File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/126bb592a14f19a6a72dd5aee527a7/.command.log
Size
7.2 KB
Task
NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS (BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/ebb8d66d0e4680eaed709c7ce41c82/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ctat_ref_annot.interval_list
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/126bb592a14f19a6a72dd5aee527a7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/126bb592a14f19a6a72dd5aee527a7/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/ref_annot.gtf.refflat
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4d20a971c93be1dc46f16704254326/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (6 inputs)

/usr/local/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
May 28, 2026 8:11:15 PM com.intel.gkl.NativeLibraryLoader load
INFO: Loading libgkl_compression.so from jar:file:/usr/local/share/picard-3.1.0-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu May 28 20:11:15 GMT 2026] CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --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 May 28 20:11:15 GMT 2026] Executing as ?@nf-04126bb592a14f19a6a72dd5aee527a7-95182-wf6rb on Linux 6.12.83 amd64; OpenJDK 64-Bit Server VM 20-internal-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:3.1.0
INFO	2026-05-28 20:11:20	CollectRnaSeqMetrics	Loaded 58279 genes.
INFO	2026-05-28 20:11:39	SinglePassSamProgram	Processed     1,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:   18s.  Last read position: chr1:114,464,347
INFO	2026-05-28 20:11:57	SinglePassSamProgram	Processed     2,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:   18s.  Last read position: chr2:13,227,518
INFO	2026-05-28 20:12:10	SinglePassSamProgram	Processed     3,000,000 records.  Elapsed time: 00:00:49s.  Time for last 1,000,000:   12s.  Last read position: chr2:178,681,115
INFO	2026-05-28 20:12:30	SinglePassSamProgram	Processed     4,000,000 records.  Elapsed time: 00:01:10s.  Time for last 1,000,000:   20s.  Last read position: chr3:105,577,790
INFO	2026-05-28 20:12:46	SinglePassSamProgram	Processed     5,000,000 records.  Elapsed time: 00:01:25s.  Time for last 1,000,000:   15s.  Last read position: chr4:188,533,863
INFO	2026-05-28 20:12:59	SinglePassSamProgram	Processed     6,000,000 records.  Elapsed time: 00:01:38s.  Time for last 1,000,000:   13s.  Last read position: chr6:3,224,944
INFO	2026-05-28 20:13:16	SinglePassSamProgram	Processed     7,000,000 records.  Elapsed time: 00:01:55s.  Time for last 1,000,000:   16s.  Last read position: chr6:151,223,784
INFO	2026-05-28 20:13:34	SinglePassSamProgram	Processed     8,000,000 records.  Elapsed time: 00:02:13s.  Time for last 1,000,000:   17s.  Last read position: chr7:137,908,315
INFO	2026-05-28 20:13:47	SinglePassSamProgram	Processed     9,000,000 records.  Elapsed time: 00:02:26s.  Time for last 1,000,000:   13s.  Last read position: chr8:143,866,188
INFO	2026-05-28 20:14:02	SinglePassSamProgram	Processed    10,000,000 records.  Elapsed time: 00:02:42s.  Time for last 1,000,000:   15s.  Last read position: chr10:11,096,338
INFO	2026-05-28 20:14:18	SinglePassSamProgram	Processed    11,000,000 records.  Elapsed time: 00:02:57s.  Time for last 1,000,000:   15s.  Last read position: chr11:44,970,703
INFO	2026-05-28 20:14:36	SinglePassSamProgram	Processed    12,000,000 records.  Elapsed time: 00:03:15s.  Time for last 1,000,000:   17s.  Last read position: chr12:6,581,150
INFO	2026-05-28 20:14:53	SinglePassSamProgram	Processed    13,000,000 records.  Elapsed time: 00:03:33s.  Time for last 1,000,000:   17s.  Last read position: chr12:128,971,632
INFO	2026-05-28 20:15:09	SinglePassSamProgram	Processed    14,000,000 records.  Elapsed time: 00:03:49s.  Time for last 1,000,000:   15s.  Last read position: chr14:104,893,056
INFO	2026-05-28 20:15:19	SinglePassSamProgram	Processed    15,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:   10s.  Last read position: chr15:99,131,351
INFO	2026-05-28 20:15:30	SinglePassSamProgram	Processed    16,000,000 records.  Elapsed time: 00:04:10s.  Time for last 1,000,000:   10s.  Last read position: chr16:66,604,864
INFO	2026-05-28 20:15:41	SinglePassSamProgram	Processed    17,000,000 records.  Elapsed time: 00:04:20s.  Time for last 1,000,000:   10s.  Last read position: chr17:41,624,493
INFO	2026-05-28 20:15:52	SinglePassSamProgram	Processed    18,000,000 records.  Elapsed time: 00:04:32s.  Time for last 1,000,000:   11s.  Last read position: chr18:44,949,891
INFO	2026-05-28 20:16:04	SinglePassSamProgram	Processed    19,000,000 records.  Elapsed time: 00:04:44s.  Time for last 1,000,000:   11s.  Last read position: chr19:35,095,511
INFO	2026-05-28 20:16:13	SinglePassSamProgram	Processed    20,000,000 records.  Elapsed time: 00:04:53s.  Time for last 1,000,000:    8s.  Last read position: chr20:17,825,458
INFO	2026-05-28 20:16:17	SinglePassSamProgram	Processed    21,000,000 records.  Elapsed time: 00:04:57s.  Time for last 1,000,000:    3s.  Last read position: chr21:8,216,846
INFO	2026-05-28 20:16:18	SinglePassSamProgram	Processed    22,000,000 records.  Elapsed time: 00:04:58s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,397,478
INFO	2026-05-28 20:16:20	SinglePassSamProgram	Processed    23,000,000 records.  Elapsed time: 00:05:00s.  Time for last 1,000,000:    1s.  Last read position: chr21:8,442,047
INFO	2026-05-28 20:16:24	SinglePassSamProgram	Processed    24,000,000 records.  Elapsed time: 00:05:03s.  Time for last 1,000,000:    3s.  Last read position: chr22:20,566,657
INFO	2026-05-28 20:16:33	SinglePassSamProgram	Processed    25,000,000 records.  Elapsed time: 00:05:13s.  Time for last 1,000,000:    9s.  Last read position: chrX:154,349,653
INFO	2026-05-28 20:16:35	SinglePassSamProgram	Processed    26,000,000 records.  Elapsed time: 00:05:14s.  Time for last 1,000,000:    1s.  Last read position: GL000220.1:116,801
INFO	2026-05-28 20:16:36	SinglePassSamProgram	Processed    27,000,000 records.  Elapsed time: 00:05:15s.  Time for last 1,000,000:    0s.  Last read position: KI270733.1:126,207
INFO	2026-05-28 20:16:37	SinglePassSamProgram	Processed    28,000,000 records.  Elapsed time: 00:05:16s.  Time for last 1,000,000:    0s.  Last read position: KI270733.1:173,231
INFO	2026-05-28 20:16:38	SinglePassSamProgram	Processed    29,000,000 records.  Elapsed time: 00:05:17s.  Time for last 1,000,000:    0s.  Last read position: */*
[Thu May 28 20:16:39 GMT 2026] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 5.40 minutes.
Runtime.totalMemory()=2781347840