Class picard.sam.CreateSequenceDictionaryTest

7

tests

0

failures

0

ignored

0.103s

duration

100%

successful

Tests

Test Duration Result
testAltNames 0.016s passed
testBasic 0.011s passed
testDefaultOutputFile 0.010s passed
testForEquivalence 0.011s passed
testNonUniqueSequenceName 0.010s passed
testPunctuationInReferenceNames 0.011s passed
testSequenceMD5sRespectLineEndings 0.034s passed

Standard error

[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --OUTPUT /tmp/CreateSequenceDictionaryTest.10827121097138734673.dict --TRUNCATE_NAMES_AT_WHITESPACE true --ALT_NAMES /tmp/CreateSequenceDictionaryTest11833702376125509316.alt --REFERENCE testdata/picard/sam/basic.fasta --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --OUTPUT /tmp/CreateSequenceDictionaryTest.4246563989576467480.dict --TRUNCATE_NAMES_AT_WHITESPACE false --REFERENCE testdata/picard/sam/basic.fasta --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 13:03:52	CreateSequenceDictionary	Output dictionary will be written in /mounts/lovelace/software/picard/picard/testdata/picard/sam/basic.dict
[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --TRUNCATE_NAMES_AT_WHITESPACE false --REFERENCE testdata/picard/sam/basic.fasta --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --OUTPUT /tmp/CreateSequenceDictionaryTest.12065609877850521272.dict --TRUNCATE_NAMES_AT_WHITESPACE false --REFERENCE testdata/picard/reference/test.fasta --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --OUTPUT /tmp/CreateSequenceDictionaryTest.5678120632987650121.dict --TRUNCATE_NAMES_AT_WHITESPACE true --REFERENCE testdata/picard/sam/duplicate_sequence_names.fasta --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
INFO	2025-04-24 13:03:52	CreateSequenceDictionary	Output dictionary will be written in /mounts/lovelace/software/picard/picard/testdata/picard/sam/special.dict
[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --TRUNCATE_NAMES_AT_WHITESPACE false --ALT_NAMES testdata/picard/sam/special.alt --REFERENCE testdata/picard/sam/special.fasta --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --OUTPUT /tmp/CreateSequenceDictionaryTest_unix.17433466312262798671.dict --REFERENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/test.fasta --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --OUTPUT /tmp/CreateSequenceDictionaryTest_dos.8432093636250319151.dict --REFERENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/test_dos_line_endings.fasta --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:03:52 EDT 2025] CreateSequenceDictionary --OUTPUT /tmp/CreateSequenceDictionaryTest_dos_gz.855825350655910275.dict --REFERENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/test_dos_line_endings.fasta.gz --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --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 13:03:52 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 13:03:52 EDT 2025] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824