[Thu Apr 24 13:04:13 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_basic.sam --OUTPUT /tmp/picardRevertSamTest17167545283827750747 --OUTPUT_BY_READGROUP true --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_basic.sam --OUTPUT /tmp/reverted1935402754686956192.sam --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_CLEAR XT --SAMPLE_ALIAS Hey,Dad! --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_basic.sam --OUTPUT /tmp/reverted11431265869376401435.sam --RESTORE_ORIGINAL_QUALITIES false --REMOVE_DUPLICATE_INFORMATION false --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_CLEAR XT --SAMPLE_ALIAS Hey,Dad! --LIBRARY_NAME NewLibraryName --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:13 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_basic.sam --OUTPUT /tmp/reverted9509405003251267520.sam --RESTORE_HARDCLIPS false --RESTORE_ORIGINAL_QUALITIES false --REMOVE_DUPLICATE_INFORMATION false --REMOVE_ALIGNMENT_INFORMATION false --OUTPUT_BY_READGROUP false --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
USAGE: RevertSam [arguments]
Reverts SAM/BAM/CRAM files to a previous state. This tool removes or restores certain properties of the SAM records,
including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It
is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score
recalibration (BQSR) if theoriginal qualities were retained.
<h3>Examples</h3>
<h4>Example with single output:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
O=reverted.bam
<h4>Example outputting by read group with output map:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
OUTPUT_BY_READGROUP=true \
OUTPUT_MAP=reverted_bam_paths.tsv
Will output a BAM/SAM file per read group.
<h4>Example outputting by read group without output map:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
OUTPUT_BY_READGROUP=true \
O=/write/reverted/read/group/bams/in/this/dir
Will output one file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option.
Note: If the program fails due to a validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT or
SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will be
obviated when the REMOVE_ALIGNMENT_INFORMATION option is used).
Version:null
Required Arguments:
--INPUT,-I <PicardHtsPath> The input SAM/BAM/CRAM file to revert the state of. Required.
--OUTPUT,-O <PicardHtsPath> The output SAM/BAM/CRAM file to create, or an output directory if OUTPUT_BY_READGROUP is
true. Required. Cannot be used in conjunction with argument(s) OUTPUT_MAP (OM)
--OUTPUT_MAP,-OM <PicardHtsPath>
Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only
used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjunction with
argument(s) OUTPUT (O)
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.
--ATTRIBUTE_TO_CLEAR <String> When removing alignment information, the set of optional tags to remove. This argument
may be specified 0 or more times. Default value: [NM, UQ, PG, MD, MQ, SA, MC, AS].
--ATTRIBUTE_TO_REVERSE,-RV <String>
Attributes on negative strand reads that need to be reversed. This argument may be
specified 0 or more times. Default value: [OQ, U2].
--ATTRIBUTE_TO_REVERSE_COMPLEMENT,-RC <String>
Attributes on negative strand reads that need to be reverse complemented. This argument
may be specified 0 or more times. Default value: [E2, SQ].
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--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}
--KEEP_FIRST_DUPLICATE <Boolean>
If SANITIZE=true keep the first record when we find more than one record with the same
name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1
and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the
duplicate flag in the FLAG field, but instead reads with the same name. Default value:
false. Possible values: {true, false}
--LIBRARY_NAME,-LIB <String> The library name to use in the reverted output file. This will override the existing
sample alias in the file and is used only if all the read groups in the input file have
the same library name. Default value: null.
--MAX_DISCARD_FRACTION <Double>
If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to
sanitization then the program will exit with an Exception instead of exiting cleanly.
Output BAM will still be valid. Default value: 0.01.
--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: 100.
--OUTPUT_BY_READGROUP,-OBR <Boolean>
When true, outputs each read group in a separate file. Default value: false. Possible
values: {true, false}
--OUTPUT_BY_READGROUP_FILE_FORMAT,-OBRFF <FileType>
When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format.
Default value: dynamic. sam (Generate SAM files.)
bam (Generate BAM files.)
cram (Generate CRAM files.)
dynamic (Generate files based on the extention of INPUT.)
--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.
--REMOVE_ALIGNMENT_INFORMATION <Boolean>
Remove all alignment information from the file. Default value: true. Possible values:
{true, false}
--REMOVE_DUPLICATE_INFORMATION <Boolean>
Remove duplicate read flags from all reads. Note that if this is false and
REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes
desirable trait of having unmapped reads that are marked as duplicates. Default value:
true. Possible values: {true, false}
--RESTORE_HARDCLIPS,-RHC <Boolean>
When true, restores reads and qualities of records with hard-clips containing XB and XQ
tags. Default value: true. Possible values: {true, false}
--RESTORE_ORIGINAL_QUALITIES,-OQ <Boolean>
True to restore original qualities from the OQ field to the QUAL field if available.
Default value: true. Possible values: {true, false}
--SAMPLE_ALIAS,-ALIAS <String>The sample alias to use in the reverted output file. This will override the existing
sample alias in the file and is used only if all the read groups in the input file have
the same sample alias. Default value: null.
--SANITIZE <Boolean> WARNING: This option is potentially destructive. If enabled will discard reads in order to
produce a consistent output BAM. Reads discarded include (but are not limited to) paired
reads with missing mates, duplicated records, records with mismatches in length of bases
and qualities. This option can only be enabled if the output sort order is queryname and
will always cause sorting to occur. Default value: false. Possible values: {true, false}
--SORT_ORDER,-SO <SortOrder> The sort order to create the reverted output file with. Default value: queryname.
Possible values: {unsorted, queryname, coordinate, duplicate, unknown}
--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}
[Thu Apr 24 13:04:14 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam --OUTPUT /tmp/test-output-hard-clipped-round-trip-mba1974854357716713441.sam --HARD_CLIP_OVERLAPPING_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:04:14 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam]
INFO 2025-04-24 13:04:14 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT /tmp/test-output-hard-clipped-round-trip-mba1974854357716713441.sam --OUTPUT /tmp/test-output-hard-clipped-round-trip-reverted10394093584548419359.sam --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP false --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
USAGE: RevertSam [arguments]
Reverts SAM/BAM/CRAM files to a previous state. This tool removes or restores certain properties of the SAM records,
including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It
is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score
recalibration (BQSR) if theoriginal qualities were retained.
<h3>Examples</h3>
<h4>Example with single output:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
O=reverted.bam
<h4>Example outputting by read group with output map:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
OUTPUT_BY_READGROUP=true \
OUTPUT_MAP=reverted_bam_paths.tsv
Will output a BAM/SAM file per read group.
<h4>Example outputting by read group without output map:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
OUTPUT_BY_READGROUP=true \
O=/write/reverted/read/group/bams/in/this/dir
Will output one file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option.
Note: If the program fails due to a validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT or
SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will be
obviated when the REMOVE_ALIGNMENT_INFORMATION option is used).
Version:null
Required Arguments:
--INPUT,-I <PicardHtsPath> The input SAM/BAM/CRAM file to revert the state of. Required.
--OUTPUT,-O <PicardHtsPath> The output SAM/BAM/CRAM file to create, or an output directory if OUTPUT_BY_READGROUP is
true. Required. Cannot be used in conjunction with argument(s) OUTPUT_MAP (OM)
--OUTPUT_MAP,-OM <PicardHtsPath>
Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only
used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjunction with
argument(s) OUTPUT (O)
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.
--ATTRIBUTE_TO_CLEAR <String> When removing alignment information, the set of optional tags to remove. This argument
may be specified 0 or more times. Default value: [NM, UQ, PG, MD, MQ, SA, MC, AS].
--ATTRIBUTE_TO_REVERSE,-RV <String>
Attributes on negative strand reads that need to be reversed. This argument may be
specified 0 or more times. Default value: [OQ, U2].
--ATTRIBUTE_TO_REVERSE_COMPLEMENT,-RC <String>
Attributes on negative strand reads that need to be reverse complemented. This argument
may be specified 0 or more times. Default value: [E2, SQ].
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--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}
--KEEP_FIRST_DUPLICATE <Boolean>
If SANITIZE=true keep the first record when we find more than one record with the same
name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1
and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the
duplicate flag in the FLAG field, but instead reads with the same name. Default value:
false. Possible values: {true, false}
--LIBRARY_NAME,-LIB <String> The library name to use in the reverted output file. This will override the existing
sample alias in the file and is used only if all the read groups in the input file have
the same library name. Default value: null.
--MAX_DISCARD_FRACTION <Double>
If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to
sanitization then the program will exit with an Exception instead of exiting cleanly.
Output BAM will still be valid. Default value: 0.01.
--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: 100.
--OUTPUT_BY_READGROUP,-OBR <Boolean>
When true, outputs each read group in a separate file. Default value: false. Possible
values: {true, false}
--OUTPUT_BY_READGROUP_FILE_FORMAT,-OBRFF <FileType>
When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format.
Default value: dynamic. sam (Generate SAM files.)
bam (Generate BAM files.)
cram (Generate CRAM files.)
dynamic (Generate files based on the extention of INPUT.)
--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.
--REMOVE_ALIGNMENT_INFORMATION <Boolean>
Remove all alignment information from the file. Default value: true. Possible values:
{true, false}
--REMOVE_DUPLICATE_INFORMATION <Boolean>
Remove duplicate read flags from all reads. Note that if this is false and
REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes
desirable trait of having unmapped reads that are marked as duplicates. Default value:
true. Possible values: {true, false}
--RESTORE_HARDCLIPS,-RHC <Boolean>
When true, restores reads and qualities of records with hard-clips containing XB and XQ
tags. Default value: true. Possible values: {true, false}
--RESTORE_ORIGINAL_QUALITIES,-OQ <Boolean>
True to restore original qualities from the OQ field to the QUAL field if available.
