USAGE: CrosscheckReadGroupFingerprints [arguments]
DEPRECATED: USE CrosscheckFingerprints.
Version:null
Required Arguments:
--HAPLOTYPE_MAP,-H <File> The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for
fingerprinting. See
https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for
details. Required.
--INPUT,-I <String> One or more input files (or lists of files) with which to compare fingerprints. This
argument must be specified at least once. Required.
Optional Arguments:
--ALLOW_DUPLICATE_READS <Boolean>
Allow the use of duplicate reads in performing the comparison. Can be useful when
duplicate marking has been overly aggressive and coverage is low. Default value: false.
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.
--CALCULATE_TUMOR_AWARE_RESULTS <Boolean>
Specifies whether the Tumor-aware result should be calculated. These are time consuming
and can roughly double the runtime of the tool. When crosschecking many groups not
calculating the tumor-aware results can result in a significant speedup. Default value:
true. Possible values: {true, false}
--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}
--CROSSCHECK_BY <DataType> Specifies which data-type should be used as the basic comparison unit. Fingerprints from
readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared.
Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP.
Possible values: {FILE, SAMPLE, LIBRARY, READGROUP}
--CROSSCHECK_LIBRARIES <Boolean>
Instead of producing the normal comparison of read-groups, roll fingerprints up to the
library level and print out a library x library matrix with LOD scores. Default value:
false. Possible values: {true, false}
--CROSSCHECK_MODE <CrosscheckMode>
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
Default value: CHECK_SAME_SAMPLE. CHECK_SAME_SAMPLE (In this mode, each sample in INPUT
will only be checked against a single corresponding sample in SECOND_INPUT. If a
corresponding sample cannot be found, the program will proceed, but report the missing
samples and return the value specified in EXIT_CODE_WHEN_MISMATCH. The corresponding
samples are those that equal each other, after possible renaming via INPUT_SAMPLE_MAP and
SECOND_INPUT_SAMPLE_MAP. In this mode CROSSCHECK_BY must be SAMPLE.)
CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the
samples in SECOND_INPUT.)
--CROSSCHECK_SAMPLES <Boolean>Instead of producing the normal comparison of read-groups, roll fingerprints up to the
sample level and print out a sample x sample matrix with LOD scores. Default value:
false. Possible values: {true, false}
--EXIT_CODE_WHEN_MISMATCH <Integer>
When one or more mismatches between groups is detected, exit with this value instead of 0.
Default value: 1.
--EXIT_CODE_WHEN_NO_VALID_CHECKS <Integer>
When all LOD scores are zero, exit with this value. Default value: 1.
--EXPECT_ALL_GROUPS_TO_MATCH <Boolean>
Expect all groups' fingerprints to match, irrespective of their sample names. By default
(with this value set to false), groups (readgroups, libraries, files, or samples) with
different sample names are expected to mismatch, and those with the same sample name are
expected to match. Default value: false. Possible values: {true, false} Cannot be used
in conjunction with argument(s) EXPECT_ALL_READ_GROUPS_TO_MATCH
--EXPECT_ALL_READ_GROUPS_TO_MATCH <Boolean>
Expect all read groups' fingerprints to match, irrespective of their sample names. By
default (with this value set to false), read groups with different sample names are
expected to mismatch, and those with the same sample name are expected to match. Default
value: false. Possible values: {true, false} Cannot be used in conjunction with
argument(s) EXPECT_ALL_GROUPS_TO_MATCH
--GENOTYPING_ERROR_RATE <Double>
This argument is DEPRECATED (No longer used in fingerprint checking. Will be removed in a
future release.). Assumed genotyping error rate that provides a floor on the probability
that a genotype comes from the expected sample. Must be greater than zero. Default
value: 0.01.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--INPUT_INDEX_MAP <File> A tsv with two columns and no header which maps the input files to corresponding indices;
to be used when index files are not located next to input files. First column must match
the list of inputs. Default value: null.
--INPUT_SAMPLE_FILE_MAP <File>A tsv with two columns representing the sample as it should be used for comparisons to
SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in
the second column). Need only to include the samples that change. Values in column 1
should be unique even in union with the remaining unmapped samples. Values in column 2
should be unique in the file. Will error if more than one sample is found in a file
(multi-sample VCF) pointed to in column 2. Should only be used in the presence of
SECOND_INPUT. Default value: null. Cannot be used in conjunction with argument(s)
INPUT_SAMPLE_MAP
--INPUT_SAMPLE_MAP <File> A tsv with two columns representing the sample as it appears in the INPUT data (in column
1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second
column). Need only include the samples that change. Values in column 1 should be unique.
Values in column 2 should be unique even in union with the remaining unmapped samples.
Should only be used with SECOND_INPUT. Default value: null. Cannot be used in
conjunction with argument(s) INPUT_SAMPLE_FILE_MAP
--LOD_THRESHOLD,-LOD <Double> If any two groups (with the same sample name) match with a LOD score lower than the
threshold the tool will exit with a non-zero code to indicate error. Program will also
exit with an error if it finds two groups with different sample name that match with a LOD
score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different
individuals, negative LOD score -N, mean 10^N time more likely that the groups are from
different individuals, and +N means 10^N times more likely that the groups are from the
same individual. Default value: 0.0.
--LOSS_OF_HET_RATE <Double> The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via
loss of heterozygosity) in the tumor (model assumes independent events, so this needs to
be larger than reality). Default value: 0.5.
--MATRIX_OUTPUT,-MO <File> Optional output file to write matrix of LOD scores to. This is less informative than the
metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of
Heterozygosity). It is however sometimes easier to use visually. Default value: null.
Cannot be used in conjunction with argument(s) SECOND_INPUT (SI)
--MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK <Double>
Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood
difference between the different values for the three possible genotypes). Default value:
3.0.
--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.
--NUM_THREADS <Integer> The number of threads to use to process files and generate fingerprints. Default value:
1.
--OUTPUT,-O <File> Optional output file to write metrics to. Default is to write to stdout. Default value:
null.
--OUTPUT_ERRORS_ONLY <Boolean>If true, then only groups that do not relate to each other as expected will have their
LODs reported. Default value: false. Possible values: {true, false}
--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.
