Class picard.vcf.GatherVcfsTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| TestGatherFiles[0]([file:/tmp/shard1.18294915163721530627.vcf, file:/tmp/shard2.11084708081190958222.vcf, file:/tmp/shard310402849899490187635.vcf], /tmp/whole.10470126824156385644.vcf, 0, false) | 0.026s | passed |
| TestGatherFiles[1]([file:/tmp/shard310402849899490187635.vcf, file:/tmp/shard1.18294915163721530627.vcf, file:/tmp/shard2.11084708081190958222.vcf], /tmp/whole.10470126824156385644.vcf, 0, true) | 0.027s | passed |
| TestGatherFiles[2]([file:/tmp/shard1.18294915163721530627.vcf, file:/tmp/shard2_bad.7645964417906643632.vcf, file:/tmp/shard310402849899490187635.vcf], /tmp/whole.10470126824156385644.vcf, 1, false) | 0.021s | passed |
| TestGatherFiles[3]([file:/tmp/shard1.18294915163721530627.vcf, file:/tmp/shard310402849899490187635.vcf, file:/tmp/shard2.11084708081190958222.vcf], /tmp/whole.10470126824156385644.vcf, 1, false) | 0.012s | passed |
| TestGatherFiles[4]([file:/tmp/shard310402849899490187635.vcf, file:/tmp/shard1.18294915163721530627.vcf, file:/tmp/shard2.11084708081190958222.vcf], /tmp/whole.10470126824156385644.vcf, 1, false) | 0.010s | passed |
| TestGatherFiles[5]([file:/tmp/shard1.8525341143730961265.vcf.gz, file:/tmp/shard2.13011038560983988326.vcf.gz, file:/tmp/shard310402849899490187635.vcf], /tmp/whole.8912846718657487448.vcf.gz, 0, false) | 0.029s | passed |
| TestGatherFiles[6]([file:/tmp/shard1.8525341143730961265.vcf.gz, file:/tmp/shard2_bad.16438601585542964643.vcf.gz, file:/tmp/shard310402849899490187635.vcf], /tmp/whole.8912846718657487448.vcf.gz, 1, false) | 0.022s | passed |
| TestGatherFiles[7]([file:/tmp/shard1.8525341143730961265.vcf.gz, file:/tmp/shard3.1388249229175671791.vcf.gz, file:/tmp/shard2.11084708081190958222.vcf], /tmp/whole.8912846718657487448.vcf.gz, 1, false) | 0.013s | passed |
| TestGatherFiles[8]([file:/tmp/shard3.1388249229175671791.vcf.gz, file:/tmp/shard1.8525341143730961265.vcf.gz, file:/tmp/shard2.11084708081190958222.vcf], /tmp/whole.8912846718657487448.vcf.gz, 1, false) | 0.012s | passed |
| TestGatherFiles[9]([file:/tmp/shard3.1388249229175671791.vcf.gz, file:/tmp/shard1.8525341143730961265.vcf.gz, file:/tmp/shard2.11084708081190958222.vcf], /tmp/whole.8912846718657487448.vcf.gz, 0, true) | 0.031s | passed |
Standard error
[Thu Apr 24 13:18:09 EDT 2025] GatherVcfs --INPUT file:/tmp/shard1.18294915163721530627.vcf --INPUT file:/tmp/shard2.11084708081190958222.vcf --INPUT file:/tmp/shard310402849899490187635.vcf --OUTPUT /tmp/result1477771175666593761.vcf --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2025-04-24 13:18:09 GatherVcfs Gathering by conventional means. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] GatherVcfs --INPUT file:/tmp/shard310402849899490187635.vcf --INPUT file:/tmp/shard1.18294915163721530627.vcf --INPUT file:/tmp/shard2.11084708081190958222.vcf --OUTPUT /tmp/result17052446002768907412.vcf --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2025-04-24 13:18:09 GatherVcfs Gathering by conventional means. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] GatherVcfs --INPUT file:/tmp/shard1.18294915163721530627.vcf --INPUT file:/tmp/shard2_bad.7645964417906643632.vcf --INPUT file:/tmp/shard310402849899490187635.vcf --OUTPUT /tmp/result6211450369643057758.vcf --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2025-04-24 13:18:09 GatherVcfs Gathering by conventional means. ERROR 2025-04-24 13:18:09 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First variant in file /tmp/shard2_bad.7645964417906643632.vcf is at 22:17283967 but last variant in earlier file /tmp/shard1.18294915163721530627.vcf is at 22:17283967 [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs 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] GatherVcfs --INPUT file:/tmp/shard1.18294915163721530627.vcf --INPUT file:/tmp/shard310402849899490187635.vcf --INPUT