Task started

+ echo Task started

+ cd /mnt/workflow/3316253/20240610_171352_HaplotypeCallerGvcf_GATK4/call-MergeGVCFs/work

+ bash ../command

++ tee -a ../stdout.txt

++ tee -a ../stderr.txt

MergeGVCFs

+ /gatk/gatk --java-options -Xmx6G MergeVcfs --INPUT --OUTPUT ERR194159-30x.hg38.g.vcf.gz

USAGE: MergeVcfs [arguments]

<p>Combines multiple variant files into a single variant file.</p><h3>Inputs</h3><ul> <li>One or more input file in

VCF format (can be gzipped, i.e. ending in ".vcf.gz", or binary compressed, i.e. ending in ".bcf").</li>

<li>Optionally a sequence dictionary file (typically name ending in .dict) if the input VCF does not contain a

complete contig list and if the output index is to be created (true by default).</li> </ul> <p> The input variant

data must adhere to the following rules:</p> <ul> <li>If there are samples, those must be the same across

all input files.</li> <li>Input file headers must be contain compatible declarations for common annotations

(INFO, FORMAT fields) and filters.</li> <li>Input files variant records must be sorted by their contig and

position following the sequence dictionary provided or the header contig list.</li> </ul> <p>You can either

directly specify the list of files by specifying <code>INPUT</code> multiple times, or provide a list in a file with

name ending in ".list" to <code>INPUT</code>.</p> <h3>Outputs</h3> <p>A VCF sorted (i) according to the dictionary and

(ii) by coordinate.</p> <h3>Usage examples</h3> <h4>Example 1:</h4> <p>We combine several variant files in different

formats, where at least one of them contains the contig list in its header.</p> <pre>java -jar picard.jar MergeVcfs \

I=input_variants.01.vcf \

I=input_variants.02.vcf.gz \

O=output_variants.vcf.gz</pre> <h4>Example 2:</h4> <p>Similar to example 1 but we use an input list file to specify the

input files:</p> <pre>java -jar picard.jar MergeVcfs \

I=input_variant_files.list \

O=output_variants.vcf.gz</pre><hr/>

Version:4.2.6.1

Required Arguments:

--INPUT,-I <PicardHtsPath> VCF or BCF input files (File format is determined by file extension), or a file having a

'.list' suffix containing the path to the files, one per line. This argument must be

specified at least once. Required.

--OUTPUT,-O <File> The merged VCF or BCF file. File format is determined by file extension. Required.

Optional Arguments:

--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.

--COMMENT,-CO <String> Comment(s) to include in the merged output file's header. This argument may be specified

0 or more times. Default value: null.

--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.

--CREATE_INDEX <Boolean> Whether to create an index when writing VCF or coordinate sorted BAM output. Default

value: true. Possible values: {true, false}

--CREATE_MD5_FILE <Boolean> Whether to create an MD5 digest for any BAM or FASTQ files created. Default value:

false. Possible values: {true, false}

--GA4GH_CLIENT_SECRETS <String>

Google Genomics API client_secrets.json file path. Default value: client_secrets.json.

--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}

--MAX_RECORDS_IN_RAM <Integer>When writing files that need to be sorted, this will specify the number of records stored

in RAM before spilling to disk. Increasing this number reduces the number of file handles

needed to sort the file, and increases the amount of RAM needed. Default value: 500000.

--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible

values: {true, false}

--REFERENCE_SEQUENCE,-R <File>Reference sequence file. Default value: null.

--SEQUENCE_DICTIONARY,-D <PicardHtsPath>

The index sequence dictionary to use instead of the sequence dictionary in the input files

Default value: null.

--TMP_DIR <File> One or more directories with space available to be used by this program for temporary

storage of working files This argument may be specified 0 or more times. Default value:

null.

--USE_JDK_DEFLATER,-use_jdk_deflater <Boolean>

Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default

value: false. Possible values: {true, false}

--USE_JDK_INFLATER,-use_jdk_inflater <Boolean>

Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default

value: false. Possible values: {true, false}

--VALIDATION_STRINGENCY <ValidationStringency>

Validation stringency for all SAM files read by this program. Setting stringency to

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: STRICT.

Possible values: {STRICT, LENIENT, SILENT}

--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:

--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}

Illegal argument value: Positional arguments were provided ',ERR194159-30x.hg38.g.vcf.gz}' but no positional argument is defined for this tool.

Tool returned:

1

Using GATK jar /gatk/gatk-package-4.2.6.1-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 -Xmx6G -jar /gatk/gatk-package-4.2.6.1-local.jar MergeVcfs --INPUT --OUTPUT ERR194159-30x.hg38.g.vcf.gz

+ EXIT_CODE=4

+ '[' 4 -eq 0 ']'

+ echo Task failed

Task failed

+ exit 4