--REQUIRE_INDEX_FILES <Boolean>
A boolean value to determine whether input files should only be parsed if index files are
available. Without turning this option on, the tool will need to read through the entirety
of input files without index files either provided via the INPUT_INDEX_MAP or locally
accessible relative to the input, which significantly increases runtime. If set to true
and no index is found for a file, an exception will be thrown. This applies for both the
INPUT and SECOND_INPUT files. Default value: false. Possible values: {true, false}
--SAMPLE_INDIVIDUAL_MAP <File>A tsv with two columns representing the individual with which each sample is associated.
The first column is the sample id, and the second column is the associated individual id.
Values in the first column must be unique. If INPUT_SAMPLE_MAP or SECOND_INPUT_SAMPLE_MAP
is also specified, then the values in the first column of this file should be the sample
aliases specified in the second columns of INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP,
respectively. When this input is specified, expectations for matches will be based on the
equality or inequality of the individual ids associated with two samples, as opposed to
the sample ids themselves. Samples which are not listed in this file will have their
sample id used as their individual id, for the purposes of match expectations. This means
that one sample id could be used as the individual id for another sample, but not included
in the map itself, and these two samples would be considered to have come from the same
individual. Note that use of this parameter only affects labelling of matches and
mismatches as EXPECTED or UNEXPECTED. It has no affect on how data is grouped for
crosschecking. Default value: null.
--SECOND_INPUT,-SI <String> A second set of input files (or lists of files) with which to compare fingerprints. If
this option is provided the tool compares each sample in INPUT with the sample from
SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE
regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in
INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool
will proceed to check the matching samples, but report the missing samples and return a
non-zero error-code. This argument may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s) MATRIX_OUTPUT (MO)
--SECOND_INPUT_INDEX_MAP <File>
A tsv with two columns and no header which maps the second input files to corresponding
indices; to be used when index files are not located next to second input files. First
column must match the list of second inputs. Default value: null.
--SECOND_INPUT_SAMPLE_MAP <File>
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in
column 1) and the sample as it should be used for comparisons to INPUT (in the second
column). Note that in case of unrolling files (file-of-filenames) one would need to
reference the final file, i.e. the file that contains the genomic data. Need only include
the samples that change. Values in column 1 should be unique. Values in column 2 should be
unique even in union with the remaining unmapped samples. Should only be used with
SECOND_INPUT. 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}
When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value LIBRARY
Use CrosscheckFingerprints if you would like to do that.
USAGE: CrosscheckReadGroupFingerprints [arguments]
DEPRECATED: USE CrosscheckFingerprints.
Version:null
Required Arguments:
--HAPLOTYPE_MAP,-H <File> The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for
fingerprinting. See
https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for
details. Required.
--INPUT,-I <String> One or more input files (or lists of files) with which to compare fingerprints. This
argument must be specified at least once. Required.
Optional Arguments:
--ALLOW_DUPLICATE_READS <Boolean>
Allow the use of duplicate reads in performing the comparison. Can be useful when
duplicate marking has been overly aggressive and coverage is low. Default value: false.
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.
--CALCULATE_TUMOR_AWARE_RESULTS <Boolean>
Specifies whether the Tumor-aware result should be calculated. These are time consuming
and can roughly double the runtime of the tool. When crosschecking many groups not
calculating the tumor-aware results can result in a significant speedup. Default value:
true. Possible values: {true, false}
--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}
--CROSSCHECK_BY <DataType> Specifies which data-type should be used as the basic comparison unit. Fingerprints from
readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared.
Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP.
Possible values: {FILE, SAMPLE, LIBRARY, READGROUP}
--CROSSCHECK_LIBRARIES <Boolean>
Instead of producing the normal comparison of read-groups, roll fingerprints up to the
library level and print out a library x library matrix with LOD scores. Default value:
false. Possible values: {true, false}
--CROSSCHECK_MODE <CrosscheckMode>
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
Default value: CHECK_SAME_SAMPLE. CHECK_SAME_SAMPLE (In this mode, each sample in INPUT
will only be checked against a single corresponding sample in SECOND_INPUT. If a
corresponding sample cannot be found, the program will proceed, but report the missing
samples and return the value specified in EXIT_CODE_WHEN_MISMATCH. The corresponding
samples are those that equal each other, after possible renaming via INPUT_SAMPLE_MAP and
SECOND_INPUT_SAMPLE_MAP. In this mode CROSSCHECK_BY must be SAMPLE.)
CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the
samples in SECOND_INPUT.)
--CROSSCHECK_SAMPLES <Boolean>Instead of producing the normal comparison of read-groups, roll fingerprints up to the
sample level and print out a sample x sample matrix with LOD scores. Default value:
false. Possible values: {true, false}
--EXIT_CODE_WHEN_MISMATCH <Integer>
When one or more mismatches between groups is detected, exit with this value instead of 0.
Default value: 1.
--EXIT_CODE_WHEN_NO_VALID_CHECKS <Integer>
When all LOD scores are zero, exit with this value. Default value: 1.
--EXPECT_ALL_GROUPS_TO_MATCH <Boolean>
Expect all groups' fingerprints to match, irrespective of their sample names. By default
(with this value set to false), groups (readgroups, libraries, files, or samples) with
different sample names are expected to mismatch, and those with the same sample name are
expected to match. Default value: false. Possible values: {true, false} Cannot be used
in conjunction with argument(s) EXPECT_ALL_READ_GROUPS_TO_MATCH
--EXPECT_ALL_READ_GROUPS_TO_MATCH <Boolean>
Expect all read groups' fingerprints to match, irrespective of their sample names. By
default (with this value set to false), read groups with different sample names are
expected to mismatch, and those with the same sample name are expected to match. Default
value: false. Possible values: {true, false} Cannot be used in conjunction with
argument(s) EXPECT_ALL_GROUPS_TO_MATCH
--GENOTYPING_ERROR_RATE <Double>
This argument is DEPRECATED (No longer used in fingerprint checking. Will be removed in a
future release.). Assumed genotyping error rate that provides a floor on the probability
that a genotype comes from the expected sample. Must be greater than zero. Default
value: 0.01.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--INPUT_INDEX_MAP <File> A tsv with two columns and no header which maps the input files to corresponding indices;
to be used when index files are not located next to input files. First column must match
the list of inputs. Default value: null.
