Class picard.vcf.FixVcfHeaderTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testFixVcfHeader[0](-1, file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true) | 0.022s | passed |
| testFixVcfHeader[1](-1, file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false) | 0.015s | passed |
| testFixVcfHeader[2](-1, file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false) | 0.013s | passed |
| testFixVcfHeader[3](-1, null, true) | 0.013s | passed |
| testFixVcfHeader[4](2, null, true) | 0.012s | passed |
| testFixVcfHeader[5](2147483647, null, true) | 0.014s | passed |
| testMissingFilterNotInFirstNRecords | 0.008s | passed |
| testReplaceHeaderWithDifferentSamplesError | 0.002s | passed |
Standard error
[Thu Apr 24 13:18:08 EDT 2025] FixVcfHeader --INPUT file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/input.vcf --OUTPUT /tmp/output.3526166331478034788.vcf --CHECK_FIRST_N_RECORDS -1 --HEADER file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/header.vcf --ENFORCE_SAME_SAMPLES true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:18:08 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 INFO 2025-04-24 13:18:08 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter INFO 2025-04-24 13:18:08 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG INFO 2025-04-24 13:18:08 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD INFO 2025-04-24 13:18:08 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT INFO 2025-04-24 13:18:08 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ INFO 2025-04-24 13:18:08 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT INFO 2025-04-24 13:18:08 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL INFO 2025-04-24 13:18:08 FixVcfHeader Writing the output VCF. [Thu Apr 24 13:18:08 EDT 2025] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] FixVcfHeader --INPUT file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/input.vcf --OUTPUT /tmp/output.4801699274872077216.vcf --CHECK_FIRST_N_RECORDS -1 --HEADER file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/header.vcf --ENFORCE_SAME_SAMPLES false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:18:09 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 INFO 2025-04-24 13:18:09 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter INFO 2025-04-24 13:18:09 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL INFO 2025-04-24 13:18:09 FixVcfHeader Writing the output VCF. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] FixVcfHeader --INPUT file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/input.vcf --OUTPUT /tmp/output.3923330220005619747.vcf --CHECK_FIRST_N_RECORDS -1 --HEADER file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf --ENFORCE_SAME_SAMPLES false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:18:09 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 INFO 2025-04-24 13:18:09 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter INFO 2025-04-24 13:18:09 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT INFO 2025-04-24 13:18:09 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL INFO 2025-04-24 13:18:09 FixVcfHeader Writing the output VCF. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] FixVcfHeader --INPUT file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/input.vcf --OUTPUT /tmp/output.11231359052077599873.vcf --CHECK_FIRST_N_RECORDS -1 --ENFORCE_SAME_SAMPLES true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:18:09 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 INFO 2025-04-24 13:18:09 FixVcfHeader Reading in records to re-build the header. INFO 2025-04-24 13:18:09 FixVcfHeader Will add an INFO line with id: PLNCIIonWG INFO 2025-04-24 13:18:09 FixVcfHeader Will add an FILTER line with id: MissingFilter INFO 2025-04-24 13:18:09 FixVcfHeader VCF header re-built. INFO 2025-04-24 13:18:09 FixVcfHeader Writing the output VCF. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] FixVcfHeader --INPUT file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/input.vcf --OUTPUT /tmp/output.5415600677554277834.vcf --CHECK_FIRST_N_RECORDS 2 --ENFORCE_SAME_SAMPLES true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:18:09 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 INFO 2025-04-24 13:18:09 FixVcfHeader Reading in records to re-build the header. INFO 2025-04-24 13:18:09 FixVcfHeader Will add an INFO line with id: PLNCIIonWG INFO 2025-04-24 13:18:09 FixVcfHeader Will add an FILTER line with id: MissingFilter INFO 2025-04-24 13:18:09 FixVcfHeader VCF header re-built. INFO 2025-04-24 13:18:09 FixVcfHeader Writing the output VCF. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] FixVcfHeader --INPUT file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/input.vcf --OUTPUT /tmp/output.1929092824367027369.vcf --CHECK_FIRST_N_RECORDS 2147483647 --ENFORCE_SAME_SAMPLES true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:18:09 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 INFO 2025-04-24 13:18:09 FixVcfHeader Reading in records to re-build the header. INFO 2025-04-24 13:18:09 FixVcfHeader Will add an INFO line with id: PLNCIIonWG INFO 2025-04-24 13:18:09 FixVcfHeader Will add an FILTER line with id: MissingFilter INFO 2025-04-24 13:18:09 FixVcfHeader VCF header re-built. INFO 2025-04-24 13:18:09 FixVcfHeader Writing the output VCF. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] FixVcfHeader --INPUT file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/input.vcf --OUTPUT /tmp/output.17555994794732425879.vcf --CHECK_FIRST_N_RECORDS 1 --ENFORCE_SAME_SAMPLES true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:18:09 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 INFO 2025-04-24 13:18:09 FixVcfHeader Reading in records to re-build the header. INFO 2025-04-24 13:18:09 FixVcfHeader Will add an INFO line with id: PLNCIIonWG INFO 2025-04-24 13:18:09 FixVcfHeader VCF header re-built. INFO 2025-04-24 13:18:09 FixVcfHeader Writing the output VCF. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:18:09 EDT 2025] FixVcfHeader --INPUT file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/input.vcf --OUTPUT /tmp/output.13951155577275749195.vcf --CHECK_FIRST_N_RECORDS -1 --HEADER file:/mounts/lovelace/software/picard/picard/testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf --ENFORCE_SAME_SAMPLES true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:18:09 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 13:18:09 EDT 2025] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp