Error found with v2.4-9 not if using v2.3-9

bigeybigey Montpellier, FranceMember

Problem with GATK v2.4-9 PrintReads

Look at the log below:

INFO  12:28:00,176 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  12:28:00,178 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.4-9-g532efad, Compiled 2013/03/19 07:35:36 
INFO  12:28:00,178 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  12:28:00,178 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  12:28:00,181 HelpFormatter - Program Args: -T PrintReads -R /home/bigey/VinVoile/RefGenome/SACE_s288c_all_chromosomes_numeric_2011-05-16.fasta -I ../IndelRealigner/40.IndelRealigner.bam --num_threads 1 -BQSR 40.recalibration.gpr --out 40.BaseQualityRecalibration.bam 
INFO  12:28:00,181 HelpFormatter - Date/Time: 2013/04/24 12:28:00 
INFO  12:28:00,181 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  12:28:00,181 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  12:28:00,246 GenomeAnalysisEngine - Strictness is SILENT 
INFO  12:28:00,673 ContextCovariate -       Context sizes: base substitution model 2, indel substitution model 3 
INFO  12:28:00,726 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  12:28:00,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  12:28:00,743 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  12:28:00,790 GenomeAnalysisEngine - Creating shard strategy for 1 BAM files 
INFO  12:28:00,794 GenomeAnalysisEngine - Done creating shard strategy 
INFO  12:28:00,794 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  12:28:00,794 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining 
INFO  12:28:00,800 ReadShardBalancer$1 - Loading BAM index data for next contig 
INFO  12:28:00,800 ReadShardBalancer$1 - Done loading BAM index data for next contig 
INFO  12:28:31,059 ProgressMeter -    chr01:107790        4.00e+05   30.0 s       75.0 s      0.9%        56.4 m    55.9 m 
INFO  12:29:01,060 ProgressMeter -    chr01:225642        8.00e+05   60.0 s       75.0 s      1.9%        53.9 m    52.9 m 
INFO  12:29:31,596 ProgressMeter -     chr02:90412        1.30e+06   90.0 s       70.0 s      2.6%        56.9 m    55.4 m 
INFO  12:30:01,626 ProgressMeter -    chr02:216912        1.70e+06  120.0 s       71.0 s      3.7%        54.4 m    52.4 m 
INFO  12:30:41,627 ProgressMeter -    chr02:425243        2.30e+06    2.7 m       70.0 s      5.4%        49.5 m    46.8 m 
INFO  12:31:21,628 ProgressMeter -    chr02:587712        2.90e+06    3.3 m       69.0 s      6.7%        49.6 m    46.2 m 
INFO  12:31:51,628 ProgressMeter -    chr02:711040        3.30e+06    3.8 m       70.0 s      7.7%        49.5 m    45.7 m 
INFO  12:32:21,629 ProgressMeter -    chr02:802525        3.80e+06    4.3 m       68.0 s      8.5%        51.0 m    46.7 m 
INFO  12:33:01,630 ProgressMeter -    chr03:113540        4.44e+06    5.0 m       67.0 s      9.5%        52.6 m    47.6 m 
INFO  12:33:42,221 ProgressMeter -    chr03:276446        5.04e+06    5.7 m       67.0 s     10.9%        52.4 m    46.7 m 
INFO  12:34:12,222 ProgressMeter -     chr04:72182        5.47e+06    6.2 m       67.0 s     11.8%        52.5 m    46.3 m 
INFO  12:34:52,233 ProgressMeter -    chr04:239901        6.07e+06    6.9 m       67.0 s     13.2%        52.1 m    45.2 m 
INFO  12:35:22,233 ProgressMeter -    chr04:370095        6.57e+06    7.4 m       67.0 s     14.2%        51.7 m    44.3 m 
INFO  12:35:52,234 ProgressMeter -    chr04:528963        7.07e+06    7.9 m       66.0 s     15.5%        50.5 m    42.7 m 
INFO  12:36:32,235 ProgressMeter -    chr04:748019        7.77e+06    8.5 m       65.0 s     17.3%        49.1 m    40.6 m 
INFO  12:37:12,236 ProgressMeter -    chr04:922953        8.37e+06    9.2 m       65.0 s     18.8%        48.9 m    39.7 m 
INFO  12:37:42,236 ProgressMeter -   chr04:1053992        8.77e+06    9.7 m       66.0 s     19.8%        48.8 m    39.1 m 
INFO  12:38:12,237 ProgressMeter -   chr04:1196317        9.27e+06   10.2 m       65.0 s     21.0%        48.5 m    38.3 m 
INFO  12:38:52,238 ProgressMeter -   chr04:1369332        9.87e+06   10.9 m       66.0 s     22.4%        48.4 m    37.5 m 
INFO  12:39:22,238 ProgressMeter -   chr04:1495234        1.04e+07   11.4 m       65.0 s     23.5%        48.4 m    37.0 m 
INFO  12:39:52,239 ProgressMeter -     chr05:89034        1.09e+07   11.9 m       65.0 s     24.5%        48.4 m    36.5 m 
INFO  12:40:32,409 ProgressMeter -    chr05:316377        1.15e+07   12.5 m       65.0 s     26.4%        47.5 m    34.9 m 
INFO  12:41:02,432 ProgressMeter -    chr05:467016        1.20e+07   13.0 m       65.0 s     27.6%        47.1 m    34.1 m 
INFO  12:41:42,433 ProgressMeter -     chr06:60550        1.27e+07   13.7 m       64.0 s     29.0%        47.2 m    33.5 m 
INFO  12:42:12,433 ProgressMeter -    chr06:213631        1.31e+07   14.2 m       65.0 s     30.3%        46.8 m    32.7 m 
INFO  12:42:42,434 ProgressMeter -     chr07:39164        1.37e+07   14.7 m       64.0 s     31.1%        47.3 m    32.6 m 
INFO  12:43:22,435 ProgressMeter -    chr07:219007        1.43e+07   15.4 m       64.0 s     32.5%        47.2 m    31.8 m 
INFO  12:43:52,435 ProgressMeter -    chr07:342472        1.48e+07   15.9 m       64.0 s     33.6%        47.2 m    31.4 m 
INFO  12:44:22,436 ProgressMeter -    chr07:493648        1.53e+07   16.4 m       64.0 s     34.8%        47.0 m    30.6 m 
INFO  12:44:52,437 ProgressMeter -    chr07:672762        1.58e+07   16.9 m       64.0 s     36.3%        46.5 m    29.6 m 
INFO  12:45:32,438 ProgressMeter -    chr07:900322        1.65e+07   17.5 m       63.0 s     38.1%        45.9 m    28.4 m 
INFO  12:46:03,148 ProgressMeter -   chr07:1037661        1.69e+07   18.0 m       64.0 s     39.3%        45.9 m    27.9 m 
INFO  12:46:33,149 ProgressMeter -     chr08:93032        1.73e+07   18.5 m       64.0 s     40.5%        45.8 m    27.3 m 
INFO  12:47:03,781 ProgressMeter -    chr08:235180        1.78e+07   19.0 m       64.0 s     41.6%        45.7 m    26.7 m 
INFO  12:47:33,796 ProgressMeter -    chr08:353516        1.83e+07   19.6 m       64.0 s     42.6%        45.9 m    26.3 m 
INFO  12:48:03,796 ProgressMeter -    chr08:474566        1.88e+07   20.1 m       63.0 s     43.6%        46.0 m    25.9 m 
INFO  12:48:33,797 ProgressMeter -     chr09:44787        1.94e+07   20.6 m       63.0 s     44.7%        46.0 m    25.4 m 
INFO  12:49:03,798 ProgressMeter -    chr09:168676        1.98e+07   21.1 m       63.0 s     45.7%        46.0 m    25.0 m 
INFO  12:49:43,799 ProgressMeter -    chr09:370745        2.05e+07   21.7 m       63.0 s     47.4%        45.8 m    24.1 m 
INFO  12:50:13,825 ProgressMeter -     chr10:58236        2.10e+07   22.2 m       63.0 s     48.4%        45.9 m    23.7 m 
INFO  12:50:53,826 ProgressMeter -    chr10:241411        2.16e+07   22.9 m       63.0 s     49.9%        45.8 m    22.9 m 
INFO  12:51:20,776 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.4-9-g532efad): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: There is no space left on the device, so writing failed
##### ERROR ------------------------------------------------------------------------------------------
ERROR: PrintReads
EXIT: 1
Killing process ./gatk_BaseQualityRecalibration_VinVoile.sh
kill 10106... ok
kill 10112... ok
kill 10157... 

