Class picard.sam.CleanSamTest

all > picard.sam > CleanSamTest

tests

failures

ignored

0.417s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testCleanSamTester[0](100M, 100M, 101, 2)	0.032s	passed
testCleanSamTester[1](100M, 99M1S, 101, 3)	0.029s	passed
testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)	0.029s	passed
testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)	0.029s	passed
testCleanSamTester[4](99M1I, 99M1I, 101, 3)	0.028s	passed
testCleanSamTester[5](90M10I, 90M10I, 101, 3)	0.029s	passed
testCleanSam[0](simple_fits.sam, 100M)	0.058s	passed
testCleanSam[1](simple_overhang.sam, 99M1S)	0.070s	passed
testCleanSam[2](fits_with_deletion.sam, 91M2D9M)	0.029s	passed
testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)	0.028s	passed
testCleanSam[4](trailing_insertion.sam, 99M1I)	0.028s	passed
testCleanSam[5](long_trailing_insertion.sam, 90M10I)	0.028s	passed

Standard output

No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found

Standard error

[Tue Aug 16 04:11:17 CDT 2016] picard.sam.CleanSam INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CleanSam/simple_fits.sam OUTPUT=/tmp/simple_fits.sam.1325058040579666727.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:17 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
[Tue Aug 16 04:11:17 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CleanSam/simple_overhang.sam OUTPUT=/tmp/simple_overhang.sam.6974391526438716169.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
Ignoring SAM validation error: ERROR: Read name simple_overhang, Read CIGAR M operator maps off end of reference
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CleanSam/fits_with_deletion.sam OUTPUT=/tmp/fits_with_deletion.sam.7206729476510622839.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CleanSam/overhang_with_deletion.sam OUTPUT=/tmp/overhang_with_deletion.sam.7764659582931647614.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
Ignoring SAM validation error: ERROR: Read name overhang_with_deletion, Read CIGAR M operator maps off end of reference
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CleanSam/trailing_insertion.sam OUTPUT=/tmp/trailing_insertion.sam.2314203085098278657.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CleanSam/long_trailing_insertion.sam OUTPUT=/tmp/long_trailing_insertion.sam.8951243443784796007.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.1013893286055927541.tmp/input.sam OUTPUT=/tmp/CleanSamTester.1013893286055927541.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.6574238655960531005.tmp/input.sam OUTPUT=/tmp/CleanSamTester.6574238655960531005.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.5342343640779560448.tmp/input.sam OUTPUT=/tmp/CleanSamTester.5342343640779560448.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.7165874304952893920.tmp/input.sam OUTPUT=/tmp/CleanSamTester.7165874304952893920.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.6118196157523925017.tmp/input.sam OUTPUT=/tmp/CleanSamTester.6118196157523925017.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.1548525597946772184.tmp/input.sam OUTPUT=/tmp/CleanSamTester.1548525597946772184.tmp/output.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:18 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
[Tue Aug 16 04:11:18 CDT 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120