Default value: true. Possible values: {true, false}
--SAMPLE_ALIAS,-ALIAS <String>The sample alias to use in the reverted output file. This will override the existing
sample alias in the file and is used only if all the read groups in the input file have
the same sample alias. Default value: null.
--SANITIZE <Boolean> WARNING: This option is potentially destructive. If enabled will discard reads in order to
produce a consistent output BAM. Reads discarded include (but are not limited to) paired
reads with missing mates, duplicated records, records with mismatches in length of bases
and qualities. This option can only be enabled if the output sort order is queryname and
will always cause sorting to occur. Default value: false. Possible values: {true, false}
--SORT_ORDER,-SO <SortOrder> The sort order to create the reverted output file with. Default value: queryname.
Possible values: {unsorted, queryname, coordinate, duplicate, unknown}
--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}
Argument 'OUTPUT' cannot be used in conjunction with argument(s) OUTPUT_MAP
USAGE: RevertSam [arguments]
Reverts SAM/BAM/CRAM files to a previous state. This tool removes or restores certain properties of the SAM records,
including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It
is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score
recalibration (BQSR) if theoriginal qualities were retained.
<h3>Examples</h3>
<h4>Example with single output:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
O=reverted.bam
<h4>Example outputting by read group with output map:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
OUTPUT_BY_READGROUP=true \
OUTPUT_MAP=reverted_bam_paths.tsv
Will output a BAM/SAM file per read group.
<h4>Example outputting by read group without output map:</h4>
java -jar picard.jar RevertSam \
I=input.bam \
OUTPUT_BY_READGROUP=true \
O=/write/reverted/read/group/bams/in/this/dir
Will output one file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option.
Note: If the program fails due to a validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT or
SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will be
obviated when the REMOVE_ALIGNMENT_INFORMATION option is used).
Version:null
Required Arguments:
--INPUT,-I <PicardHtsPath> The input SAM/BAM/CRAM file to revert the state of. Required.
--OUTPUT,-O <PicardHtsPath> The output SAM/BAM/CRAM file to create, or an output directory if OUTPUT_BY_READGROUP is
true. Required. Cannot be used in conjunction with argument(s) OUTPUT_MAP (OM)
--OUTPUT_MAP,-OM <PicardHtsPath>
Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only
used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjunction with
argument(s) OUTPUT (O)
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.
--ATTRIBUTE_TO_CLEAR <String> When removing alignment information, the set of optional tags to remove. This argument
may be specified 0 or more times. Default value: [NM, UQ, PG, MD, MQ, SA, MC, AS].
--ATTRIBUTE_TO_REVERSE,-RV <String>
Attributes on negative strand reads that need to be reversed. This argument may be
specified 0 or more times. Default value: [OQ, U2].
--ATTRIBUTE_TO_REVERSE_COMPLEMENT,-RC <String>
Attributes on negative strand reads that need to be reverse complemented. This argument
may be specified 0 or more times. Default value: [E2, SQ].
--COMPRESSION_LEVEL <Integer> Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5.
--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}
--KEEP_FIRST_DUPLICATE <Boolean>
If SANITIZE=true keep the first record when we find more than one record with the same
name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1
and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the
duplicate flag in the FLAG field, but instead reads with the same name. Default value:
false. Possible values: {true, false}
--LIBRARY_NAME,-LIB <String> The library name to use in the reverted output file. This will override the existing
sample alias in the file and is used only if all the read groups in the input file have
the same library name. Default value: null.
--MAX_DISCARD_FRACTION <Double>
If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to
sanitization then the program will exit with an Exception instead of exiting cleanly.
Output BAM will still be valid. Default value: 0.01.
--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: 100.
--OUTPUT_BY_READGROUP,-OBR <Boolean>
When true, outputs each read group in a separate file. Default value: false. Possible
values: {true, false}
--OUTPUT_BY_READGROUP_FILE_FORMAT,-OBRFF <FileType>
When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format.
Default value: dynamic. sam (Generate SAM files.)
bam (Generate BAM files.)
cram (Generate CRAM files.)
dynamic (Generate files based on the extention of INPUT.)
--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.
