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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
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Picard CollectMultipleMetrics error in R script

Hello!

I run CollectMultipleMetrics in a RNAseq pipeline, and I encounter this error:

[Wed Jan 13 11:50:10 EST 2016] picard.analysis.CollectMultipleMetrics INPUT=sorted.mdup.bam REFERENCE_SEQUENCE=Mus_musculus.GRCm38.fa OUTPUT=metrics PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectBaseDistributionByCycle, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] TMP_DIR=[/scratch] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=2000000 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Jan 13 11:50:10 EST 2016] Executing as me@machine on Linux 2.6.32-573.12.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-ea-b07; Picard version: 1.123(286a232caea2fdc8fdd88574c09c460b46386fff_1413818736) IntelDeflater INFO 2016-01-13 11:50:19 SinglePassSamProgram Processed 1 000 000 records. Elapsed time: 00:00:08s. Time for last 1 000 000: 7s. Last read position: 1:24 615 160 INFO 2016-01-13 11:50:26 SinglePassSamProgram Processed 2 000 000 records. Elapsed time: 00:00:15s. Time for last 1 000 000: 6s. Last read position: 1:58 405 526 INFO 2016-01-13 11:50:33 SinglePassSamProgram Processed 3 000 000 records. Elapsed time: 00:00:22s. Time for last 1 000 000: 7s. Last read position: 1:84 726 212 INFO 2016-01-13 11:50:39 SinglePassSamProgram Processed 4 000 000 records. Elapsed time: 00:00:28s. Time for last 1 000 000: 6s. Last read position: 1:131 258 270 INFO 2016-01-13 11:50:46 SinglePassSamProgram Processed 5 000 000 records. Elapsed time: 00:00:35s. Time for last 1 000 000: 6s. Last read position: 1:162 699 014 INFO 2016-01-13 11:50:53 SinglePassSamProgram Processed 6 000 000 records. Elapsed time: 00:00:42s. Time for last 1 000 000: 6s. Last read position: 1:180 423 776 INFO 2016-01-13 11:51:00 SinglePassSamProgram Processed 7 000 000 records. Elapsed time: 00:00:49s. Time for last 1 000 000: 7s. Last read position: 10:40 288 148 INFO 2016-01-13 11:51:07 SinglePassSamProgram Processed 8 000 000 records. Elapsed time: 00:00:56s. Time for last 1 000 000: 6s. Last read position: 10:60 300 791 INFO 2016-01-13 11:51:14 SinglePassSamProgram Processed 9 000 000 records. Elapsed time: 00:01:03s. Time for last 1 000 000: 6s. Last read position: 10:78 194 008 INFO 2016-01-13 11:51:21 SinglePassSamProgram Processed 10 000 000 records. Elapsed time: 00:01:10s. Time for last 1 000 000: 7s. Last read position: 10:81 369 411 INFO 2016-01-13 11:51:27 SinglePassSamProgram Processed 11 000 000 records. Elapsed time: 00:01:17s. Time for last 1 000 000: 6s. Last read position: 10:117 277 576 INFO 2016-01-13 11:51:33 SinglePassSamProgram Processed 12 000 000 records. Elapsed time: 00:01:23s. Time for last 1 000 000: 6s. Last read position: 10:117 282 106 INFO 2016-01-13 11:51:40 SinglePassSamProgram Processed 13 000 000 records. Elapsed time: 00:01:30s. Time for last 1 000 000: 6s. Last read position: 10:128 492 616 INFO 2016-01-13 11:51:47 SinglePassSamProgram Processed 14 000 000 records. Elapsed time: 00:01:37s. Time for last 1 000 000: 7s. Last read position: 11:20 077 246 INFO 2016-01-13 11:51:54 SinglePassSamProgram Processed 15 000 000 records. Elapsed time: 00:01:43s. Time for last 1 000 000: 6s. Last read position: 11:50 284 406 INFO 2016-01-13 11:52:00 SinglePassSamProgram Processed 16 000 000 records. Elapsed time: 00:01:49s. Time for last 1 000 000: 6s. Last read position: 11:62 594 925 INFO 2016-01-13 11:52:07 SinglePassSamProgram Processed 17 000 000 records. Elapsed time: 00:01:56s. Time for last 1 000 000: 7s. Last read position: 11:75 576 108 INFO 2016-01-13 11:52:14 SinglePassSamProgram Processed 18 000 000 records. Elapsed time: 