The process generates enormous quantity of temporary files in /temp:

-rw-rw-r-- 1 bigey   bigey   230744134 avril 24 12:28 sortingcollection.9024565749384412155.tmp
-rw-rw-r-- 1 bigey   bigey   219511537 avril 24 12:28 sortingcollection.8973503823555804377.tmp
-rw-rw-r-- 1 bigey   bigey   231792190 avril 24 12:29 sortingcollection.7216091881937794353.tmp
-rw-rw-r-- 1 bigey   bigey   219118116 avril 24 12:29 sortingcollection.6679446087497261536.tmp
-rw-rw-r-- 1 bigey   bigey   219542120 avril 24 12:29 sortingcollection.8006535209972409188.tmp
-rw-rw-r-- 1 bigey   bigey   229852260 avril 24 12:29 sortingcollection.3246683484034351926.tmp
-rw-rw-r-- 1 bigey   bigey   219839674 avril 24 12:30 sortingcollection.1199958687270672912.tmp

...skip...

Over 10GB and keep growing until /tmp is full and GATK -T PrintReads exit:

$ du -ch /tmp | grep total
17G     total

Bam files are created but empty. Note that sufficient space is avalaible in the current directory.

No problem with GATK v2.3-9

Everything is ok if running the same processing using GATK v2.3-9. Output bam(s) are generated on the fly in the current directory...

