Class picard.analysis.CollectAlignmentSummaryMetricsTest
Tests
| Test |
Duration |
Result |
| test |
0.025s |
passed |
| testAdapterReads |
0.016s |
passed |
| testBisulfite |
0.014s |
passed |
| testBisulfiteButNot |
0.014s |
passed |
| testChimeras |
0.014s |
passed |
| testMultipleLevelsOfMetrics |
0.020s |
passed |
| testNoPFReads |
0.012s |
passed |
| testNoReference |
0.012s |
passed |
| testReadLengthHistogram[0](summary_alignment_stats_test.sam, true) |
0.386s |
passed |
| testReadLengthHistogram[0](true) |
0.526s |
passed |
| testReadLengthHistogram[1](false) |
0.025s |
passed |
| testReadLengthHistogram[1](summary_alignment_stats_test2.sam, true) |
0.424s |
passed |
| testReadLengthHistogram[2](summary_alignment_stats_test3.sam, true) |
0.406s |
passed |
| testReadLengthHistogram[3](summary_alignment_stats_test_empty.sam, false) |
0.220s |
passed |
| testZeroLengthReads |
0.023s |
passed |
Standard error
[Thu Apr 24 12:59:12 EDT 2025] CollectAlignmentSummaryMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/test6087715144492670185.txt --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:12 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 12:59:12 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:12 EDT 2025] CollectAlignmentSummaryMetrics --MAX_INSERT_SIZE 200 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_adapter_reads.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testAdapterReads11474971553381395631.txt --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:12 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
WARNING 2025-04-24 12:59:12 SinglePassSamProgram File reports sort order 'unsorted', assuming it's coordinate sorted anyway.
[Thu Apr 24 12:59:12 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --IS_BISULFITE_SEQUENCED true --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testBisulfite15881072622723403381.txt --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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 12:59:13 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --IS_BISULFITE_SEQUENCED false --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testBisulfiteButNot251558583141582804.txt --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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 12:59:13 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --MAX_INSERT_SIZE 20 --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_chimeras.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testChimeras4116905033142784543.txt --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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 12:59:13 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --METRIC_ACCUMULATION_LEVEL ALL_READS --METRIC_ACCUMULATION_LEVEL SAMPLE --METRIC_ACCUMULATION_LEVEL READ_GROUP --METRIC_ACCUMULATION_LEVEL LIBRARY --COLLECT_ALIGNMENT_INFORMATION false --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_multiple.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testMultipleLevelsOfMetrics12539654648949085726.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --IS_BISULFITE_SEQUENCED false --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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 12:59:13 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/null.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/test11968863501202382307.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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
WARNING 2025-04-24 12:59:13 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway.
WARNING 2025-04-24 12:59:13 CollectAlignmentSummaryMetrics /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/null.sam has no sequence dictionary. If any reads in the file are aligned, then alignment summary metrics collection will fail.
WARNING 2025-04-24 12:59:13 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected!
[Thu Apr 24 12:59:13 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --COLLECT_ALIGNMENT_INFORMATION false --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testNoReference1851765572584324775.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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 12:59:13 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:13 RExecutor Executing R script via command: Rscript /tmp/script3529129383906121248.R
INFO 2025-04-24 12:59:13 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --HISTOGRAM_FILE /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram3434604594119657288.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram13733946471850311382.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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
WARNING 2025-04-24 12:59:13 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected!
INFO 2025-04-24 12:59:13 RExecutor Executing R script via command: Rscript /tmp/script17973723736702664401.R /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram13733946471850311382.txt /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram3434604594119657288.pdf summary_alignment_stats_test3.sam
INFO 2025-04-24 12:59:13 ProcessExecutor null device
INFO 2025-04-24 12:59:13 ProcessExecutor 1
[Thu Apr 24 12:59:13 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram18345649150296110288.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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
WARNING 2025-04-24 12:59:13 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected!
[Thu Apr 24 12:59:13 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:13 RExecutor Executing R script via command: Rscript /tmp/script8025350900248467625.R
INFO 2025-04-24 12:59:13 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:13 EDT 2025] CollectAlignmentSummaryMetrics --HISTOGRAM_FILE /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram7596307529925872115.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram11339798806068054394.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:13 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
WARNING 2025-04-24 12:59:13 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected!
INFO 2025-04-24 12:59:13 RExecutor Executing R script via command: Rscript /tmp/script2507098073912275527.R /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram11339798806068054394.txt /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram7596307529925872115.pdf summary_alignment_stats_test.sam
INFO 2025-04-24 12:59:14 ProcessExecutor null device
INFO 2025-04-24 12:59:14 ProcessExecutor 1
[Thu Apr 24 12:59:14 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:14 RExecutor Executing R script via command: Rscript /tmp/script2159574685033805096.R
INFO 2025-04-24 12:59:14 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:14 EDT 2025] CollectAlignmentSummaryMetrics --HISTOGRAM_FILE /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram12975654123068690897.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram15767181913643012343.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:14 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
WARNING 2025-04-24 12:59:14 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected!
INFO 2025-04-24 12:59:14 RExecutor Executing R script via command: Rscript /tmp/script9604628499824843909.R /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram15767181913643012343.txt /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram12975654123068690897.pdf summary_alignment_stats_test2.sam
INFO 2025-04-24 12:59:14 ProcessExecutor null device
INFO 2025-04-24 12:59:14 ProcessExecutor 1
[Thu Apr 24 12:59:14 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:14 RExecutor Executing R script via command: Rscript /tmp/script2725137396821368667.R
INFO 2025-04-24 12:59:14 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:14 EDT 2025] CollectAlignmentSummaryMetrics --HISTOGRAM_FILE /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram10854901532900653809.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram17469656708756208897.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:14 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
WARNING 2025-04-24 12:59:14 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected!
INFO 2025-04-24 12:59:14 RExecutor Executing R script via command: Rscript /tmp/script5907055484863020544.R /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram17469656708756208897.txt /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram10854901532900653809.pdf summary_alignment_stats_test3.sam
INFO 2025-04-24 12:59:14 ProcessExecutor null device
INFO 2025-04-24 12:59:14 ProcessExecutor 1
[Thu Apr 24 12:59:14 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO 2025-04-24 12:59:14 RExecutor Executing R script via command: Rscript /tmp/script427205297545063308.R
INFO 2025-04-24 12:59:15 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 12:59:15 EDT 2025] CollectAlignmentSummaryMetrics --HISTOGRAM_FILE /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram14800360926056943081.pdf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_empty.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testReadLengthHistogram14722487235284746108.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:15 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
WARNING 2025-04-24 12:59:15 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected!
WARNING 2025-04-24 12:59:15 CollectAlignmentSummaryMetrics No Read length histograms to plot.
[Thu Apr 24 12:59:15 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:15 EDT 2025] CollectAlignmentSummaryMetrics --COLLECT_ALIGNMENT_INFORMATION false --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam --OUTPUT /tmp/picard.analysis.CollectAlignmentSummaryMetricsTest2750889733958695465/testZeroLengthReads4787944667227030000.txt --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:15 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 12:59:15 EDT 2025] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824