00:02:04s. Time for last 1 000 000: 7s. Last read position: 11:86 815 079 INFO 2016-01-13 11:52:21 SinglePassSamProgram Processed 19 000 000 records. Elapsed time: 00:02:10s. Time for last 1 000 000: 6s. Last read position: 11:100 781 869 INFO 2016-01-13 11:52:28 SinglePassSamProgram Processed 20 000 000 records. Elapsed time: 00:02:17s. Time for last 1 000 000: 7s. Last read position: 11:109 668 732 INFO 2016-01-13 11:52:35 SinglePassSamProgram Processed 21 000 000 records. Elapsed time: 00:02:24s. Time for last 1 000 000: 6s. Last read position: 11:120 347 082 INFO 2016-01-13 11:52:42 SinglePassSamProgram Processed 22 000 000 records. Elapsed time: 00:02:31s. Time for last 1 000 000: 6s. Last read position: 12:32 851 067 INFO 2016-01-13 11:52:48 SinglePassSamProgram Processed 23 000 000 records. Elapsed time: 00:02:38s. Time for last 1 000 000: 6s. Last read position: 12:86 883 769 INFO 2016-01-13 11:52:55 SinglePassSamProgram Processed 24 000 000 records. Elapsed time: 00:02:45s. Time for last 1 000 000: 6s. Last read position: 12:113 153 306 INFO 2016-01-13 11:53:03 SinglePassSamProgram Processed 25 000 000 records. Elapsed time: 00:02:52s. Time for last 1 000 000: 7s. Last read position: 13:52 611 052 INFO 2016-01-13 11:53:09 SinglePassSamProgram Processed 26 000 000 records. Elapsed time: 00:02:58s. Time for last 1 000 000: 6s. Last read position: 13:74 720 979 INFO 2016-01-13 11:53:16 SinglePassSamProgram Processed 27 000 000 records. Elapsed time: 00:03:05s. Time for last 1 000 000: 6s. Last read position: 14:14 116 451 INFO 2016-01-13 11:53:23 SinglePassSamProgram Processed 28 000 000 records. Elapsed time: 00:03:12s. Time for last 1 000 000: 6s. Last read position: 14:45 597 948 INFO 2016-01-13 11:53:29 SinglePassSamProgram Processed 29 000 000 records. Elapsed time: 00:03:18s. Time for last 1 000 000: 6s. Last read position: 14:63 521 977 INFO 2016-01-13 11:53:36 SinglePassSamProgram Processed 30 000 000 records. Elapsed time: 00:03:25s. Time for last 1 000 000: 6s. Last read position: 15:5 116 661 INFO 2016-01-13 11:53:43 SinglePassSamProgram Processed 31 000 000 records. Elapsed time: 00:03:32s. Time for last 1 000 000: 6s. Last read position: 15:73 809 694 INFO 2016-01-13 11:53:50 SinglePassSamProgram Processed 32 000 000 records. Elapsed time: 00:03:39s. Time for last 1 000 000: 6s. Last read position: 15:79 534 754 INFO 2016-01-13 11:53:57 SinglePassSamProgram Processed 33 000 000 records. Elapsed time: 00:03:46s. Time for last 1 000 000: 7s. Last read position: 15:98 931 497 INFO 2016-01-13 11:54:04 SinglePassSamProgram Processed 34 000 000 records. Elapsed time: 00:03:53s. Time for last 1 000 000: 6s. Last read position: 16:5 008 851 INFO 2016-01-13 11:54:11 SinglePassSamProgram Processed 35 000 000 records. Elapsed time: 00:04:00s. Time for last 1 000 000: 6s. Last read position: 16:35 022 587 INFO 2016-01-13 11:54:18 SinglePassSamProgram Processed 36 000 000 records. Elapsed time: 00:04:08s. Time for last 1 000 000: 7s. Last read position: 17:6 132 340 INFO 2016-01-13 11:54:25 SinglePassSamProgram Processed 37 000 000 records. Elapsed time: 00:04:14s. Time for last 1 000 000: 6s. Last read position: 17:26 646 052 INFO 2016-01-13 11:54:32 SinglePassSamProgram Processed 38 000 000 records. Elapsed time: 00:04:21s. Time for last 1 000 000: 6s. Last read position: 17:33 952 419 INFO 2016-01-13 11:54:38 SinglePassSamProgram Processed 39 000 000 records. Elapsed time: 00:04:28s. Time for last 1 000 000: 6s. Last read position: 17:39 847 693 INFO 2016-01-13 11:54:46 SinglePassSamProgram Processed 40 000 000 records. Elapsed time: 00:04:35s. Time for last 1 000 000: 7s. Last read position: 17:70 974 194 INFO 2016-01-13 11:54:53 SinglePassSamProgram Processed 41 000 000 records. Elapsed time: 00:04:42s. Time for last 1 000 