file:/tmp/shard2.11084708081190958222.vcf --OUTPUT /tmp/result9172220451854418876.vcf --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. ERROR 2025-04-24 13:18:09 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard2.11084708081190958222.vcf is not after first record in previous file /tmp/shard310402849899490187635.vcf [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs 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] GatherVcfs --INPUT file:/tmp/shard310402849899490187635.vcf --INPUT file:/tmp/shard1.18294915163721530627.vcf --INPUT file:/tmp/shard2.11084708081190958222.vcf --OUTPUT /tmp/result9975202727091318113.vcf --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. ERROR 2025-04-24 13:18:09 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard1.18294915163721530627.vcf is not after first record in previous file /tmp/shard310402849899490187635.vcf [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs 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] GatherVcfs --INPUT file:/tmp/shard1.8525341143730961265.vcf.gz --INPUT file:/tmp/shard2.13011038560983988326.vcf.gz --INPUT file:/tmp/shard310402849899490187635.vcf --OUTPUT /tmp/result15952403192547524139.vcf.gz --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2025-04-24 13:18:09 GatherVcfs Gathering by conventional means. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:18:09 EDT 2025] GatherVcfs --INPUT file:/tmp/shard1.8525341143730961265.vcf.gz --INPUT file:/tmp/shard2_bad.16438601585542964643.vcf.gz --INPUT file:/tmp/shard310402849899490187635.vcf --OUTPUT /tmp/result9585794716994253738.vcf.gz --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2025-04-24 13:18:09 GatherVcfs Gathering by conventional means. ERROR 2025-04-24 13:18:09 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First variant in file /tmp/shard2_bad.16438601585542964643.vcf.gz is at 22:17283967 but last variant in earlier file /tmp/shard1.8525341143730961265.vcf.gz is at 22:17283967 [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs 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] GatherVcfs --INPUT file:/tmp/shard1.8525341143730961265.vcf.gz --INPUT file:/tmp/shard3.1388249229175671791.vcf.gz --INPUT file:/tmp/shard2.11084708081190958222.vcf --OUTPUT /tmp/result9862676588159562376.vcf.gz --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. ERROR 2025-04-24 13:18:09 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard2.11084708081190958222.vcf is not after first record in previous file /tmp/shard3.1388249229175671791.vcf.gz [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs 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] GatherVcfs --INPUT file:/tmp/shard3.1388249229175671791.vcf.gz --INPUT file:/tmp/shard1.8525341143730961265.vcf.gz --INPUT file:/tmp/shard2.11084708081190958222.vcf --OUTPUT /tmp/result11225144642316445718.vcf.gz --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. ERROR 2025-04-24 13:18:09 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard1.8525341143730961265.vcf.gz is not after first record in previous file /tmp/shard3.1388249229175671791.vcf.gz [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs 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] GatherVcfs --INPUT file:/tmp/shard3.1388249229175671791.vcf.gz --INPUT file:/tmp/shard1.8525341143730961265.vcf.gz --INPUT file:/tmp/shard2.11084708081190958222.vcf --OUTPUT /tmp/result10629086478052777495.vcf.gz --COMMENT This is a comment --REORDER_INPUT_BY_FIRST_VARIANT true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX true --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 GatherVcfs Checking inputs. INFO 2025-04-24 13:18:09 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2025-04-24 13:18:09 GatherVcfs Gathering by conventional means. [Thu Apr 24 13:18:09 EDT 2025] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824