Class picard.analysis.CollectUmiPrevalenceMetricsTest
Tests
| Test |
Duration |
Result |
| integrationTest |
0.015s |
passed |
Standard error
[Thu Apr 24 12:59:25 EDT 2025] CollectUmiPrevalenceMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/independent_replicates/twopairsWithManyUmis.sam --OUTPUT /tmp/test5538131497801544994.umi_hist --MINIMUM_MQ 20 --BARCODE_TAG RX --BARCODE_BQ BQ --MINIMUM_BARCODE_BQ 30 --FILTER_UNPAIRED_READS true --PROGRESS_STEP_INTERVAL 1000000 --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 12:59:25 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 12:59:25 CollectUmiPrevalenceMetrics Queried BAM, getting duplicate sets.
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Duplicate set iterator initializing.
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Duplicate set iterator initialized.
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Starting iteration on duplicate sets
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Iteration done. Emitting metrics.
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Processed 6 sets
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Filtered 0 unpaired reads
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Filtered 0 unaligned reads
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Filtered 0 low mapQ reads
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Filtered 0 Secondary or Supplementary reads
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Filtered 0 reads that had no UMI tag
INFO 2025-04-24 12:59:25 CollectUmiPrevalenceMetrics Filtered 0 reads that had poor quality UMI
[Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectUmiPrevalenceMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824