--INPUT_SAMPLE_FILE_MAP <File>A tsv with two columns representing the sample as it should be used for comparisons to
SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in
the second column). Need only to include the samples that change. Values in column 1
should be unique even in union with the remaining unmapped samples. Values in column 2
should be unique in the file. Will error if more than one sample is found in a file
(multi-sample VCF) pointed to in column 2. Should only be used in the presence of
SECOND_INPUT. Default value: null. Cannot be used in conjunction with argument(s)
INPUT_SAMPLE_MAP
--INPUT_SAMPLE_MAP <File> A tsv with two columns representing the sample as it appears in the INPUT data (in column
1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second
column). Need only include the samples that change. Values in column 1 should be unique.
Values in column 2 should be unique even in union with the remaining unmapped samples.
Should only be used with SECOND_INPUT. Default value: null. Cannot be used in
conjunction with argument(s) INPUT_SAMPLE_FILE_MAP
--LOD_THRESHOLD,-LOD <Double> If any two groups (with the same sample name) match with a LOD score lower than the
threshold the tool will exit with a non-zero code to indicate error. Program will also
exit with an error if it finds two groups with different sample name that match with a LOD
score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different
individuals, negative LOD score -N, mean 10^N time more likely that the groups are from
different individuals, and +N means 10^N times more likely that the groups are from the
same individual. Default value: 0.0.
--LOSS_OF_HET_RATE <Double> The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via
loss of heterozygosity) in the tumor (model assumes independent events, so this needs to
be larger than reality). Default value: 0.5.
--MATRIX_OUTPUT,-MO <File> Optional output file to write matrix of LOD scores to. This is less informative than the
metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of
Heterozygosity). It is however sometimes easier to use visually. Default value: null.
Cannot be used in conjunction with argument(s) SECOND_INPUT (SI)
--MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK <Double>
Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood
difference between the different values for the three possible genotypes). Default value:
3.0.
--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.
--NUM_THREADS <Integer> The number of threads to use to process files and generate fingerprints. Default value:
1.
--OUTPUT,-O <File> Optional output file to write metrics to. Default is to write to stdout. Default value:
null.
--OUTPUT_ERRORS_ONLY <Boolean>If true, then only groups that do not relate to each other as expected will have their
LODs reported. Default value: false. Possible values: {true, false}
--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.
--REQUIRE_INDEX_FILES <Boolean>
A boolean value to determine whether input files should only be parsed if index files are
available. Without turning this option on, the tool will need to read through the entirety
of input files without index files either provided via the INPUT_INDEX_MAP or locally
accessible relative to the input, which significantly increases runtime. If set to true
and no index is found for a file, an exception will be thrown. This applies for both the
INPUT and SECOND_INPUT files. Default value: false. Possible values: {true, false}
--SAMPLE_INDIVIDUAL_MAP <File>A tsv with two columns representing the individual with which each sample is associated.
The first column is the sample id, and the second column is the associated individual id.
Values in the first column must be unique. If INPUT_SAMPLE_MAP or SECOND_INPUT_SAMPLE_MAP
is also specified, then the values in the first column of this file should be the sample
aliases specified in the second columns of INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP,
respectively. When this input is specified, expectations for matches will be based on the
equality or inequality of the individual ids associated with two samples, as opposed to
the sample ids themselves. Samples which are not listed in this file will have their
sample id used as their individual id, for the purposes of match expectations. This means
that one sample id could be used as the individual id for another sample, but not included
in the map itself, and these two samples would be considered to have come from the same
individual. Note that use of this parameter only affects labelling of matches and
mismatches as EXPECTED or UNEXPECTED. It has no affect on how data is grouped for
crosschecking. Default value: null.
--SECOND_INPUT,-SI <String> A second set of input files (or lists of files) with which to compare fingerprints. If
this option is provided the tool compares each sample in INPUT with the sample from
SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE
regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in
INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool
will proceed to check the matching samples, but report the missing samples and return a
non-zero error-code. This argument may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s) MATRIX_OUTPUT (MO)
--SECOND_INPUT_INDEX_MAP <File>
A tsv with two columns and no header which maps the second input files to corresponding
indices; to be used when index files are not located next to second input files. First
column must match the list of second inputs. Default value: null.
--SECOND_INPUT_SAMPLE_MAP <File>
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in
column 1) and the sample as it should be used for comparisons to INPUT (in the second
column). Note that in case of unrolling files (file-of-filenames) one would need to
reference the final file, i.e. the file that contains the genomic data. Need only include
the samples that change. Values in column 1 should be unique. Values in column 2 should be
unique even in union with the remaining unmapped samples. Should only be used with
SECOND_INPUT. 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}
When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value SAMPLE
Use CrosscheckFingerprints if you would like to do that.
USAGE: CrosscheckReadGroupFingerprints [arguments]
DEPRECATED: USE CrosscheckFingerprints.
Version:null
Required Arguments:
--HAPLOTYPE_MAP,-H <File> The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for
fingerprinting. See
https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for
details. Required.
--INPUT,-I <String> One or more input files (or lists of files) with which to compare fingerprints. This
argument must be specified at least once. Required.
Optional Arguments:
--ALLOW_DUPLICATE_READS <Boolean>
Allow the use of duplicate reads in performing the comparison. Can be useful when
duplicate marking has been overly aggressive and coverage is low. Default value: false.
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.
--CALCULATE_TUMOR_AWARE_RESULTS <Boolean>
Specifies whether the Tumor-aware result should be calculated. These are time consuming
and can roughly double the runtime of the tool. When crosschecking many groups not
calculating the tumor-aware results can result in a significant speedup. Default value:
true. Possible values: {true, false}
--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}
--CROSSCHECK_BY <DataType> Specifies which data-type should be used as the basic comparison unit. Fingerprints from
readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared.
Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP.
