod-cutoff <Double>
LOD score cutoff for selecting bad variants Default value: -5.0.
--debug-stdev-thresholding <Boolean>
Output variants that fail standard deviation thresholding to the log for debugging
purposes. Redirection of stdout to a file is recommended. Default value: false. Possible
values: {true, false}
--dirichlet <Double> The dirichlet parameter in the variational Bayes algorithm. Default value: 0.001.
--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}
--dont-run-rscript <Boolean> Disable the RScriptExecutor to allow RScript to be generated but not run Default value:
false. Possible values: {true, false}
--k-means-iterations <Integer>Number of k-means iterations Default value: 100.
--max-attempts <Integer> Number of attempts to build a model before failing Default value: 1.
--max-gaussians <Integer> Max number of Gaussians for the positive model Default value: 8.
--max-iterations <Integer> Maximum number of VBEM iterations Default value: 150.
--max-negative-gaussians <Integer>
Max number of Gaussians for the negative model Default value: 2.
--maximum-training-variants <Integer>
Maximum number of training data Default value: 2500000.
--minimum-bad-variants <Integer>
Minimum number of bad variants Default value: 1000.
--mq-cap-for-logit-jitter-transform,-mq-cap <Integer>
Apply logit transform and jitter to MQ values Default value: 0.
--mq-jitter <Double> Amount of jitter (as a multiplier to a Normal(0,1) distribution) to add to the AS_MQ and
transformed MQ values Default value: 0.05.
--prior-counts <Double> The number of prior counts to use in the variational Bayes algorithm. Default value:
20.0.
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
--shrinkage <Double> The shrinkage parameter in the variational Bayes algorithm. Default value: 1.0.
--standard-deviation-threshold,-std <Double>
Annotation value divergence threshold (number of standard deviations from the means)
Default value: 10.0.
--trust-all-polymorphic <Boolean>
Trust that all the input training sets' unfiltered records contain only polymorphic sites
to drastically speed up the computation. Default value: false. Possible values: {true,
false}
***********************************************************************
A USER ERROR has occurred: Argument resource was missing: Argument 'resource' is required
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
bash: -resource:hapmap,known=false,training=true,truth=true,prior=15.0: command not found
bash: $'\302\240': command not found
Could you point out the mistakes of my commands and what should i do to work it out? Thanks for your help.
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I am closing this topic as you already have one on going with the same issue.
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