No temporary files in /temp:

$ du -ch /tmp | grep total
132K    total

Log of the complete process below:

INFO  14:34:27,043 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:34:27,044 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-ge5ebf34, Compiled 2013/01/11 22:43:14 
INFO  14:34:27,044 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  14:34:27,045 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  14:34:27,048 HelpFormatter - Program Args: -T PrintReads -R /home/bigey/VinVoile/RefGenome/SACE_s288c_all_chromosomes_numeric_2011-05-16.fasta -I ../IndelRealigner/40.IndelRealigner.bam --num_threads 1 -BQSR 40.recalibration.gpr --out 40.BaseQualityRecalibration.bam 
INFO  14:34:27,048 HelpFormatter - Date/Time: 2013/04/23 14:34:27 
INFO  14:34:27,048 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:34:27,048 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  14:34:27,576 ContextCovariate -       Context sizes: base substitution model 2, indel substitution model 3 
INFO  14:34:27,578 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 3] 
INFO  14:34:27,578 NestedIntegerArray - Pre-allocating first 2 dimensions 
INFO  14:34:27,578 NestedIntegerArray - Done pre-allocating first 2 dimensions 
INFO  14:34:27,578 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 3] 
INFO  14:34:27,578 NestedIntegerArray - Pre-allocating first 2 dimensions 
INFO  14:34:27,579 NestedIntegerArray - Done pre-allocating first 2 dimensions 
INFO  14:34:27,579 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1012, 3] 
INFO  14:34:27,580 NestedIntegerArray - Pre-allocating first 2 dimensions 
INFO  14:34:27,580 NestedIntegerArray - Done pre-allocating first 2 dimensions 
INFO  14:34:27,580 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1002, 3] 
INFO  14:34:27,580 NestedIntegerArray - Pre-allocating first 2 dimensions 
INFO  14:34:27,580 NestedIntegerArray - Done pre-allocating first 2 dimensions 
INFO  14:34:27,629 GenomeAnalysisEngine - Strictness is SILENT 
INFO  14:34:27,710 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  14:34:27,716 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  14:34:27,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 
INFO  14:34:27,751 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  14:34:27,751 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining 
INFO  14:34:27,786 ReadShardBalancer$1 - Loading BAM index data for next contig 
INFO  14:34:27,788 ReadShardBalancer$1 - Done loading BAM index data for next contig 
INFO  14:34:57,755 ProgressMeter -     chr01:48732        4.40e+05   30.0 s       68.1 s      0.4%         2.1 h     2.1 h 
INFO  14:35:27,756 ProgressMeter -    chr01:105016        9.11e+05   60.0 s       65.9 s      0.9%       115.8 m   114.8 m 
INFO  14:35:57,757 ProgressMeter -    chr01:171762        1.39e+06   90.0 s       64.7 s      1.4%       106.2 m   104.7 m 
INFO  14:36:27,758 ProgressMeter -      chr02:6914        1.87e+06    2.0 m       64.3 s      1.9%       102.6 m   100.6 m 
INFO  14:37:07,759 ProgressMeter -     chr02:66548        2.49e+06    2.7 m       64.3 s      2.4%       109.3 m   106.6 m 
INFO  14:37:37,760 ProgressMeter -    chr02:131769        2.95e+06    3.2 m       64.5 s      3.0%       106.4 m   103.2 m 
INFO  14:38:17,761 ProgressMeter -    chr02:240845        3.57e+06    3.8 m       64.5 s      3.9%        99.0 m    95.2 m 
INFO  14:38:47,762 ProgressMeter -    chr02:329251        4.04e+06    4.3 m       64.4 s      4.6%        94.2 m    89.9 m 
INFO  14:39:17,762 ProgressMeter -    chr02:409396        4.51e+06    4.8 m       64.3 s      5.3%        91.9 m    87.1 m 
INFO  14:39:47,763 ProgressMeter -    chr02:482158        4.97e+06    5.3 m       64.4 s      5.9%        91.1 m    85.7 m 
INFO  14:40:27,764 ProgressMeter -    chr02:580208        5.59e+06    6.0 m       64.4 s      6.7%        90.1 m    84.1 m 
INFO  14:41:07,764 ProgressMeter -    chr02:674955        6.20e+06    6.7 m       64.5 s      7.4%        89.6 m    82.9 m 
