Class picard.sam.CleanSamTest

12

tests

0

failures

0

ignored

0.131s

duration

100%

successful

Tests

Test Duration Result
testCleanSamTester[0](100M, 100M, 101, 2) 0.011s passed
testCleanSamTester[1](100M, 99M1S, 101, 3) 0.016s passed
testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1) 0.009s passed
testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1) 0.012s passed
testCleanSamTester[4](99M1I, 99M1I, 101, 3) 0.009s passed
testCleanSamTester[5](90M10I, 90M10I, 101, 3) 0.010s passed
testCleanSam[0](simple_fits.sam, 100M) 0.019s passed
testCleanSam[1](simple_overhang.sam, 99M1S) 0.010s passed
testCleanSam[2](fits_with_deletion.sam, 91M2D9M) 0.009s passed
testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S) 0.009s passed
testCleanSam[4](trailing_insertion.sam, 99M1I) 0.008s passed
testCleanSam[5](long_trailing_insertion.sam, 90M10I) 0.009s 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

[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CleanSam/simple_fits.sam --OUTPUT /tmp/simple_fits.sam.17319280685478794794.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CleanSam/simple_overhang.sam --OUTPUT /tmp/simple_overhang.sam.10523310048694688774.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name simple_overhang, Read CIGAR M operator maps off end of reference
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CleanSam/fits_with_deletion.sam --OUTPUT /tmp/fits_with_deletion.sam.15707627720103338037.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CleanSam/overhang_with_deletion.sam --OUTPUT /tmp/overhang_with_deletion.sam.7093559815308163940.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name overhang_with_deletion, Read CIGAR M operator maps off end of reference
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CleanSam/trailing_insertion.sam --OUTPUT /tmp/trailing_insertion.sam.12976417239461639218.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/CleanSam/long_trailing_insertion.sam --OUTPUT /tmp/long_trailing_insertion.sam.5096495058108390460.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /tmp/CleanSamTester.tmp7423408031733889511/input.sam --OUTPUT /tmp/CleanSamTester.tmp7423408031733889511/output.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /tmp/CleanSamTester.tmp3724823798181207732/input.sam --OUTPUT /tmp/CleanSamTester.tmp3724823798181207732/output.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference
Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /tmp/CleanSamTester.tmp7581854468175258627/input.sam --OUTPUT /tmp/CleanSamTester.tmp7581854468175258627/output.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /tmp/CleanSamTester.tmp1926014930438084543/input.sam --OUTPUT /tmp/CleanSamTester.tmp1926014930438084543/output.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference
Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /tmp/CleanSamTester.tmp17821559153446576538/input.sam --OUTPUT /tmp/CleanSamTester.tmp17821559153446576538/output.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:46 EDT 2025] CleanSam --INPUT /tmp/CleanSamTester.tmp9385799791884605460/input.sam --OUTPUT /tmp/CleanSamTester.tmp9385799791884605460/output.sam --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:03:46 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
[Thu Apr 24 13:03:46 EDT 2025] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824