Galaxy tool MarkDuplicates run at 12/05/2011 14:34:29
The following output files were created (click the filename to view/download a copy):
Picard on line resources
Picard output (transposed to make it easier to see)
| ## net.sf.picard.metrics.StringHeader | 
| # net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | 
| ## net.sf.picard.metrics.StringHeader | 
| # Started on: Thu May 12 14:34:28 EDT 2011 | 
| ## METRICS CLASS	net.sf.picard.sam.DuplicationMetrics | 
| LIBRARY |  | 
| UNPAIRED_READS_EXAMINED | 1 | 
| READ_PAIRS_EXAMINED | 3 | 
| UNMAPPED_READS | 1 | 
| UNPAIRED_READ_DUPLICATES | 1 | 
| READ_PAIR_DUPLICATES | 1 | 
| READ_PAIR_OPTICAL_DUPLICATES | 0 | 
| PERCENT_DUPLICATION | 0.428571 | 
| ESTIMATED_LIBRARY_SIZE | 3 | 
| ## HISTOGRAM	java.lang.Double | 
| BIN	VALUE | 
| 1.0	0.948181 | 
| 2.0	1.296997 | 
| 3.0	1.425319 | 
| 4.0	1.472527 | 
| 5.0	1.489893 | 
| 6.0	1.496282 | 
| 7.0	1.498632 | 
| 8.0	1.499497 | 
| 9.0	1.499815 | 
| 10.0	1.499932 | 
| 11.0	1.499975 | 
| 12.0	1.499991 | 
| 13.0	1.499997 | 
| 14.0	1.499999 | 
| 15.0	1.5 | 
| 16.0	1.5 | 
| 17.0	1.5 | 
| 18.0	1.5 | 
| 19.0	1.5 | 
| 20.0	1.5 | 
| 21.0	1.5 | 
| 22.0	1.5 | 
| 23.0	1.5 | 
| 24.0	1.5 | 
| 25.0	1.5 | 
| 26.0	1.5 | 
| 27.0	1.5 | 
| 28.0	1.5 | 
| 29.0	1.5 | 
| 30.0	1.5 | 
| 31.0	1.5 | 
| 32.0	1.5 | 
| 33.0	1.5 | 
| 34.0	1.5 | 
| 35.0	1.5 | 
| 36.0	1.5 | 
| 37.0	1.5 | 
| 38.0	1.5 | 
| 39.0	1.5 | 
| 40.0	1.5 | 
| 41.0	1.5 | 
| 42.0	1.5 | 
| 43.0	1.5 | 
| 44.0	1.5 | 
| 45.0	1.5 | 
| 46.0	1.5 | 
| 47.0	1.5 | 
| 48.0	1.5 | 
| 49.0	1.5 | 
| 50.0	1.5 | 
| 51.0	1.5 | 
| 52.0	1.5 | 
| 53.0	1.5 | 
| 54.0	1.5 | 
| 55.0	1.5 | 
| 56.0	1.5 | 
| 57.0	1.5 | 
| 58.0	1.5 | 
| 59.0	1.5 | 
| 60.0	1.5 | 
| 61.0	1.5 | 
| 62.0	1.5 | 
| 63.0	1.5 | 
| 64.0	1.5 | 
| 65.0	1.5 | 
| 66.0	1.5 | 
| 67.0	1.5 | 
| 68.0	1.5 | 
| 69.0	1.5 | 
| 70.0	1.5 | 
| 71.0	1.5 | 
| 72.0	1.5 | 
| 73.0	1.5 | 
| 74.0	1.5 | 
| 75.0	1.5 | 
| 76.0	1.5 | 
| 77.0	1.5 | 
| 78.0	1.5 | 
| 79.0	1.5 | 
| 80.0	1.5 | 
| 81.0	1.5 | 
| 82.0	1.5 | 
| 83.0	1.5 | 
| 84.0	1.5 | 
| 85.0	1.5 | 
| 86.0	1.5 | 
| 87.0	1.5 | 
| 88.0	1.5 | 
| 89.0	1.5 | 
| 90.0	1.5 | 
| 91.0	1.5 | 
| 92.0	1.5 | 
| 93.0	1.5 | 
| 94.0	1.5 | 
| 95.0	1.5 | 
| 96.0	1.5 | 
| 97.0	1.5 | 
| 98.0	1.5 | 
| 99.0	1.5 | 
Picard Tool Run Log
Thu, 12 May 2011 14:34:29 INFO
 ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/MarkDuplicates.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 0 and stderr: 
[Thu May 12 14:34:28 EDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
INFO	2011-05-12 14:34:28	MarkDuplicates	Start of doWork freeMemory: 8644632; totalMemory: 9109504; maxMemory: 1908932608
INFO	2011-05-12 14:34:28	MarkDuplicates	Reading input file and constructing read end information.
INFO	2011-05-12 14:34:28	MarkDuplicates	Will retain up to 7575129 data points before spilling to disk.
INFO	2011-05-12 14:34:28	MarkDuplicates	Read 7 records. 0 pairs never matched.
INFO	2011-05-12 14:34:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 8316168; totalMemory: 130351104; maxMemory: 1908932608
INFO	2011-05-12 14:34:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
INFO	2011-05-12 14:34:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2011-05-12 14:34:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2011-05-12 14:34:29	MarkDuplicates	Sorting list of duplicate records.
INFO	2011-05-12 14:34:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 129615120; totalMemory: 607649792; maxMemory: 1908932608
INFO	2011-05-12 14:34:29	MarkDuplicates	Marking 3 records as duplicates.
INFO	2011-05-12 14:34:29	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2011-05-12 14:34:29	MarkDuplicates	Before output close freeMemory: 128997520; totalMemory: 607649792; maxMemory: 1908932608
INFO	2011-05-12 14:34:29	MarkDuplicates	After output close freeMemory: 128997280; totalMemory: 607649792; maxMemory: 1908932608
[Thu May 12 14:34:29 EDT 2011] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=607649792
The freely available 
Picard software 
generated all outputs reported here running as a 
Galaxy tool