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Created May 2, 2016 09:23
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gistfile1.txt
[Fri Apr 29 21:29:39 CEST 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar INPUT=[/home/kong/Haiying/Projects/Melanoma/Primary/ILSE530X_B20/Lock/Picard/T15520.sorted.sam] OUTPUT=/home/kong/Haiying/Projects/Melanoma/Primary/ILS
E530X_B20/Lock/Picard/T15520.dedupped.bam METRICS_FILE=/home/kong/Haiying/Projects/Melanoma/Primary/ILSE530X_B20/Lock/Picard/T15520.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGA
R=true BLOCK_SIZE=100000 DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX=<optimized capture of last three ':' separated fields as nu
meric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Fri Apr 29 21:29:39 CEST 2016] Executing as kong@hpc19 on Linux 3.2.53-1.el5.elrepo amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_60-b27; Picard version: 2.2.4(920e3247c340720b009f2398c1b93cce132c9bed_1461793281) IntelDeflater
WARNING 2016-04-29 21:29:42 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: SN7001427:194:C87EVANXX:2:1204:9575:49281 2/2 125b aligned read.
INFO 2016-04-29 21:29:59 MarkDuplicatesWithMateCigar Read 1,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 17s. Last read position: 1:9,799,705
INFO 2016-04-29 21:29:59 MarkDuplicatesWithMateCigar freeMemory: 1512642936; totalMemory: 1545601024; maxMemory: 3817865216; output buffer size: 585; duplicate queue size: 1
INFO 2016-04-29 21:30:17 MarkDuplicatesWithMateCigar Read 2,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 17s. Last read position: 1:17,724,121
INFO 2016-04-29 21:30:17 MarkDuplicatesWithMateCigar freeMemory: 1375019136; totalMemory: 1405091840; maxMemory: 3817865216; output buffer size: 123; duplicate queue size: 1
INFO 2016-04-29 21:30:33 MarkDuplicatesWithMateCigar Read 3,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 16s. Last read position: 1:26,498,035
INFO 2016-04-29 21:30:33 MarkDuplicatesWithMateCigar freeMemory: 1213042368; totalMemory: 1243611136; maxMemory: 3817865216; output buffer size: 3732; duplicate queue size: 1
INFO 2016-04-29 21:30:51 MarkDuplicatesWithMateCigar Read 4,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 17s. Last read position: 1:35,847,318
INFO 2016-04-29 21:30:51 MarkDuplicatesWithMateCigar freeMemory: 1031089440; totalMemory: 1058537472; maxMemory: 3817865216; output buffer size: 4128; duplicate queue size: 1
INFO 2016-04-29 21:31:07 MarkDuplicatesWithMateCigar Read 5,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 16s. Last read position: 1:44,422,394
INFO 2016-04-29 21:31:07 MarkDuplicatesWithMateCigar freeMemory: 850557200; totalMemory: 871890944; maxMemory: 3817865216; output buffer size: 481; duplicate queue size: 1
INFO 2016-04-29 21:31:25 MarkDuplicatesWithMateCigar Read 6,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 17s. Last read position: 1:55,158,095
INFO 2016-04-29 21:31:25 MarkDuplicatesWithMateCigar freeMemory: 686923912; totalMemory: 708313088; maxMemory: 3817865216; output buffer size: 3528; duplicate queue size: 1
INFO 2016-04-29 21:31:41 MarkDuplicatesWithMateCigar Read 7,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 16s. Last read position: 1:75,455,569
INFO 2016-04-29 21:31:42 MarkDuplicatesWithMateCigar freeMemory: 516005584; totalMemory: 545259520; maxMemory: 3817865216; output buffer size: 14121; duplicate queue size: 1
record #1: SN7001427:194:C87EVANXX:2:2303:15414:57980 121 1 77643940 40 42S83M = 77643940 0 CGATCCTTCTAGAAGTATGAAGGCCTCCTGGCAATCTTCTCTTTAACCCACATCACAGGTTAAAGAGAACTTTGCCAGGAGGCCTTCATACTTCTAGAAGG
GCATCATTTGTTAGGTCCTTTTTC GFGGGGGGGGGGGGGGGGGGGGGBGGFEGGGGGGGGGEGEGGGGDDGFGGCGCDGGGD>EGGGEGEGGGGGFGGCFGGGEGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGCCCCC SA:Z:1,77643955,+,77S44M4S,11,1; XA:Z:1,-55428102,42S83M,4; MD:Z:
28A54 NM:i:1 AS:i:78 XS:i:63
record #2: SN7001427:194:C87EVANXX:2:2303:15414:57980 2121 1 77643955 11 77H44M4H = 77643955 0 GGTTAAAGAGAAGATTGCCAGGAGGCCTTCATACTTCTAGAAGG FGDDGGGGEGEGGGGGGGGGEFGGBGGGGGGGGGGGGGGGGGGGSA:Z:1,77643940,-,42S83M,40,1; XA:Z:1,+55428115,75S46M4S,2;2,+31055770,78S43M4S,2; MD:Z:12C31 NM:i:1 AS:i:39 XS:i:36
[Fri Apr 29 21:31:43 CEST 2016] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 2.08 minutes.
Runtime.totalMemory()=529006592
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" picard.PicardException: Found a samRecordWithOrdinal with sufficiently large clipping that we may have
missed including it in an early duplicate marking iteration. Please increase the minimum distance to at least 143bp
to ensure it is considered (was 120).
Record was: SN7001427:194:C87EVANXX:2:2303:15414:57980 121 1 77643940 40 42S83M = 77643940 0 CGATCCTTCTAGAAGTATGAAGGCCTCCTGGCAATCTTCTCTTTAACCCACATCACAGGTTAAAGAGAACTTTGCCAGGAGGCCTTCATACTTCTAGAAGG
GCATCATTTGTTAGGTCCTTTTTC GFGGGGGGGGGGGGGGGGGGGGGBGGFEGGGGGGGGGEGEGGGGDDGFGGCGCDGGGD>EGGGEGEGGGGGFGGCFGGGEGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGCCCCC SA:Z:1,77643955,+,77S44M4S,11,1; XA:Z:1,-55428102,42S83M,4; MD:Z:
28A54 NM:i:1 AS:i:78 XS:i:63
at picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator.checkForMinimumDistanceFailure(MarkDuplicatesWithMateCigarIterator.java:332)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator.markDuplicatesAndGetTheNextAvailable(MarkDuplicatesWithMateCigarIterator.java:421)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator.next(MarkDuplicatesWithMateCigarIterator.java:219)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator.next(MarkDuplicatesWithMateCigarIterator.java:47)
at picard.sam.markduplicates.MarkDuplicatesWithMateCigar.doWork(MarkDuplicatesWithMateCigar.java:158)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
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