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Picard CollectMultipleMetrics error in R script

emixaMemixaM CanadaMember Posts: 33

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 Posts: 11,414 admin

    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?

    Geraldine Van der Auwera, PhD

  • emixaMemixaM CanadaMember Posts: 33

    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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