[Fri Mar 28 22:31:36 UTC 2025] NormalizeFasta --INPUT /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/picard/fastq/NormalizeFasta/testfasta.fasta --OUTPUT /tmp/normalized8915571723466664286.fasta --LINE_LENGTH 5 --TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Mar 28 22:31:37 UTC 2025] Executing as runner@fv-az1690-153 on Linux 6.8.0-1021-azure amd64; OpenJDK 64-Bit Server VM 17.0.6+10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.3.0
[Fri Mar 28 22:31:37 UTC 2025] picard.reference.NormalizeFasta done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
USAGE: NormalizeFasta [arguments]
Normalizes lines of sequence in a FASTA file to be of the same length.This tool takes any FASTA-formatted file and
reformats the sequence to ensure that all of the sequence record lines are of the same length (with the exception of the
last line). Although the default setting is 100 bases per line, a custom line_length can be specified by the user. In
addition, record names can be truncated at the first instance of a whitespace character to ensure downstream
compatibility.<br /><h4>Usage example:</h4><pre>java -jar picard.jar NormalizeFasta \<br /> I=input_sequence.fasta
\<br /> O=normalized_sequence.fasta</pre><hr />
Version:3.3.0
Required Arguments:
--INPUT,-I <File> The input FASTA file to normalize. Required.
--OUTPUT,-O <File> The output FASTA file to write. 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.
--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: false. 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}
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--LINE_LENGTH <Integer> The line length to be used for the output FASTA file. Default value: 100.
--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 <PicardHtsPath>
Reference sequence file. 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.
--TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE <Boolean>
Truncate sequence names at first whitespace. Default value: false. Possible values:
{true, false}
--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}
input is not a recognized option