000: 7s. Last read position: 18:34 349 659 INFO 2016-01-13 11:54:59 SinglePassSamProgram Processed 42 000 000 records. Elapsed time: 00:04:49s. Time for last 1 000 000: 6s. Last read position: 18:65 809 480 INFO 2016-01-13 11:55:06 SinglePassSamProgram Processed 43 000 000 records. Elapsed time: 00:04:56s. Time for last 1 000 000: 6s. Last read position: 19:4 316 395 INFO 2016-01-13 11:55:14 SinglePassSamProgram Processed 44 000 000 records. Elapsed time: 00:05:03s. Time for last 1 000 000: 7s. Last read position: 19:7 215 445 INFO 2016-01-13 11:55:20 SinglePassSamProgram Processed 45 000 000 records. Elapsed time: 00:05:09s. Time for last 1 000 000: 6s. Last read position: 19:21 276 603 INFO 2016-01-13 11:55:27 SinglePassSamProgram Processed 46 000 000 records. Elapsed time: 00:05:16s. Time for last 1 000 000: 6s. Last read position: 19:56 439 778 INFO 2016-01-13 11:55:34 SinglePassSamProgram Processed 47 000 000 records. Elapsed time: 00:05:23s. Time for last 1 000 000: 6s. Last read position: 2:24 405 695 INFO 2016-01-13 11:55:41 SinglePassSamProgram Processed 48 000 000 records. Elapsed time: 00:05:30s. Time for last 1 000 000: 7s. Last read position: 2:34 810 968 INFO 2016-01-13 11:55:48 SinglePassSamProgram Processed 49 000 000 records. Elapsed time: 00:05:37s. Time for last 1 000 000: 6s. Last read position: 2:79 662 361 INFO 2016-01-13 11:55:54 SinglePassSamProgram Processed 50 000 000 records. Elapsed time: 00:05:43s. Time for last 1 000 000: 6s. Last read position: 2:120 721 272 INFO 2016-01-13 11:56:01 SinglePassSamProgram Processed 51 000 000 records. Elapsed time: 00:05:50s. Time for last 1 000 000: 6s. Last read position: 2:148 872 896 INFO 2016-01-13 11:56:08 SinglePassSamProgram Processed 52 000 000 records. Elapsed time: 00:05:57s. Time for last 1 000 000: 6s. Last read position: 2:162 934 652 INFO 2016-01-13 11:56:15 SinglePassSamProgram Processed 53 000 000 records. Elapsed time: 00:06:04s. Time for last 1 000 000: 6s. Last read position: 2:178 035 820 INFO 2016-01-13 11:56:21 SinglePassSamProgram Processed 54 000 000 records. Elapsed time: 00:06:11s. Time for last 1 000 000: 6s. Last read position: 3:65 380 183 INFO 2016-01-13 11:56:28 SinglePassSamProgram Processed 55 000 000 records. Elapsed time: 00:06:18s. Time for last 1 000 000: 6s. Last read position: 3:90 605 083 INFO 2016-01-13 11:56:35 SinglePassSamProgram Processed 56 000 000 records. Elapsed time: 00:06:25s. Time for last 1 000 000: 6s. Last read position: 3:103 044 640 INFO 2016-01-13 11:56:42 SinglePassSamProgram Processed 57 000 000 records. Elapsed time: 00:06:31s. Time for last 1 000 000: 6s. Last read position: 3:142 567 677 INFO 2016-01-13 11:56:49 SinglePassSamProgram Processed 58 000 000 records. Elapsed time: 00:06:38s. Time for last 1 000 000: 7s. Last read position: 4:43 549 937 INFO 2016-01-13 11:56:56 SinglePassSamProgram Processed 59 000 000 records. Elapsed time: 00:06:45s. Time for last 1 000 000: 6s. Last read position: 4:103 564 637 INFO 2016-01-13 11:57:02 SinglePassSamProgram Processed 60 000 000 records. Elapsed time: 00:06:51s. Time for last 1 000 000: 6s. Last read position: 4:126 232 636 INFO 2016-01-13 11:57:09 SinglePassSamProgram Processed 61 000 000 records. Elapsed time: 00:06:58s. Time for last 1 000 000: 6s. Last read position: 4:134 161 336 INFO 2016-01-13 11:57:16 SinglePassSamProgram Processed 62 000 000 records. Elapsed time: 00:07:05s. Time for last 1 000 000: 6s. Last read position: 4:145 213 984 INFO 2016-01-13 11:57:22 SinglePassSamProgram Processed 63 000 000 records. Elapsed time: 00:07:12s. Time for last 1 000 000: 6s. Last read position: 5:5 783 143 INFO 2016-01-13 11:57:29 SinglePassSamProgram Processed 64 000 000 records. Elapsed time: 00:07:18s. Time for last 1 000 000: 6s. Last read position: 5:44 176 835 INFO 