Possible values: {FILE, SAMPLE, LIBRARY, READGROUP}
--CROSSCHECK_LIBRARIES <Boolean>
Instead of producing the normal comparison of read-groups, roll fingerprints up to the
library level and print out a library x library matrix with LOD scores. Default value:
false. Possible values: {true, false}
--CROSSCHECK_MODE <CrosscheckMode>
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
Default value: CHECK_SAME_SAMPLE. CHECK_SAME_SAMPLE (In this mode, each sample in INPUT
will only be checked against a single corresponding sample in SECOND_INPUT. If a
corresponding sample cannot be found, the program will proceed, but report the missing
samples and return the value specified in EXIT_CODE_WHEN_MISMATCH. The corresponding
samples are those that equal each other, after possible renaming via INPUT_SAMPLE_MAP and
SECOND_INPUT_SAMPLE_MAP. In this mode CROSSCHECK_BY must be SAMPLE.)
CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the
samples in SECOND_INPUT.)
--CROSSCHECK_SAMPLES <Boolean>Instead of producing the normal comparison of read-groups, roll fingerprints up to the
sample level and print out a sample x sample matrix with LOD scores. Default value:
false. Possible values: {true, false}
--EXIT_CODE_WHEN_MISMATCH <Integer>
When one or more mismatches between groups is detected, exit with this value instead of 0.
Default value: 1.
--EXIT_CODE_WHEN_NO_VALID_CHECKS <Integer>
When all LOD scores are zero, exit with this value. Default value: 1.
--EXPECT_ALL_GROUPS_TO_MATCH <Boolean>
Expect all groups' fingerprints to match, irrespective of their sample names. By default
(with this value set to false), groups (readgroups, libraries, files, or samples) with
different sample names are expected to mismatch, and those with the same sample name are
expected to match. Default value: false. Possible values: {true, false} Cannot be used
in conjunction with argument(s) EXPECT_ALL_READ_GROUPS_TO_MATCH
--EXPECT_ALL_READ_GROUPS_TO_MATCH <Boolean>
Expect all read groups' fingerprints to match, irrespective of their sample names. By
default (with this value set to false), read groups with different sample names are
expected to mismatch, and those with the same sample name are expected to match. Default
value: false. Possible values: {true, false} Cannot be used in conjunction with
argument(s) EXPECT_ALL_GROUPS_TO_MATCH
--GENOTYPING_ERROR_RATE <Double>
This argument is DEPRECATED (No longer used in fingerprint checking. Will be removed in a
future release.). Assumed genotyping error rate that provides a floor on the probability
that a genotype comes from the expected sample. Must be greater than zero. Default
value: 0.01.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--INPUT_INDEX_MAP <File> A tsv with two columns and no header which maps the input files to corresponding indices;
to be used when index files are not located next to input files. First column must match
the list of inputs. Default value: null.
--INPUT_SAMPLE_FILE_MAP <File>A tsv with two columns representing the sample as it should be used for comparisons to
SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in
the second column). Need only to include the samples that change. Values in column 1
should be unique even in union with the remaining unmapped samples. Values in column 2
should be unique in the file. Will error if more than one sample is found in a file
(multi-sample VCF) pointed to in column 2. Should only be used in the presence of
SECOND_INPUT. Default value: null. Cannot be used in conjunction with argument(s)
INPUT_SAMPLE_MAP
--INPUT_SAMPLE_MAP <File> A tsv with two columns representing the sample as it appears in the INPUT data (in column
1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second
column). Need only include the samples that change. Values in column 1 should be unique.
Values in column 2 should be unique even in union with the remaining unmapped samples.
Should only be used with SECOND_INPUT. Default value: null. Cannot be used in
conjunction with argument(s) INPUT_SAMPLE_FILE_MAP
--LOD_THRESHOLD,-LOD <Double> If any two groups (with the same sample name) match with a LOD score lower than the
threshold the tool will exit with a non-zero code to indicate error. Program will also
exit with an error if it finds two groups with different sample name that match with a LOD
score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different
individuals, negative LOD score -N, mean 10^N time more likely that the groups are from
different individuals, and +N means 10^N times more likely that the groups are from the
same individual. Default value: 0.0.
--LOSS_OF_HET_RATE <Double> The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via
loss of heterozygosity) in the tumor (model assumes independent events, so this needs to
be larger than reality). Default value: 0.5.
--MATRIX_OUTPUT,-MO <File> Optional output file to write matrix of LOD scores to. This is less informative than the
metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of
Heterozygosity). It is however sometimes easier to use visually. Default value: null.
Cannot be used in conjunction with argument(s) SECOND_INPUT (SI)
--MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK <Double>
Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood
difference between the different values for the three possible genotypes). Default value:
3.0.
--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.
--NUM_THREADS <Integer> The number of threads to use to process files and generate fingerprints. Default value:
1.
--OUTPUT,-O <File> Optional output file to write metrics to. Default is to write to stdout. Default value:
null.
--OUTPUT_ERRORS_ONLY <Boolean>If true, then only groups that do not relate to each other as expected will have their
LODs reported. Default value: false. Possible values: {true, false}
--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.
--REQUIRE_INDEX_FILES <Boolean>
A boolean value to determine whether input files should only be parsed if index files are
available. Without turning this option on, the tool will need to read through the entirety
of input files without index files either provided via the INPUT_INDEX_MAP or locally
accessible relative to the input, which significantly increases runtime. If set to true
and no index is found for a file, an exception will be thrown. This applies for both the
INPUT and SECOND_INPUT files. Default value: false. Possible values: {true, false}
--SAMPLE_INDIVIDUAL_MAP <File>A tsv with two columns representing the individual with which each sample is associated.
The first column is the sample id, and the second column is the associated individual id.
Values in the first column must be unique. If INPUT_SAMPLE_MAP or SECOND_INPUT_SAMPLE_MAP
is also specified, then the values in the first column of this file should be the sample
aliases specified in the second columns of INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP,
respectively. When this input is specified, expectations for matches will be based on the
equality or inequality of the individual ids associated with two samples, as opposed to
the sample ids themselves. Samples which are not listed in this file will have their
sample id used as their individual id, for the purposes of match expectations. This means
that one sample id could be used as the individual id for another sample, but not included
in the map itself, and these two samples would be considered to have come from the same
individual. Note that use of this parameter only affects labelling of matches and
mismatches as EXPECTED or UNEXPECTED. It has no affect on how data is grouped for
crosschecking. Default value: null.
