FRACTION must be a value between 0 and 1, found: -1.0
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
FRACTION must be a value between 0 and 1, found: -1.0E-5
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
FRACTION must be a value between 0 and 1, found: -5.0
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
FRACTION must be a value between 0 and 1, found: 1.00001
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
FRACTION must be a value between 0 and 1, found: 5.0
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
FRACTION must be a value between 0 and 1, found: 50.0
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
FRACTION must be a value between 0 and 1, found: 1.7976931348623157E308
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
FRACTION must be a value between 0 and 1, found: Infinity
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
FRACTION must be a value between 0 and 1, found: -Infinity
USAGE: PositionBasedDownsampleSam [options]
Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam
Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither
end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence
the read came from. The downsampling is based on this position. Results with the exact same input will produce the
same results.
Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your
BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly.
This has been designed with Illumina MiSeq/HiSeq in mind.
Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile.
Note 3: Downsampling twice with this program is not supported.
Note 4: You should call MarkDuplicates after downsampling.
Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample
fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling
percentage will not be accurately determined by the input argument FRACTION.
Version: null
Options:
--help
-h Displays options specific to this tool.
--stdhelp
-H Displays options specific to this tool AND options common to all Picard command line
tools.
--version Displays program version.
INPUT=File
I=File The input SAM or BAM file to downsample. Required.
OUTPUT=File
O=File The output, downsampled, SAM or BAM file to write. Required.
FRACTION=Double
F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required.
STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null.
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean
Allow Downsampling again despite this being a bad idea with possibly unexpected results.
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
REMOVE_DUPLICATE_INFORMATION=Boolean
Determines whether the duplicate tag should be reset since the downsampling requires
re-marking duplicates. Default value: true. This option can be set to 'null' to clear
the default value. Possible values: {true, false}
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam3662035949969180207.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:59 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:59 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:11:59 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Second pass done.
WARNING 2016-08-16 04:12:00 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.069400.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Finished! Kept 1388 out of 20000 reads (P=0.0694000).
[Tue Aug 16 04:12:00 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:12:00 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam3662035949969180207.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6899806406877126154.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=true REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:00 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
WARNING 2016-08-16 04:12:00 PositionBasedDownsampleSam Found previous Program Record that indicates that this BAM has been downsampled already with this program. Operation not supported! Previous PG: SAMProgramRecord{PN=PositionBasedDownsampleSam, CL=picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam3662035949969180207.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json}
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Second pass done.
WARNING 2016-08-16 04:12:00 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.998559.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Finished! Kept 1386 out of 1388 reads (P=0.998559).
[Tue Aug 16 04:12:00 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:12:00 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam1002365835490896720.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:00 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Second pass done.
WARNING 2016-08-16 04:12:00 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.069400.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Finished! Kept 1388 out of 20000 reads (P=0.0694000).
[Tue Aug 16 04:12:00 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:12:00 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam1002365835490896720.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6706934487771485176.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:00 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
ERROR 2016-08-16 04:12:00 PositionBasedDownsampleSam Found previous Program Record that indicates that this BAM has been downsampled already with this program. Operation not supported! Previous PG: SAMProgramRecord{PN=PositionBasedDownsampleSam, CL=picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam1002365835490896720.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json}
[Tue Aug 16 04:12:00 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:12:00 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam1301748042476697512.bam FRACTION=0.3 CREATE_INDEX=true ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:00 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:00 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Second pass done.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Finished! Kept 5544 out of 20000 reads (P=0.277200).
[Tue Aug 16 04:12:01 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:12:01 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam2340777749136583910.bam FRACTION=0.4 CREATE_INDEX=true ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:01 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Second pass done.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Finished! Kept 7652 out of 20000 reads (P=0.382600).
[Tue Aug 16 04:12:01 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:12:01 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam4580547754486873211.bam FRACTION=0.5 CREATE_INDEX=true ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:01 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:01 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Second pass done.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Finished! Kept 9688 out of 20000 reads (P=0.484400).
[Tue Aug 16 04:12:02 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:12:02 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam3159266239324397019.bam FRACTION=0.6 CREATE_INDEX=true ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Second pass done.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Finished! Kept 12348 out of 20000 reads (P=0.617400).
[Tue Aug 16 04:12:02 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:12:02 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6940239644590731208.bam FRACTION=0.7 CREATE_INDEX=true ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Second pass done.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Finished! Kept 14456 out of 20000 reads (P=0.722800).
[Tue Aug 16 04:12:02 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:12:02 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6304769691997859152.bam FRACTION=0.7999999999999999 CREATE_INDEX=true ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Second pass done.
INFO 2016-08-16 04:12:02 PositionBasedDownsampleSam Finished! Kept 16642 out of 20000 reads (P=0.832100).
[Tue Aug 16 04:12:02 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:12:03 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam1957396784279892627.bam FRACTION=0.8999999999999999 CREATE_INDEX=true ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Second pass done.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Finished! Kept 18612 out of 20000 reads (P=0.930600).
[Tue Aug 16 04:12:03 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:12:03 CDT 2016] picard.sam.PositionBasedDownsampleSam INPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam6780390235111282523.bam OUTPUT=/tmp/pds_test4352352573427974784PositionalDownsampling/PositionalDownsampleSam5928137520971500062.bam FRACTION=0.9999999999999999 CREATE_INDEX=true ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false REMOVE_DUPLICATE_INFORMATION=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam First pass done.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Starting second pass. Outputting reads.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Second pass done.
INFO 2016-08-16 04:12:03 PositionBasedDownsampleSam Finished! Kept 20000 out of 20000 reads (P=1.00000).
[Tue Aug 16 04:12:03 CDT 2016] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376