--REMOVE_ALIGNMENT_INFORMATION <Boolean>
Remove all alignment information from the file. Default value: true. Possible values:
{true, false}
--REMOVE_DUPLICATE_INFORMATION <Boolean>
Remove duplicate read flags from all reads. Note that if this is false and
REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes
desirable trait of having unmapped reads that are marked as duplicates. Default value:
true. Possible values: {true, false}
--RESTORE_HARDCLIPS,-RHC <Boolean>
When true, restores reads and qualities of records with hard-clips containing XB and XQ
tags. Default value: true. Possible values: {true, false}
--RESTORE_ORIGINAL_QUALITIES,-OQ <Boolean>
True to restore original qualities from the OQ field to the QUAL field if available.
Default value: true. Possible values: {true, false}
--SAMPLE_ALIAS,-ALIAS <String>The sample alias to use in the reverted output file. This will override the existing
sample alias in the file and is used only if all the read groups in the input file have
the same sample alias. Default value: null.
--SANITIZE <Boolean> WARNING: This option is potentially destructive. If enabled will discard reads in order to
produce a consistent output BAM. Reads discarded include (but are not limited to) paired
reads with missing mates, duplicated records, records with mismatches in length of bases
and qualities. This option can only be enabled if the output sort order is queryname and
will always cause sorting to occur. Default value: false. Possible values: {true, false}
--SORT_ORDER,-SO <SortOrder> The sort order to create the reverted output file with. Default value: queryname.
Possible values: {unsorted, queryname, coordinate, duplicate, unknown}
--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}
Argument INPUT was missing: Argument 'INPUT' is required
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam --OUTPUT . --OUTPUT_BY_READGROUP true --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam --OUTPUT /tmp/no-rg-reverted16776706915894193461.sam --SANITIZE true --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:04:14 RevertSam Discarded 0 out of 240 (0.000%) reads in order to sanitize output.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_basic.sam --OUTPUT_MAP /tmp/picardRevertSamTestOutputMap5056260895004666165.txt --OUTPUT_BY_READGROUP true --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_CLEAR NM --SAMPLE_ALIAS test_sample_1 --LIBRARY_NAME test_library_1 --REFERENCE_SEQUENCE testdata/picard/reference/test.fasta --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_sample_library_override.sam --OUTPUT /tmp/bad4542198853247133607.sam --SAMPLE_ALIAS NewSample --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_sample_library_override.sam --OUTPUT /tmp/bad3560865146898507444.sam --LIBRARY_NAME NewLibrary --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_sample_library_override.sam --OUTPUT /tmp/bad7664386690921065381.sam --SAMPLE_ALIAS NewSample --LIBRARY_NAME NewLibrary --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT /tmp/test-input-santize-and-deduplicate-records9912361360090162919.sam --OUTPUT /tmp/test-output-santize-and-deduplicate-records1970844450994209700.sam --SANITIZE true --MAX_DISCARD_FRACTION 1.0 --KEEP_FIRST_DUPLICATE true --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
WARNING 2025-04-24 13:04:14 RevertSam Skipping read group 3 with no reads
INFO 2025-04-24 13:04:14 RevertSam Detected quality format for 0: Standard
INFO 2025-04-24 13:04:14 RevertSam Detected quality format for 1: Standard
INFO 2025-04-24 13:04:14 RevertSam Detected quality format for 2: Standard
INFO 2025-04-24 13:04:14 RevertSam Discarded 4 out of 12 (33.333%) reads in order to sanitize output.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_single_end.sam --OUTPUT /tmp/single_end_reverted120381782179592335.sam --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --SANITIZE false --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
WARNING 2025-04-24 13:04:14 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:14 EDT 2025] RevertSam --INPUT testdata/picard/sam/RevertSam/revert_sam_single_end.sam --OUTPUT /tmp/single_end_reverted16639604740794295690.sam --SANITIZE true --OUTPUT_BY_READGROUP false --RESTORE_HARDCLIPS true --OUTPUT_BY_READGROUP_FILE_FORMAT dynamic --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES true --REMOVE_DUPLICATE_INFORMATION true --REMOVE_ALIGNMENT_INFORMATION true --ATTRIBUTE_TO_CLEAR NM --ATTRIBUTE_TO_CLEAR UQ --ATTRIBUTE_TO_CLEAR PG --ATTRIBUTE_TO_CLEAR MD --ATTRIBUTE_TO_CLEAR MQ --ATTRIBUTE_TO_CLEAR SA --ATTRIBUTE_TO_CLEAR MC --ATTRIBUTE_TO_CLEAR AS --ATTRIBUTE_TO_REVERSE OQ --ATTRIBUTE_TO_REVERSE U2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTE_TO_REVERSE_COMPLEMENT SQ --MAX_DISCARD_FRACTION 0.01 --KEEP_FIRST_DUPLICATE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:04:14 RevertSam Detected quality format for A: Standard
INFO 2025-04-24 13:04:14 RevertSam Discarded 0 out of 3 (0.000%) reads in order to sanitize output.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.RevertSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824