--SECOND_INPUT,-SI <String> A second set of input files (or lists of files) with which to compare fingerprints. If
this option is provided the tool compares each sample in INPUT with the sample from
SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE
regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in
INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool
will proceed to check the matching samples, but report the missing samples and return a
non-zero error-code. This argument may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s) MATRIX_OUTPUT (MO)
--SECOND_INPUT_INDEX_MAP <File>
A tsv with two columns and no header which maps the second input files to corresponding
indices; to be used when index files are not located next to second input files. First
column must match the list of second inputs. Default value: null.
--SECOND_INPUT_SAMPLE_MAP <File>
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in
column 1) and the sample as it should be used for comparisons to INPUT (in the second
column). Note that in case of unrolling files (file-of-filenames) one would need to
reference the final file, i.e. the file that contains the genomic data. Need only include
the samples that change. Values in column 1 should be unique. Values in column 2 should be
unique even in union with the remaining unmapped samples. Should only be used with
SECOND_INPUT. 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}
When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value FILE
Use CrosscheckFingerprints if you would like to do that.
USAGE: CrosscheckReadGroupFingerprints [arguments]
DEPRECATED: USE CrosscheckFingerprints.
Version:null
Required Arguments:
--HAPLOTYPE_MAP,-H <File> The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for
fingerprinting. See
https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for
details. Required.
--INPUT,-I <String> One or more input files (or lists of files) with which to compare fingerprints. This
argument must be specified at least once. Required.
Optional Arguments:
--ALLOW_DUPLICATE_READS <Boolean>
Allow the use of duplicate reads in performing the comparison. Can be useful when
duplicate marking has been overly aggressive and coverage is low. Default value: false.
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.
--CALCULATE_TUMOR_AWARE_RESULTS <Boolean>
Specifies whether the Tumor-aware result should be calculated. These are time consuming
and can roughly double the runtime of the tool. When crosschecking many groups not
calculating the tumor-aware results can result in a significant speedup. Default value:
true. Possible values: {true, false}
--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}
--CROSSCHECK_BY <DataType> Specifies which data-type should be used as the basic comparison unit. Fingerprints from
readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared.
Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP.
Possible values: {FILE, SAMPLE, LIBRARY, READGROUP}
--CROSSCHECK_LIBRARIES <Boolean>
Instead of producing the normal comparison of read-groups, roll fingerprints up to the
library level and print out a library x library matrix with LOD scores. Default value:
false. Possible values: {true, false}
--CROSSCHECK_MODE <CrosscheckMode>
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
Default value: CHECK_SAME_SAMPLE. CHECK_SAME_SAMPLE (In this mode, each sample in INPUT
will only be checked against a single corresponding sample in SECOND_INPUT. If a
corresponding sample cannot be found, the program will proceed, but report the missing
samples and return the value specified in EXIT_CODE_WHEN_MISMATCH. The corresponding
samples are those that equal each other, after possible renaming via INPUT_SAMPLE_MAP and
SECOND_INPUT_SAMPLE_MAP. In this mode CROSSCHECK_BY must be SAMPLE.)
CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the
samples in SECOND_INPUT.)
--CROSSCHECK_SAMPLES <Boolean>Instead of producing the normal comparison of read-groups, roll fingerprints up to the
sample level and print out a sample x sample matrix with LOD scores. Default value:
false. Possible values: {true, false}
--EXIT_CODE_WHEN_MISMATCH <Integer>
When one or more mismatches between groups is detected, exit with this value instead of 0.
Default value: 1.
--EXIT_CODE_WHEN_NO_VALID_CHECKS <Integer>
When all LOD scores are zero, exit with this value. Default value: 1.
--EXPECT_ALL_GROUPS_TO_MATCH <Boolean>
Expect all groups' fingerprints to match, irrespective of their sample names. By default
(with this value set to false), groups (readgroups, libraries, files, or samples) with
different sample names are expected to mismatch, and those with the same sample name are
expected to match. Default value: false. Possible values: {true, false} Cannot be used
in conjunction with argument(s) EXPECT_ALL_READ_GROUPS_TO_MATCH
--EXPECT_ALL_READ_GROUPS_TO_MATCH <Boolean>
Expect all read groups' fingerprints to match, irrespective of their sample names. By
default (with this value set to false), read groups with different sample names are
expected to mismatch, and those with the same sample name are expected to match. Default
value: false. Possible values: {true, false} Cannot be used in conjunction with
argument(s) EXPECT_ALL_GROUPS_TO_MATCH
--GENOTYPING_ERROR_RATE <Double>
This argument is DEPRECATED (No longer used in fingerprint checking. Will be removed in a
future release.). Assumed genotyping error rate that provides a floor on the probability
that a genotype comes from the expected sample. Must be greater than zero. Default
value: 0.01.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--INPUT_INDEX_MAP <File> A tsv with two columns and no header which maps the input files to corresponding indices;
to be used when index files are not located next to input files. First column must match
the list of inputs. Default value: null.
--INPUT_SAMPLE_FILE_MAP <File>A tsv with two columns representing the sample as it should be used for comparisons to
SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in
the second column). Need only to include the samples that change. Values in column 1
should be unique even in union with the remaining unmapped samples. Values in column 2
should be unique in the file. Will error if more than one sample is found in a file
(multi-sample VCF) pointed to in column 2. Should only be used in the presence of
SECOND_INPUT. Default value: null. Cannot be used in conjunction with argument(s)
INPUT_SAMPLE_MAP
--INPUT_SAMPLE_MAP <File> A tsv with two columns representing the sample as it appears in the INPUT data (in column
1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second
column). Need only include the samples that change. Values in column 1 should be unique.
Values in column 2 should be unique even in union with the remaining unmapped samples.
Should only be used with SECOND_INPUT. Default value: null. Cannot be used in
conjunction with argument(s) INPUT_SAMPLE_FILE_MAP
--LOD_THRESHOLD,-LOD <Double> If any two groups (with the same sample name) match with a LOD score lower than the
threshold the tool will exit with a non-zero code to indicate error. Program will also
exit with an error if it finds two groups with different sample name that match with a LOD
score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different
individuals, negative LOD score -N, mean 10^N time more likely that the groups are from
different individuals, and +N means 10^N times more likely that the groups are from the
same individual. Default value: 0.0.