INFO  14:41:37,765 ProgressMeter -    chr02:742044        6.67e+06    7.2 m       64.5 s      8.0%        89.7 m    82.5 m 
INFO  14:42:07,766 ProgressMeter -    chr02:796735        7.14e+06    7.7 m       64.4 s      8.4%        90.8 m    83.1 m 
INFO  14:42:47,767 ProgressMeter -     chr03:17233        7.76e+06    8.3 m       64.4 s      8.7%        95.6 m    87.2 m 
INFO  14:43:17,767 ProgressMeter -     chr03:70771        8.22e+06    8.8 m       64.5 s      9.2%        96.4 m    87.6 m 
INFO  14:43:47,768 ProgressMeter -    chr03:142899        8.69e+06    9.3 m       64.4 s      9.8%        95.7 m    86.4 m 
INFO  14:44:27,769 ProgressMeter -    chr03:236520        9.30e+06   10.0 m       64.5 s     10.5%        95.0 m    85.0 m 
INFO  14:45:07,769 ProgressMeter -    chr03:307397        9.93e+06   10.7 m       64.4 s     11.1%        96.1 m    85.4 m 
INFO  14:45:37,770 ProgressMeter -     chr04:57438        1.04e+07   11.2 m       64.4 s     11.7%        95.8 m    84.7 m 
INFO  14:46:07,771 ProgressMeter -    chr04:126159        1.09e+07   11.7 m       64.4 s     12.2%        95.5 m    83.8 m 
INFO  14:46:47,772 ProgressMeter -    chr04:217909        1.15e+07   12.3 m       64.4 s     13.0%        95.1 m    82.7 m 
INFO  14:47:17,772 ProgressMeter -    chr04:292138        1.20e+07   12.8 m       64.3 s     13.6%        94.5 m    81.6 m 
INFO  14:47:47,773 ProgressMeter -    chr04:371723        1.24e+07   13.3 m       64.4 s     14.2%        93.7 m    80.3 m 
INFO  14:48:27,774 ProgressMeter -    chr04:482317        1.31e+07   14.0 m       64.3 s     15.1%        92.4 m    78.4 m 
INFO  14:48:57,774 ProgressMeter -    chr04:566989        1.35e+07   14.5 m       64.4 s     15.8%        91.5 m    77.0 m 
INFO  14:49:27,775 ProgressMeter -    chr04:652084        1.40e+07   15.0 m       64.4 s     16.5%        90.7 m    75.7 m 
INFO  14:49:57,776 ProgressMeter -    chr04:726356        1.44e+07   15.5 m       64.5 s     17.2%        90.4 m    74.9 m 
INFO  14:50:37,777 ProgressMeter -    chr04:823751        1.50e+07   16.2 m       64.5 s     18.0%        90.0 m    73.9 m 
INFO  14:51:07,777 ProgressMeter -    chr04:900534        1.55e+07   16.7 m       64.6 s     18.6%        89.7 m    73.0 m 
INFO  14:51:37,778 ProgressMeter -    chr04:976221        1.60e+07   17.2 m       64.6 s     19.2%        89.4 m    72.2 m 
INFO  14:52:17,779 ProgressMeter -   chr04:1075082        1.66e+07   17.8 m       64.6 s     20.0%        89.1 m    71.2 m 
INFO  14:52:47,788 ProgressMeter -   chr04:1156525        1.70e+07   18.3 m       64.6 s     20.7%        88.6 m    70.3 m 
INFO  14:53:17,789 ProgressMeter -   chr04:1239588        1.75e+07   18.8 m       64.6 s     21.4%        88.1 m    69.3 m 
INFO  14:53:47,790 ProgressMeter -   chr04:1310429        1.80e+07   19.3 m       64.6 s     22.0%        88.1 m    68.7 m 
INFO  14:54:27,791 ProgressMeter -   chr04:1397193        1.86e+07   20.0 m       64.5 s     22.7%        88.2 m    68.2 m 
INFO  14:54:57,791 ProgressMeter -   chr04:1462402        1.91e+07   20.5 m       64.5 s     23.2%        88.3 m    67.8 m 
INFO  14:55:27,792 ProgressMeter -   chr04:1515912        1.95e+07   21.0 m       64.5 s     23.6%        88.8 m    67.8 m 
INFO  14:55:57,793 ProgressMeter -     chr05:37863        2.00e+07   21.5 m       64.5 s     24.1%        89.3 m    67.8 m 
INFO  14:56:37,793 ProgressMeter -    chr05:134175        2.06e+07   22.2 m       64.5 s     24.9%        89.1 m    66.9 m 
INFO  14:57:07,794 ProgressMeter -    chr05:213413        2.11e+07   22.7 m       64.5 s     25.5%        88.8 m    66.1 m 
INFO  14:57:37,795 ProgressMeter -    chr05:294177        2.16e+07   23.2 m       64.5 s     26.2%        88.4 m    65.3 m 
INFO  14:58:17,796 ProgressMeter -    chr05:394396        2.22e+07   23.8 m       64.4 s     27.0%        88.2 m    64.4 m 
INFO  14:58:47,796 ProgressMeter -    chr05:476926        2.27e+07   24.3 m       64.4 s     27.7%        87.9 m    63.5 m 
INFO  14:59:17,797 ProgressMeter -    chr05:540246        2.31e+07   24.8 m       64.4 s     28.2%        88.0 m    63.2 m 