2016-01-13 11:57:36 SinglePassSamProgram Processed 65 000 000 records. Elapsed time: 00:07:25s. Time for last 1 000 000: 6s. Last read position: 5:107 903 709 INFO 2016-01-13 11:57:43 SinglePassSamProgram Processed 66 000 000 records. Elapsed time: 00:07:32s. Time for last 1 000 000: 6s. Last read position: 5:121 372 232 INFO 2016-01-13 11:57:49 SinglePassSamProgram Processed 67 000 000 records. Elapsed time: 00:07:38s. Time for last 1 000 000: 5s. Last read position: 5:134 620 184 INFO 2016-01-13 11:57:56 SinglePassSamProgram Processed 68 000 000 records. Elapsed time: 00:07:45s. Time for last 1 000 000: 7s. Last read position: 5:142 903 802 INFO 2016-01-13 11:58:03 SinglePassSamProgram Processed 69 000 000 records. Elapsed time: 00:07:52s. Time for last 1 000 000: 7s. Last read position: 5:151 643 744 INFO 2016-01-13 11:58:10 SinglePassSamProgram Processed 70 000 000 records. Elapsed time: 00:07:59s. Time for last 1 000 000: 7s. Last read position: 6:55 060 998 INFO 2016-01-13 11:58:17 SinglePassSamProgram Processed 71 000 000 records. Elapsed time: 00:08:06s. Time for last 1 000 000: 6s. Last read position: 6:97 221 731 INFO 2016-01-13 11:58:24 SinglePassSamProgram Processed 72 000 000 records. Elapsed time: 00:08:13s. Time for last 1 000 000: 6s. Last read position: 6:124 728 807 INFO 2016-01-13 11:58:31 SinglePassSamProgram Processed 73 000 000 records. Elapsed time: 00:08:20s. Time for last 1 000 000: 7s. Last read position: 7:3 650 845 INFO 2016-01-13 11:58:38 SinglePassSamProgram Processed 74 000 000 records. Elapsed time: 00:08:27s. Time for last 1 000 000: 6s. Last read position: 7:19 572 846 INFO 2016-01-13 11:58:44 SinglePassSamProgram Processed 75 000 000 records. Elapsed time: 00:08:34s. Time for last 1 000 000: 6s. Last read position: 7:29 149 560 INFO 2016-01-13 11:58:51 SinglePassSamProgram Processed 76 000 000 records. Elapsed time: 00:08:41s. Time for last 1 000 000: 6s. Last read position: 7:45 458 060 INFO 2016-01-13 11:58:58 SinglePassSamProgram Processed 77 000 000 records. Elapsed time: 00:08:47s. Time for last 1 000 000: 6s. Last read position: 7:80 735 551 INFO 2016-01-13 11:59:05 SinglePassSamProgram Processed 78 000 000 records. Elapsed time: 00:08:54s. Time for last 1 000 000: 6s. Last read position: 7:104 465 010 INFO 2016-01-13 11:59:12 SinglePassSamProgram Processed 79 000 000 records. Elapsed time: 00:09:01s. Time for last 1 000 000: 6s. Last read position: 7:126 699 913 INFO 2016-01-13 11:59:19 SinglePassSamProgram Processed 80 000 000 records. Elapsed time: 00:09:08s. Time for last 1 000 000: 7s. Last read position: 7:135 684 619 INFO 2016-01-13 11:59:26 SinglePassSamProgram Processed 81 000 000 records. Elapsed time: 00:09:15s. Time for last 1 000 000: 7s. Last read position: 8:13 587 009 INFO 2016-01-13 11:59:32 SinglePassSamProgram Processed 82 000 000 records. Elapsed time: 00:09:22s. Time for last 1 000 000: 6s. Last read position: 8:70 029 074 INFO 2016-01-13 11:59:39 SinglePassSamProgram Processed 83 000 000 records. Elapsed time: 00:09:29s. Time for last 1 000 000: 6s. Last read position: 8:83 725 864 INFO 2016-01-13 11:59:46 SinglePassSamProgram Processed 84 000 000 records. Elapsed time: 00:09:35s. Time for last 1 000 000: 6s. Last read position: 8:105 525 578 INFO 2016-01-13 11:59:53 SinglePassSamProgram Processed 85 000 000 records. Elapsed time: 00:09:43s. Time for last 1 000 000: 7s. Last read position: 8:122 699 229 INFO 2016-01-13 12:00:00 SinglePassSamProgram Processed 86 000 000 records. Elapsed time: 00:09:50s. Time for last 1 000 000: 7s. Last read position: 9:35 226 343 INFO 2016-01-13 12:00:07 SinglePassSamProgram Processed 87 000 000 records. Elapsed time: 00:09:56s. Time for last 1 000 000: 6s. Last read position: 9:57 627 423 INFO 2016-01-13 12:00:14 SinglePassSamProgram Processed 