--LOSS_OF_HET_RATE <Double> The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via
loss of heterozygosity) in the tumor (model assumes independent events, so this needs to
be larger than reality). Default value: 0.5.
--MATRIX_OUTPUT,-MO <File> Optional output file to write matrix of LOD scores to. This is less informative than the
metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of
Heterozygosity). It is however sometimes easier to use visually. Default value: null.
Cannot be used in conjunction with argument(s) SECOND_INPUT (SI)
--MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK <Double>
Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood
difference between the different values for the three possible genotypes). Default value:
3.0.
--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.
--NUM_THREADS <Integer> The number of threads to use to process files and generate fingerprints. Default value:
1.
--OUTPUT,-O <File> Optional output file to write metrics to. Default is to write to stdout. Default value:
null.
--OUTPUT_ERRORS_ONLY <Boolean>If true, then only groups that do not relate to each other as expected will have their
LODs reported. Default value: false. Possible values: {true, false}
--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.
--REQUIRE_INDEX_FILES <Boolean>
A boolean value to determine whether input files should only be parsed if index files are
available. Without turning this option on, the tool will need to read through the entirety
of input files without index files either provided via the INPUT_INDEX_MAP or locally
accessible relative to the input, which significantly increases runtime. If set to true
and no index is found for a file, an exception will be thrown. This applies for both the
INPUT and SECOND_INPUT files. Default value: false. Possible values: {true, false}
--SAMPLE_INDIVIDUAL_MAP <File>A tsv with two columns representing the individual with which each sample is associated.
The first column is the sample id, and the second column is the associated individual id.
Values in the first column must be unique. If INPUT_SAMPLE_MAP or SECOND_INPUT_SAMPLE_MAP
is also specified, then the values in the first column of this file should be the sample
aliases specified in the second columns of INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP,
respectively. When this input is specified, expectations for matches will be based on the
equality or inequality of the individual ids associated with two samples, as opposed to
the sample ids themselves. Samples which are not listed in this file will have their
sample id used as their individual id, for the purposes of match expectations. This means
that one sample id could be used as the individual id for another sample, but not included
in the map itself, and these two samples would be considered to have come from the same
individual. Note that use of this parameter only affects labelling of matches and
mismatches as EXPECTED or UNEXPECTED. It has no affect on how data is grouped for
crosschecking. Default value: null.
--SECOND_INPUT,-SI <String> A second set of input files (or lists of files) with which to compare fingerprints. If
this option is provided the tool compares each sample in INPUT with the sample from
SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE
regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in
INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool
will proceed to check the matching samples, but report the missing samples and return a
non-zero error-code. This argument may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s) MATRIX_OUTPUT (MO)
--SECOND_INPUT_INDEX_MAP <File>
A tsv with two columns and no header which maps the second input files to corresponding
indices; to be used when index files are not located next to second input files. First
column must match the list of second inputs. Default value: null.
--SECOND_INPUT_SAMPLE_MAP <File>
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in
column 1) and the sample as it should be used for comparisons to INPUT (in the second
column). Note that in case of unrolling files (file-of-filenames) one would need to
reference the final file, i.e. the file that contains the genomic data. Need only include
the samples that change. Values in column 1 should be unique. Values in column 2 should be
unique even in union with the remaining unmapped samples. Should only be used with
SECOND_INPUT. 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}
When calling CrosscheckReadGroupFingerprints, please refrain from supplying a MATRIX_OUTPUT argument.
(Found value matrix.file
Use CrosscheckFingerprints if you would like to do that.
USAGE: CrosscheckReadGroupFingerprints [arguments]
DEPRECATED: USE CrosscheckFingerprints.
Version:null
Required Arguments:
--HAPLOTYPE_MAP,-H <File> The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for
fingerprinting. See
https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for
details. Required.
--INPUT,-I <String> One or more input files (or lists of files) with which to compare fingerprints. This
argument must be specified at least once. Required.
Optional Arguments:
--ALLOW_DUPLICATE_READS <Boolean>
Allow the use of duplicate reads in performing the comparison. Can be useful when
duplicate marking has been overly aggressive and coverage is low. Default value: false.
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.
--CALCULATE_TUMOR_AWARE_RESULTS <Boolean>
Specifies whether the Tumor-aware result should be calculated. These are time consuming
and can roughly double the runtime of the tool. When crosschecking many groups not
calculating the tumor-aware results can result in a significant speedup. Default value:
true. Possible values: {true, false}
--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}
--CROSSCHECK_BY <DataType> Specifies which data-type should be used as the basic comparison unit. Fingerprints from
readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared.
Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP.
Possible values: {FILE, SAMPLE, LIBRARY, READGROUP}
--CROSSCHECK_LIBRARIES <Boolean>
Instead of producing the normal comparison of read-groups, roll fingerprints up to the
library level and print out a library x library matrix with LOD scores. Default value:
false. Possible values: {true, false}
--CROSSCHECK_MODE <CrosscheckMode>
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
Default value: CHECK_SAME_SAMPLE. CHECK_SAME_SAMPLE (In this mode, each sample in INPUT
will only be checked against a single corresponding sample in SECOND_INPUT. If a
corresponding sample cannot be found, the program will proceed, but report the missing
samples and return the value specified in EXIT_CODE_WHEN_MISMATCH. The corresponding
samples are those that equal each other, after possible renaming via INPUT_SAMPLE_MAP and
SECOND_INPUT_SAMPLE_MAP. In this mode CROSSCHECK_BY must be SAMPLE.)
CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the
samples in SECOND_INPUT.)
--CROSSCHECK_SAMPLES <Boolean>Instead of producing the normal comparison of read-groups, roll fingerprints up to the
sample level and print out a sample x sample matrix with LOD scores. Default value:
false. Possible values: {true, false}
--EXIT_CODE_WHEN_MISMATCH <Integer>
When one or more mismatches between groups is detected, exit with this value instead of 0.
Default value: 1.
--EXIT_CODE_WHEN_NO_VALID_CHECKS <Integer>
When all LOD scores are zero, exit with this value. Default value: 1.