INFO  14:59:47,798 ProgressMeter -      chr06:7481        2.36e+07   25.3 m       64.4 s     28.6%        88.6 m    63.3 m 
INFO  15:00:27,799 ProgressMeter -     chr06:70111        2.42e+07   26.0 m       64.4 s     29.1%        89.4 m    63.4 m 
INFO  15:00:57,799 ProgressMeter -    chr06:137989        2.47e+07   26.5 m       64.4 s     29.7%        89.4 m    62.9 m 
INFO  15:01:27,800 ProgressMeter -    chr06:206037        2.51e+07   27.0 m       64.4 s     30.2%        89.4 m    62.4 m 
INFO  15:02:07,801 ProgressMeter -      chr07:3183        2.58e+07   27.7 m       64.4 s     30.8%        89.9 m    62.3 m 
INFO  15:02:47,802 ProgressMeter -     chr07:75361        2.64e+07   28.3 m       64.4 s     31.4%        90.4 m    62.0 m 
INFO  15:03:17,802 ProgressMeter -    chr07:140480        2.69e+07   28.8 m       64.4 s     31.9%        90.4 m    61.6 m 
INFO  15:03:47,803 ProgressMeter -    chr07:215954        2.73e+07   29.3 m       64.4 s     32.5%        90.2 m    60.9 m 
INFO  15:04:27,804 ProgressMeter -    chr07:309412        2.79e+07   30.0 m       64.4 s     33.3%        90.1 m    60.1 m 
INFO  15:04:57,804 ProgressMeter -    chr07:388076        2.84e+07   30.5 m       64.5 s     33.9%        89.9 m    59.4 m 
INFO  15:05:27,805 ProgressMeter -    chr07:470201        2.89e+07   31.0 m       64.4 s     34.6%        89.6 m    58.6 m 
INFO  15:05:57,806 ProgressMeter -    chr07:558478        2.93e+07   31.5 m       64.4 s     35.3%        89.2 m    57.7 m 
INFO  15:06:37,806 ProgressMeter -    chr07:667170        3.00e+07   32.2 m       64.4 s     36.2%        88.8 m    56.6 m 
INFO  15:07:07,807 ProgressMeter -    chr07:750758        3.04e+07   32.7 m       64.4 s     36.9%        88.5 m    55.8 m 
INFO  15:07:37,808 ProgressMeter -    chr07:831620        3.09e+07   33.2 m       64.4 s     37.6%        88.3 m    55.1 m 
INFO  15:08:17,809 ProgressMeter -    chr07:930449        3.15e+07   33.8 m       64.4 s     38.4%        88.1 m    54.3 m 
INFO  15:08:47,809 ProgressMeter -   chr07:1002660        3.20e+07   34.3 m       64.4 s     39.0%        88.1 m    53.7 m 
INFO  15:09:17,810 ProgressMeter -   chr07:1059846        3.25e+07   34.8 m       64.4 s     39.5%        88.3 m    53.5 m 
INFO  15:09:57,811 ProgressMeter -     chr08:32443        3.31e+07   35.5 m       64.4 s     40.0%        88.8 m    53.3 m 
INFO  15:10:27,811 ProgressMeter -    chr08:107002        3.35e+07   36.0 m       64.4 s     40.6%        88.7 m    52.7 m 
INFO  15:10:57,812 ProgressMeter -    chr08:186235        3.40e+07   36.5 m       64.4 s     41.2%        88.5 m    52.0 m 
INFO  15:11:37,813 ProgressMeter -    chr08:291755        3.46e+07   37.2 m       64.4 s     42.1%        88.3 m    51.1 m 
INFO  15:12:07,813 ProgressMeter -    chr08:357439        3.51e+07   37.7 m       64.4 s     42.6%        88.3 m    50.7 m 
INFO  15:12:37,814 ProgressMeter -    chr08:428284        3.56e+07   38.2 m       64.4 s     43.2%        88.3 m    50.1 m 
INFO  15:13:17,815 ProgressMeter -    chr08:509757        3.62e+07   38.8 m       64.4 s     43.9%        88.5 m    49.6 m 
INFO  15:13:47,815 ProgressMeter -    chr08:558984        3.66e+07   39.3 m       64.4 s     44.3%        88.8 m    49.4 m 
INFO  15:14:17,816 ProgressMeter -     chr09:65117        3.71e+07   39.8 m       64.4 s     44.9%        88.8 m    48.9 m 
INFO  15:14:57,817 ProgressMeter -    chr09:155142        3.77e+07   40.5 m       64.4 s     45.6%        88.8 m    48.3 m 
INFO  15:15:27,817 ProgressMeter -    chr09:236980        3.82e+07   41.0 m       64.4 s     46.3%        88.6 m    47.6 m 
INFO  15:15:57,818 ProgressMeter -    chr09:312256        3.87e+07   41.5 m       64.4 s     46.9%        88.5 m    47.0 m 
INFO  15:16:27,819 ProgressMeter -    chr09:388004        3.91e+07   42.0 m       64.4 s     47.5%        88.4 m    46.4 m 
INFO  15:17:07,819 ProgressMeter -     chr10:35414        3.97e+07   42.7 m       64.4 s     48.2%        88.4 m    45.8 m 
INFO  15:17:37,820 ProgressMeter -    chr10:100511        4.02e+07   43.2 m       64.4 s     48.8%        88.5 m    45.3 m 