88 000 000 records. Elapsed time: 00:10:03s. Time for last 1 000 000: 6s. Last read position: 9:70 003 456 INFO 2016-01-13 12:00:20 SinglePassSamProgram Processed 89 000 000 records. Elapsed time: 00:10:10s. Time for last 1 000 000: 6s. Last read position: 9:96 896 206 INFO 2016-01-13 12:00:27 SinglePassSamProgram Processed 90 000 000 records. Elapsed time: 00:10:17s. Time for last 1 000 000: 7s. Last read position: 9:114 747 811 INFO 2016-01-13 12:00:34 SinglePassSamProgram Processed 91 000 000 records. Elapsed time: 00:10:24s. Time for last 1 000 000: 6s. Last read position: MT:5 758 INFO 2016-01-13 12:00:38 SinglePassSamProgram Processed 92 000 000 records. Elapsed time: 00:10:27s. Time for last 1 000 000: 3s. Last read position: MT:8 095 INFO 2016-01-13 12:00:43 SinglePassSamProgram Processed 93 000 000 records. Elapsed time: 00:10:32s. Time for last 1 000 000: 5s. Last read position: X:7 634 529 INFO 2016-01-13 12:00:50 SinglePassSamProgram Processed 94 000 000 records. Elapsed time: 00:10:39s. Time for last 1 000 000: 6s. Last read position: X:73 896 041 INFO 2016-01-13 12:00:57 SinglePassSamProgram Processed 95 000 000 records. Elapsed time: 00:10:46s. Time for last 1 000 000: 6s. Last read position: X:101 683 503 INFO 2016-01-13 12:01:04 SinglePassSamProgram Processed 96 000 000 records. Elapsed time: 00:10:53s. Time for last 1 000 000: 6s. Last read position: X:167 207 520 INFO 2016-01-13 12:01:13 SinglePassSamProgram Processed 97 000 000 records. Elapsed time: 00:11:02s. Time for last 1 000 000: 9s. Last read position: */* INFO 2016-01-13 12:01:24 SinglePassSamProgram Processed 98 000 000 records. Elapsed time: 00:11:13s. Time for last 1 000 000: 11s. Last read position: */* INFO 2016-01-13 12:01:35 SinglePassSamProgram Processed 99 000 000 records. Elapsed time: 00:11:24s. Time for last 1 000 000: 11s. Last read position: */* INFO 2016-01-13 12:01:37 RExecutor Executing R script via command: Rscript /scratch/script9078635170208800759.R metrics/ID.base_distribution_by_cycle_metrics metrics/ID.base_distribution_by_cycle.pdf sorted.mdup.bam ERROR 2016-01-13 12:01:39 ProcessExecutor Error in FUN(X[[i]], ...) : ERROR 2016-01-13 12:01:39 ProcessExecutor only defined on a data frame with all numeric variables ERROR 2016-01-13 12:01:39 ProcessExecutor Calls: plot ... plot.default -> xy.coords -> Summary.data.frame -> lapply -> FUN ERROR 2016-01-13 12:01:39 ProcessExecutor Exécution arrêtée [Wed Jan 13 12:01:39 EST 2016] picard.analysis.CollectMultipleMetrics done. Elapsed time: 11,48 minutes. Runtime.totalMemory()=761266176 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" picard.PicardException: R script nucleotideDistributionByCycle.R failed with return code 1 at picard.analysis.CollectBaseDistributionByCycle.finish(CollectBaseDistributionByCycle.java:80) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:136) at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:144) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185) at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:125) at picard.analysis.CollectMultipleMetrics.main(CollectMultipleMetrics.java:108)

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Have you run it successfully previously (suggesting a problem with this batch of data) or is it the first time you try to run it?

  • emixaMemixaM CanadaMember

    Yes actually, I apologize not editing this question sooner (problem was resolved recently).

    The issue was in my job scheduler (Moab). It was loading R but was missing bits of information. By loading directly in the submission script, not by passing arguments to the scheduler, Picard ran very smoothly, with no errors whatsoever. So not a Picard bug, more like an environment-dependant bug).

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