--EXPECT_ALL_GROUPS_TO_MATCH <Boolean>
Expect all groups' fingerprints to match, irrespective of their sample names. By default
(with this value set to false), groups (readgroups, libraries, files, or samples) with
different sample names are expected to mismatch, and those with the same sample name are
expected to match. Default value: false. Possible values: {true, false} Cannot be used
in conjunction with argument(s) EXPECT_ALL_READ_GROUPS_TO_MATCH
--EXPECT_ALL_READ_GROUPS_TO_MATCH <Boolean>
Expect all read groups' fingerprints to match, irrespective of their sample names. By
default (with this value set to false), read groups with different sample names are
expected to mismatch, and those with the same sample name are expected to match. Default
value: false. Possible values: {true, false} Cannot be used in conjunction with
argument(s) EXPECT_ALL_GROUPS_TO_MATCH
--GENOTYPING_ERROR_RATE <Double>
This argument is DEPRECATED (No longer used in fingerprint checking. Will be removed in a
future release.). Assumed genotyping error rate that provides a floor on the probability
that a genotype comes from the expected sample. Must be greater than zero. Default
value: 0.01.
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--INPUT_INDEX_MAP <File> A tsv with two columns and no header which maps the input files to corresponding indices;
to be used when index files are not located next to input files. First column must match
the list of inputs. Default value: null.
--INPUT_SAMPLE_FILE_MAP <File>A tsv with two columns representing the sample as it should be used for comparisons to
SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in
the second column). Need only to include the samples that change. Values in column 1
should be unique even in union with the remaining unmapped samples. Values in column 2
should be unique in the file. Will error if more than one sample is found in a file
(multi-sample VCF) pointed to in column 2. Should only be used in the presence of
SECOND_INPUT. Default value: null. Cannot be used in conjunction with argument(s)
INPUT_SAMPLE_MAP
--INPUT_SAMPLE_MAP <File> A tsv with two columns representing the sample as it appears in the INPUT data (in column
1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second
column). Need only include the samples that change. Values in column 1 should be unique.
Values in column 2 should be unique even in union with the remaining unmapped samples.
Should only be used with SECOND_INPUT. Default value: null. Cannot be used in
conjunction with argument(s) INPUT_SAMPLE_FILE_MAP
--LOD_THRESHOLD,-LOD <Double> If any two groups (with the same sample name) match with a LOD score lower than the
threshold the tool will exit with a non-zero code to indicate error. Program will also
exit with an error if it finds two groups with different sample name that match with a LOD
score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different
individuals, negative LOD score -N, mean 10^N time more likely that the groups are from
different individuals, and +N means 10^N times more likely that the groups are from the
same individual. Default value: 0.0.
--LOSS_OF_HET_RATE <Double> The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via
loss of heterozygosity) in the tumor (model assumes independent events, so this needs to
be larger than reality). Default value: 0.5.
--MATRIX_OUTPUT,-MO <File> Optional output file to write matrix of LOD scores to. This is less informative than the
metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of
Heterozygosity). It is however sometimes easier to use visually. Default value: null.
Cannot be used in conjunction with argument(s) SECOND_INPUT (SI)
--MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK <Double>
Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood
difference between the different values for the three possible genotypes). Default value:
3.0.
--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.
--NUM_THREADS <Integer> The number of threads to use to process files and generate fingerprints. Default value:
1.
--OUTPUT,-O <File> Optional output file to write metrics to. Default is to write to stdout. Default value:
null.
--OUTPUT_ERRORS_ONLY <Boolean>If true, then only groups that do not relate to each other as expected will have their
LODs reported. Default value: false. Possible values: {true, false}
--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.
--REQUIRE_INDEX_FILES <Boolean>
A boolean value to determine whether input files should only be parsed if index files are
available. Without turning this option on, the tool will need to read through the entirety
of input files without index files either provided via the INPUT_INDEX_MAP or locally
accessible relative to the input, which significantly increases runtime. If set to true
and no index is found for a file, an exception will be thrown. This applies for both the
INPUT and SECOND_INPUT files. Default value: false. Possible values: {true, false}
--SAMPLE_INDIVIDUAL_MAP <File>A tsv with two columns representing the individual with which each sample is associated.
The first column is the sample id, and the second column is the associated individual id.
Values in the first column must be unique. If INPUT_SAMPLE_MAP or SECOND_INPUT_SAMPLE_MAP
is also specified, then the values in the first column of this file should be the sample
aliases specified in the second columns of INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP,
respectively. When this input is specified, expectations for matches will be based on the
equality or inequality of the individual ids associated with two samples, as opposed to
the sample ids themselves. Samples which are not listed in this file will have their
sample id used as their individual id, for the purposes of match expectations. This means
that one sample id could be used as the individual id for another sample, but not included
in the map itself, and these two samples would be considered to have come from the same
individual. Note that use of this parameter only affects labelling of matches and
mismatches as EXPECTED or UNEXPECTED. It has no affect on how data is grouped for
crosschecking. Default value: null.
--SECOND_INPUT,-SI <String> A second set of input files (or lists of files) with which to compare fingerprints. If
this option is provided the tool compares each sample in INPUT with the sample from
SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE
regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in
INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool
will proceed to check the matching samples, but report the missing samples and return a
non-zero error-code. This argument may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s) MATRIX_OUTPUT (MO)
--SECOND_INPUT_INDEX_MAP <File>
A tsv with two columns and no header which maps the second input files to corresponding
indices; to be used when index files are not located next to second input files. First
column must match the list of second inputs. Default value: null.
--SECOND_INPUT_SAMPLE_MAP <File>
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in
column 1) and the sample as it should be used for comparisons to INPUT (in the second
column). Note that in case of unrolling files (file-of-filenames) one would need to
reference the final file, i.e. the file that contains the genomic data. Need only include
the samples that change. Values in column 1 should be unique. Values in column 2 should be
unique even in union with the remaining unmapped samples. Should only be used with
SECOND_INPUT. 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}
When calling CrosscheckReadGroupFingerprints, please refrain from supplying a SECOND_INPUT argument.
(Found value [/dev/stdin]
Use CrosscheckFingerprints if you would like to do that.