INFO  15:18:07,821 ProgressMeter -    chr10:171333        4.07e+07   43.7 m       64.4 s     49.4%        88.5 m    44.8 m 
INFO  15:18:37,822 ProgressMeter -    chr10:250368        4.11e+07   44.2 m       64.4 s     50.0%        88.3 m    44.2 m 
INFO  15:19:17,823 ProgressMeter -    chr10:343118        4.17e+07   44.8 m       64.4 s     50.8%        88.3 m    43.5 m 
INFO  15:19:57,824 ProgressMeter -    chr10:449972        4.24e+07   45.5 m       64.4 s     51.7%        88.1 m    42.6 m 
INFO  15:20:27,824 ProgressMeter -    chr10:537165        4.28e+07   46.0 m       64.4 s     52.4%        87.8 m    41.8 m 
INFO  15:20:57,825 ProgressMeter -    chr10:609512        4.33e+07   46.5 m       64.5 s     53.0%        87.8 m    41.3 m 
INFO  15:21:37,826 ProgressMeter -    chr10:694516        4.39e+07   47.2 m       64.5 s     53.7%        87.9 m    40.7 m 
INFO  15:22:07,826 ProgressMeter -    chr10:745143        4.44e+07   47.7 m       64.5 s     54.1%        88.1 m    40.5 m 
INFO  15:22:37,827 ProgressMeter -     chr11:27900        4.48e+07   48.2 m       64.5 s     54.3%        88.7 m    40.5 m 
INFO  15:23:17,828 ProgressMeter -    chr11:110768        4.55e+07   48.8 m       64.4 s     55.0%        88.8 m    40.0 m 
INFO  15:23:47,828 ProgressMeter -    chr11:185787        4.59e+07   49.3 m       64.5 s     55.6%        88.7 m    39.4 m 
INFO  15:24:17,829 ProgressMeter -    chr11:261348        4.64e+07   49.8 m       64.5 s     56.2%        88.6 m    38.8 m 
INFO  15:24:57,830 ProgressMeter -    chr11:368203        4.70e+07   50.5 m       64.5 s     57.1%        88.4 m    37.9 m 
INFO  15:25:37,831 ProgressMeter -    chr11:468491        4.76e+07   51.2 m       64.5 s     57.9%        88.3 m    37.2 m 
INFO  15:26:07,831 ProgressMeter -    chr11:537245        4.80e+07   51.7 m       64.5 s     58.5%        88.3 m    36.7 m 
INFO  15:26:37,832 ProgressMeter -    chr11:604855        4.85e+07   52.2 m       64.5 s     59.1%        88.3 m    36.2 m 
INFO  15:27:17,833 ProgressMeter -      chr12:3741        4.91e+07   52.8 m       64.5 s     59.6%        88.7 m    35.8 m 
INFO  15:27:47,833 ProgressMeter -     chr12:36847        4.96e+07   53.3 m       64.5 s     59.9%        89.1 m    35.8 m 
INFO  15:28:17,834 ProgressMeter -     chr12:95864        5.01e+07   53.8 m       64.5 s     60.4%        89.2 m    35.4 m 
INFO  15:28:47,835 ProgressMeter -    chr12:166783        5.05e+07   54.3 m       64.5 s     60.9%        89.2 m    34.8 m 
INFO  15:29:27,836 ProgressMeter -    chr12:269962        5.12e+07   55.0 m       64.5 s     61.8%        89.0 m    34.0 m 
INFO  15:29:57,836 ProgressMeter -    chr12:333001        5.16e+07   55.5 m       64.5 s     62.3%        89.1 m    33.6 m 
INFO  15:30:27,837 ProgressMeter -    chr12:398351        5.21e+07   56.0 m       64.5 s     62.8%        89.1 m    33.1 m 
INFO  15:31:07,838 ProgressMeter -    chr12:452656        5.27e+07   56.7 m       64.5 s     63.3%        89.5 m    32.9 m 
INFO  15:31:37,838 ProgressMeter -    chr12:454387        5.32e+07   57.2 m       64.4 s     63.3%        90.3 m    33.1 m 
INFO  15:32:07,839 ProgressMeter -    chr12:455958        5.37e+07   57.7 m       64.4 s     63.3%        91.1 m    33.4 m 
INFO  15:32:37,840 ProgressMeter -    chr12:457501        5.43e+07   58.2 m       64.3 s     63.3%        91.9 m    33.7 m 
INFO  15:33:17,841 ProgressMeter -    chr12:459707        5.49e+07   58.8 m       64.3 s     63.3%        92.9 m    34.0 m 
INFO  15:33:47,842 ProgressMeter -    chr12:461253        5.54e+07   59.3 m       64.2 s     63.4%        93.7 m    34.3 m 
INFO  15:34:27,843 ProgressMeter -    chr12:463563        5.61e+07   60.0 m       64.2 s     63.4%        94.7 m    34.7 m 
INFO  15:34:57,843 ProgressMeter -    chr12:465164        5.66e+07   60.5 m       64.1 s     63.4%        95.4 m    34.9 m 
INFO  15:35:27,844 ProgressMeter -    chr12:466654        5.71e+07   61.0 m       64.1 s     63.4%        96.2 m    35.2 m 
INFO  15:35:57,845 ProgressMeter -    chr12:468328        5.76e+07   61.5 m       64.1 s     63.4%        97.0 m    35.5 m 
INFO  15:36:37,846 ProgressMeter -    chr12:552755        5.82e+07   62.2 m       64.1 s     64.1%        97.0 m    34.8 m 
INFO  15:37:07,846 ProgressMeter -    chr12:621071        5.87e+07   62.7 m       64.1 s     64.7%        96.9 m    34.2 m 
INFO  15:37:37,847 ProgressMeter -    chr12:697165        5.91e+07   63.2 m       64.1 s     65.3%        96.7 m    33.6 m 
INFO  15:38:07,848 ProgressMeter -    chr12:769548        5.96e+07   63.7 m       64.1 s     65.9%        96.6 m    33.0 m 
INFO  15:38:37,849 ProgressMeter -    chr12:839631        6.01e+07   64.2 m       64.1 s     66.5%        96.5 m    32.4 m 
INFO  15:39:17,849 ProgressMeter -    chr12:924140        6.07e+07   64.8 m       64.1 s     67.2%        96.5 m    31.7 m 
INFO  15:39:47,850 ProgressMeter -    chr12:977882        6.11e+07   65.3 m       64.2 s     67.6%        96.6 m    31.3 m 
INFO  15:40:17,851 ProgressMeter -   chr12:1023364        6.15e+07   65.8 m       64.3 s     68.0%        96.8 m    31.0 m 
INFO  15:40:57,852 ProgressMeter -      chr13:2530        6.21e+07   66.5 m       64.3 s     68.4%        97.2 m    30.7 m 
INFO  15:41:27,853 ProgressMeter -     chr13:47293        6.25e+07   67.0 m       64.3 s     68.8%        97.4 m    30.4 m 
INFO  15:42:07,854 ProgressMeter -    chr13:133482        6.31e+07   67.7 m       64.3 s     69.5%        97.3 m    29.7 m 
INFO  15:42:47,855 ProgressMeter -    chr13:241517        6.37e+07   68.3 m       64.4 s     70.4%        97.0 m    28.7 m 
INFO  15:43:17,856 ProgressMeter -    chr13:316577        6.41e+07   68.8 m       64.4 s     71.0%        96.9 m    28.1 m 
INFO  15:43:47,856 ProgressMeter -    chr13:405725        6.46e+07   69.3 m       64.4 s     71.8%        96.6 m    27.3 m 
INFO  15:44:17,857 ProgressMeter -    chr13:483790        6.50e+07   69.8 m       64.4 s     72.4%        96.4 m    26.6 m 
INFO  15:44:47,858 ProgressMeter -    chr13:560072        6.55e+07   70.3 m       64.4 s     73.0%        96.3 m    26.0 m 
INFO  15:45:27,859 ProgressMeter -    chr13:655995        6.61e+07   71.0 m       64.4 s     73.8%        96.2 m    25.2 m 
INFO  15:45:57,859 ProgressMeter -    chr13:719183        6.66e+07   71.5 m       64.4 s     74.3%        96.2 m    24.7 m 
INFO  15:46:27,860 ProgressMeter -    chr13:786285        6.70e+07   72.0 m       64.5 s     74.9%        96.1 m    24.1 m 
INFO  15:46:57,861 ProgressMeter -    chr13:851621        6.75e+07   72.5 m       64.5 s     75.4%        96.1 m    23.6 m 
INFO  15:47:37,862 ProgressMeter -    chr13:924396        6.81e+07   73.2 m       64.5 s     76.0%        96.2 m    23.1 m 
INFO  15:48:07,862 ProgressMeter -     chr14:27832        6.84e+07   73.7 m       64.6 s     76.3%        96.6 m    22.9 m 
INFO  15:48:37,863 ProgressMeter -     chr14:73245        6.88e+07   74.2 m       64.6 s     76.6%        96.8 m    22.6 m 
INFO  15:49:07,864 ProgressMeter -    chr14:133577        6.93e+07   74.7 m       64.7 s     77.1%        96.8 m    22.1 m 
INFO  15:49:47,865 ProgressMeter -    chr14:213105        6.98e+07   75.3 m       64.7 s     77.8%        96.9 m    21.5 m 
INFO  15:50:17,865 ProgressMeter -    chr14:283904        7.03e+07   75.8 m       64.7 s     78.4%        96.8 m    20.9 m 
INFO  15:50:47,866 ProgressMeter -    chr14:355834        7.08e+07   76.3 m       64.7 s     79.0%        96.7 m    20.3 m 
INFO  15:51:27,867 ProgressMeter -    chr14:455630        7.14e+07   77.0 m       64.7 s     79.8%        96.5 m    19.5 m 
INFO  15:52:07,868 ProgressMeter -    chr14:560028        7.20e+07   77.7 m       64.7 s     80.6%        96.3 m    18.7 m 
INFO  15:52:37,868 ProgressMeter -    chr14:639841        7.25e+07   78.2 m       64.7 s     81.3%        96.2 m    18.0 m 
INFO  15:53:07,869 ProgressMeter -    chr14:705203        7.29e+07   78.7 m       64.7 s     81.8%        96.1 m    17.5 m 
INFO  15:53:47,870 ProgressMeter -    chr14:774876        7.35e+07   79.3 m       64.7 s     82.4%        96.3 m    16.9 m 
INFO  15:54:27,870 ProgressMeter -     chr15:79975        7.41e+07   80.0 m       64.7 s     83.1%        96.2 m    16.2 m 
INFO  15:54:57,871 ProgressMeter -    chr15:158166        7.46e+07   80.5 m       64.7 s     83.8%        96.1 m    15.6 m 
INFO  15:55:27,872 ProgressMeter -    chr15:226212        7.51e+07   81.0 m       64.7 s     84.3%        96.0 m    15.0 m 
INFO  15:56:07,872 ProgressMeter -    chr15:331392        7.57e+07   81.7 m       64.7 s     85.2%        95.9 m    14.2 m 
INFO  15:56:37,873 ProgressMeter -    chr15:410872        7.61e+07   82.2 m       64.8 s     85.9%        95.7 m    13.5 m 
INFO  15:57:07,874 ProgressMeter -    chr15:491167        7.66e+07   82.7 m       64.8 s     86.5%        95.6 m    12.9 m 
INFO  15:57:47,874 ProgressMeter -    chr15:589417        7.72e+07   83.3 m       64.8 s     87.3%        95.4 m    12.1 m 
INFO  15:58:17,875 ProgressMeter -    chr15:670664        7.77e+07   83.8 m       64.8 s     88.0%        95.3 m    11.4 m 
INFO  15:58:47,876 ProgressMeter -    chr15:741576        7.81e+07   84.3 m       64.8 s     88.6%        95.2 m    10.9 m 
INFO  15:59:27,877 ProgressMeter -    chr15:836878        7.87e+07   85.0 m       64.8 s     89.4%        95.1 m    10.1 m 
INFO  15:59:57,877 ProgressMeter -    chr15:908128        7.92e+07   85.5 m       64.8 s     89.9%        95.1 m     9.6 m 
INFO  16:00:27,878 ProgressMeter -    chr15:971612        7.97e+07   86.0 m       64.8 s     90.5%        95.1 m     9.1 m 
INFO  16:01:07,879 ProgressMeter -   chr15:1050337        8.03e+07   86.7 m       64.8 s     91.1%        95.1 m     8.5 m 
INFO  16:01:37,879 ProgressMeter -     chr16:16517        8.08e+07   87.2 m       64.8 s     91.6%        95.2 m     8.0 m 
INFO  16:02:07,880 ProgressMeter -     chr16:77160        8.12e+07   87.7 m       64.8 s     92.1%        95.2 m     7.5 m 
INFO  16:02:47,881 ProgressMeter -    chr16:164535        8.18e+07   88.3 m       64.8 s     92.8%        95.2 m     6.9 m 
INFO  16:03:17,881 ProgressMeter -    chr16:241374        8.23e+07   88.8 m       64.7 s     93.4%        95.1 m     6.2 m 
INFO  16:03:47,882 ProgressMeter -    chr16:317125        8.28e+07   89.3 m       64.7 s     94.1%        95.0 m     5.6 m 
INFO  16:04:27,883 ProgressMeter -    chr16:414574        8.34e+07   90.0 m       64.7 s     94.9%        94.9 m     4.9 m 
INFO  16:04:57,883 ProgressMeter -    chr16:501107        8.39e+07   90.5 m       64.7 s     95.6%        94.7 m     4.2 m 
INFO  16:05:27,884 ProgressMeter -    chr16:584240        8.43e+07   91.0 m       64.7 s     96.3%        94.5 m     3.5 m 
INFO  16:05:57,885 ProgressMeter -    chr16:665582        8.48e+07   91.5 m       64.7 s     96.9%        94.4 m     2.9 m 
INFO  16:06:37,886 ProgressMeter -    chr16:760600        8.54e+07   92.2 m       64.7 s     97.7%        94.3 m     2.2 m 
INFO  16:07:07,886 ProgressMeter -    chr16:857979        8.59e+07   92.7 m       64.7 s     98.5%        94.1 m    84.5 s 
INFO  16:07:37,887 ProgressMeter -    chr16:914913        8.63e+07   93.2 m       64.8 s     99.0%        94.1 m    58.2 s 
INFO  16:08:17,888 ProgressMeter -    2-micron:815        8.69e+07   93.8 m       64.8 s    100.0%        93.9 m     2.5 s 
INFO  16:08:47,889 ProgressMeter -          null:0        8.74e+07   94.3 m       64.8 s      0.0%      Infinity w  Infinity w 
INFO  16:09:39,278 ReadShardBalancer$1 - Loading BAM index data for next contig 
INFO  16:09:39,746 Walker - [REDUCE RESULT] Traversal result is: [email protected]c 
INFO  16:09:40,304 ProgressMeter -            done        8.81e+07   95.2 m       64.8 s      0.0%      Infinity w  Infinity w 
INFO  16:09:40,305 ProgressMeter - Total runtime 5712.55 secs, 95.21 min, 1.59 hours 
INFO  16:09:40,305 MicroScheduler - 0 reads were filtered out during traversal out of 20027 total (0.00%) 
INFO  16:09:41,697 GATKRunReport - Uploaded run statistics report to AWS S3 

Any idea ? What was wrong with my process ?

Fred

Best Answer

Answers

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