Standard error
INFO 2025-04-24 13:03:45 RExecutor Executing R script via command: Rscript /tmp/script6031147491044996446.R
INFO 2025-04-24 13:03:45 ProcessExecutor [1] "Checking if R is installed"
[Thu Apr 24 13:03:45 EDT 2025] CollectRrbsMetrics --INPUT testdata/picard/metrics/chrMReads.sam --METRICS_FILE_PREFIX /tmp/crmt.tmp9115291060255006739/READ_TEST --REFERENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_READ_LENGTH 5 --C_QUALITY_THRESHOLD 20 --NEXT_BASE_QUALITY_THRESHOLD 10 --MAX_MISMATCH_RATE 0.1 --ASSUME_SORTED false --METRIC_ACCUMULATION_LEVEL ALL_READS --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 13:03:45 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 13:03:45 RExecutor Executing R script via command: Rscript /tmp/script7837246158777583568.R /tmp/crmt.tmp9115291060255006739/READ_TEST.rrbs_detail_metrics /tmp/crmt.tmp9115291060255006739/READ_TEST.rrbs_summary_metrics /tmp/crmt.tmp9115291060255006739/READ_TEST.rrbs_qc.pdf
INFO 2025-04-24 13:03:45 ProcessExecutor null device
INFO 2025-04-24 13:03:45 ProcessExecutor 1
[Thu Apr 24 13:03:45 EDT 2025] picard.analysis.CollectRrbsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1440743424