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_LIBRARIES true --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --OUTPUT /tmp/Fingerprinting8323268972036850899NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_SAMPLES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:30 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 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Cross-checking all LIBRARY against each other
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All LIBRARYs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_LIBRARIES true --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam --OUTPUT /tmp/Fingerprinting12389693353749607146NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_SAMPLES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:30 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 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Cross-checking all LIBRARY against each other
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All LIBRARYs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_LIBRARIES true --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --OUTPUT /tmp/Fingerprinting4788572456000109311NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_SAMPLES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:30 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 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Cross-checking all LIBRARY against each other
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All LIBRARYs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_LIBRARIES true --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --OUTPUT /tmp/Fingerprinting12508951409606496692NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_SAMPLES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:30 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 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Cross-checking all LIBRARY against each other
INFO 2025-04-24 13:00:30 CrosscheckFingerprints All LIBRARYs are related as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_LIBRARIES true --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting3735573824625419925NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_SAMPLES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:30 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 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
WARNING 2025-04-24 13:00:30 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:30 CrosscheckFingerprints 2 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_LIBRARIES true --INPUT /tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting11714023573795025672NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_SAMPLES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:30 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 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam)
WARNING 2025-04-24 13:00:30 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:30 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:30 CrosscheckFingerprints 2 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:30 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:30 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_LIBRARIES true --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting13755220771599740597NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_SAMPLES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:30 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 13:00:30 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:30 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
WARNING 2025-04-24 13:00:30 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:30 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:31 CrosscheckFingerprints 2 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_LIBRARIES true --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam --OUTPUT /tmp/Fingerprinting5923141107019060834NA1291.LB.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_SAMPLES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
WARNING 2025-04-24 13:00:31 FingerprintChecker Operating without an index! We could be here for a while. (file:///mounts/lovelace/software/picard/picard/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all LIBRARY against each other
WARNING 2025-04-24 13:00:31 CrosscheckFingerprints 2 LIBRARYs did not relate as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --OUTPUT /tmp/Fingerprinting17164547847321566715NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:31 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam --OUTPUT /tmp/Fingerprinting12003716001953780539NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:31 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --OUTPUT /tmp/Fingerprinting16350086548594825842NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:31 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --OUTPUT /tmp/Fingerprinting9766255824686567044NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:31 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --OUTPUT /tmp/Fingerprinting17830603050758738082NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:31 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --OUTPUT /tmp/Fingerprinting14807145434933284122NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH false --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:31 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --OUTPUT /tmp/Fingerprinting11428507331454363827NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:31 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam --OUTPUT /tmp/Fingerprinting4501061072275424202NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:31 CrosscheckFingerprints 84 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:31 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:31 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --OUTPUT /tmp/Fingerprinting5496092492972677420NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:31 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 13:00:31 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:31 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:31 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:32 CrosscheckFingerprints 138 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --OUTPUT /tmp/Fingerprinting9983571359453730758NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 51 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all READGROUP against each other
INFO 2025-04-24 13:00:32 CrosscheckFingerprints All READGROUPs are related as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --OUTPUT /tmp/Fingerprinting7490059642669789013NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:32 CrosscheckFingerprints 188 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --OUTPUT /tmp/Fingerprinting14865556160880475273NA1291.RG.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -2.0 --EXPECT_ALL_GROUPS_TO_MATCH true --CROSSCHECK_SAMPLES false --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all READGROUP against each other
WARNING 2025-04-24 13:00:32 CrosscheckFingerprints 138 READGROUPs did not relate as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_SAMPLES true --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --OUTPUT /tmp/Fingerprinting4127184749132914252NA1291.SM.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:32 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_SAMPLES true --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam --OUTPUT /tmp/Fingerprinting802000243893990296NA1291.SM.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:32 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_SAMPLES true --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --OUTPUT /tmp/Fingerprinting18001860049940261043NA1291.SM.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:32 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_SAMPLES true --INPUT /tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam14835473084235246104.bam --OUTPUT /tmp/Fingerprinting2167965824979794756NA1291.SM.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r2.sam14474887846007297620.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam14835473084235246104.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:32 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_SAMPLES true --INPUT /tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam14835473084235246104.bam --OUTPUT /tmp/Fingerprinting16786509491285636601NA1291.SM.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r2.sam15503558537035248106.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam14835473084235246104.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 53 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all SAMPLE against each other
WARNING 2025-04-24 13:00:32 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_SAMPLES true --INPUT /tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam14835473084235246104.bam --OUTPUT /tmp/Fingerprinting512318100097825857NA1291.SM.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12892.over.fingerprints.r1.sam1519226673767840284.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam14835473084235246104.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 52 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all SAMPLE against each other
INFO 2025-04-24 13:00:32 CrosscheckFingerprints All SAMPLEs are related as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:32 EDT 2025] CrosscheckReadGroupFingerprints --CROSSCHECK_SAMPLES true --INPUT /tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam --INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam14835473084235246104.bam --OUTPUT /tmp/Fingerprinting10799591044265852069NA1291.SM.crosscheck_metrics --HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt --LOD_THRESHOLD -1.0 --CROSSCHECK_LIBRARIES false --EXPECT_ALL_READ_GROUPS_TO_MATCH false --REQUIRE_INDEX_FILES false --CROSSCHECK_MODE CHECK_SAME_SAMPLE --CROSSCHECK_BY READGROUP --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXPECT_ALL_GROUPS_TO_MATCH false --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --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
[Thu Apr 24 13:00:32 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 13:00:32 CrosscheckFingerprints Fingerprinting 2 INPUT files.
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891.over.fingerprints.r1.sam11542200148047626378.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Reading an indexed file (file:///tmp/NA12891_named_NA12892.over.fingerprints.r1.sam14835473084235246104.bam)
INFO 2025-04-24 13:00:32 FingerprintChecker Processed files. 54 fingerprints found in map.
INFO 2025-04-24 13:00:32 CrosscheckFingerprints Cross-checking all SAMPLE against each other
WARNING 2025-04-24 13:00:32 CrosscheckFingerprints 2 SAMPLEs did not relate as expected.
[Thu Apr 24 13:00:32 EDT 2025] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp