To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Failings in BadCigarFilter, BadMateFilter, and others

Hi, everyone,

I'm using GATK tools to perform local realignment around indels. For that, I run first:

java -jar $GATK -T RealignerTargetCreator -R dmel_ref.fasta -I "$i.rmdup.srt.bam" -o "$i.IndelRealigner.intervals" 2>log/GATK_RealignerTargetCreator.log

But in the end of the log file, I get some errors (failings):

INFO  21:38:09,672 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:38:09,680 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29 
INFO  21:38:09,681 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  21:38:09,681 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk 
INFO  21:38:09,681 HelpFormatter - [Wed Aug 10 21:38:09 BRT 2016] Executing on Linux 3.2.0-35-generic amd64 
INFO  21:38:09,682 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14 JdkDeflater 
INFO  21:38:09,689 HelpFormatter - Program Args: -T RealignerTargetCreator -R dmel_ref.fasta -I SRR1525697.rmdup.srt.bam -o SRR1525697.IndelRealigner.intervals 
INFO  21:38:09,694 HelpFormatter - Executing as ecoevo@ubuntu on Linux 3.2.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14. 
INFO  21:38:09,695 HelpFormatter - Date/Time: 2016/08/10 21:38:09 
INFO  21:38:09,695 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:38:09,695 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:38:09,703 GenomeAnalysisEngine - Strictness is SILENT 
INFO  21:38:09,952 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO  21:38:09,961 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:38:10,017 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05 
INFO  21:38:10,414 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  21:38:10,438 GenomeAnalysisEngine - Done preparing for traversal 
INFO  21:38:10,438 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  21:38:10,439 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  21:38:10,439 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  21:38:40,445 ProgressMeter -      2L:2672793   3037147.0    30.0 s       9.0 s        1.8%    27.8 m      27.3 m 
INFO  21:39:10,450 ProgressMeter -      2L:6086065   6445019.0    60.0 s       9.0 s        3.8%    26.2 m      25.2 m 
INFO  21:39:40,452 ProgressMeter -      2L:9561573   9918427.0    90.0 s       9.0 s        5.9%    25.5 m      24.0 m 
INFO  21:40:10,453 ProgressMeter -     2L:13016397   1.3375451E7   120.0 s       8.0 s        7.9%    25.2 m      23.2 m 
INFO  21:40:40,455 ProgressMeter -     2L:16483305   1.6848859E7     2.5 m       8.0 s       10.0%    25.0 m      22.5 m 
INFO  21:41:10,457 ProgressMeter -     2L:19879993   2.0240347E7     3.0 m       8.0 s       12.0%    25.0 m      22.0 m 
INFO  21:41:40,459 ProgressMeter -        X:871453   2.4246451E7     3.5 m       8.0 s       14.4%    24.4 m      20.9 m 
INFO  21:42:10,461 ProgressMeter -       X:7568925   3.0931123E7     4.0 m       7.0 s       18.3%    21.8 m      17.8 m 
INFO  21:42:40,463 ProgressMeter -      X:14357685   3.7730483E7     4.5 m       7.0 s       22.4%    20.1 m      15.6 m 
INFO  21:43:10,464 ProgressMeter -      X:20983221   4.4349619E7     5.0 m       6.0 s       26.3%    19.0 m      14.0 m 
INFO  21:43:40,466 ProgressMeter -      3L:2797481   4.8586206E7     5.5 m       6.0 s       28.8%    19.1 m      13.6 m 
INFO  21:44:10,469 ProgressMeter -      3L:6259589   5.2059614E7     6.0 m       6.0 s       30.9%    19.4 m      13.4 m 
INFO  21:44:40,471 ProgressMeter -      3L:9791249   5.5582174E7     6.5 m       7.0 s       32.9%    19.7 m      13.2 m 
INFO  21:45:10,472 ProgressMeter -     3L:13298625   5.908835E7     7.0 m       7.0 s       35.0%    20.0 m      13.0 m 
INFO  21:45:40,474 ProgressMeter -     3L:16762833   6.2561758E7     7.5 m       7.0 s       37.1%    20.2 m      12.7 m 
INFO  21:46:10,501 ProgressMeter -     3L:20278409   6.6067934E7     8.0 m       7.0 s       39.2%    20.4 m      12.4 m 
INFO  21:46:40,502 ProgressMeter -     3L:23709049   6.9508574E7     8.5 m       7.0 s       41.2%    20.6 m      12.1 m 
INFO  21:47:10,504 ProgressMeter -      2R:1663185   7.3351124E7     9.0 m       7.0 s       43.5%    20.7 m      11.7 m 
INFO  21:47:40,506 ProgressMeter -      2R:5138193   7.6824532E7     9.5 m       7.0 s       45.5%    20.9 m      11.4 m 
INFO  21:48:10,508 ProgressMeter -      2R:8562949   8.0248788E7    10.0 m       7.0 s       47.6%    21.0 m      11.0 m 
INFO  21:48:40,510 ProgressMeter -     2R:12060825   8.3754964E7    10.5 m       7.0 s       49.6%    21.2 m      10.7 m 
INFO  21:49:10,511 ProgressMeter -     2R:15472497   8.7162836E7    11.0 m       7.0 s       51.7%    21.3 m      10.3 m 
INFO  21:49:40,513 ProgressMeter -     2R:18919637   9.0603476E7    11.5 m       7.0 s       53.7%    21.4 m       9.9 m 
INFO  21:50:10,515 ProgressMeter -      3R:1157281   9.3989928E7    12.0 m       7.0 s       55.7%    21.5 m       9.5 m 
INFO  21:50:40,516 ProgressMeter -      3R:4548369   9.7381416E7    12.5 m       7.0 s       57.7%    21.7 m       9.2 m 
INFO  21:51:10,519 ProgressMeter -      3R:7919773   1.0075652E8    13.0 m       7.0 s       59.7%    21.8 m       8.8 m 
INFO  21:51:40,523 ProgressMeter -     3R:11339329   1.04180776E8    13.5 m       7.0 s       61.7%    21.9 m       8.4 m 
INFO  21:52:10,525 ProgressMeter -     3R:14772985   1.07605032E8    14.0 m       7.0 s       63.8%    22.0 m       8.0 m 
INFO  21:52:40,527 ProgressMeter -     3R:18176857   1.11012904E8    14.5 m       7.0 s       65.8%    22.0 m       7.5 m 
INFO  21:53:10,529 ProgressMeter -     3R:21489425   1.14322472E8    15.0 m       7.0 s       67.8%    22.1 m       7.1 m 
INFO  21:53:40,530 ProgressMeter -     3R:24927465   1.17763112E8    15.5 m       7.0 s       69.8%    22.2 m       6.7 m 
INFO  21:54:10,532 ProgressMeter -   Uextra:828401   1.21567301E8    16.0 m       7.0 s       72.1%    22.2 m       6.2 m 
INFO  21:54:40,534 ProgressMeter - Uextra:11452333   1.32184133E8    16.5 m       7.0 s       78.3%    21.1 m       4.6 m 
INFO  21:55:10,535 ProgressMeter - Uextra:24271805   1.45012805E8    17.0 m       7.0 s       85.9%    19.8 m       2.8 m 
INFO  21:55:40,537 ProgressMeter -    2RHet:662161   1.50408117E8    17.5 m       6.0 s       89.1%    19.6 m       2.1 m 
INFO  21:56:10,538 ProgressMeter -   3LHet:2500969   1.55900758E8    18.0 m       6.0 s       92.4%    19.5 m      88.0 s 
INFO  21:56:40,540 ProgressMeter -       U:3410373   1.6189126E8    18.5 m       6.0 s       95.9%    19.3 m      46.0 s 
INFO  21:57:06,212 ProgressMeter -            done   1.68736537E8    18.9 m       6.0 s      100.0%    18.9 m       0.0 s 
INFO  21:57:06,213 ProgressMeter - Total runtime 1135.77 secs, 18.93 min, 0.32 hours 
INFO  21:57:06,213 MicroScheduler - 18559258 reads were filtered out during the traversal out of approximately 73300229 total reads (25.32%) 
INFO  21:57:06,214 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter 
INFO  21:57:06,215 MicroScheduler -   -> 138531 reads (0.19% of total) failing BadMateFilter 
INFO  21:57:06,215 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter 
INFO  21:57:06,215 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter 
INFO  21:57:06,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO  21:57:06,216 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter 
INFO  21:57:06,216 MicroScheduler -   -> 18420705 reads (25.13% of total) failing MappingQualityZeroFilter 
INFO  21:57:06,216 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter 
INFO  21:57:06,216 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter 
INFO  21:57:06,217 MicroScheduler -   -> 22 reads (0.00% of total) failing UnmappedReadFilter 

And the same happens when I run the GATK IndelRealigner:

java -Xmx8G -Djava.io.tmpdir=/home/ecoevo/data/tmp -jar $GATK -T IndelRealigner -R dmel_ref.fasta -targetIntervals "$i.IndelRealigner.intervals" -I "$i.rmdup.srt.bam" -o "$i.indelrealigned.bam" 2>log/GATK_IndelRealigner.log

With STDERR:

INFO  21:57:09,651 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:57:09,655 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29 
INFO  21:57:09,655 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  21:57:09,656 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk 
INFO  21:57:09,656 HelpFormatter - [Wed Aug 10 21:57:09 BRT 2016] Executing on Linux 3.2.0-35-generic amd64 
INFO  21:57:09,656 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14 JdkDeflater 
INFO  21:57:09,662 HelpFormatter - Program Args: -T IndelRealigner -R dmel_ref.fasta -targetIntervals SRR1525697.IndelRealigner.intervals -I SRR1525697.rmdup.srt.bam -o SRR1525697.indelrealigned.bam 
INFO  21:57:09,667 HelpFormatter - Executing as ecoevo@ubuntu on Linux 3.2.0-35-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14. 
INFO  21:57:09,668 HelpFormatter - Date/Time: 2016/08/10 21:57:09 
INFO  21:57:09,668 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:57:09,668 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  21:57:09,864 GenomeAnalysisEngine - Strictness is SILENT 
INFO  21:57:09,957 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  21:57:09,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  21:57:09,994 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 
INFO  21:57:10,136 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  21:57:10,142 GenomeAnalysisEngine - Done preparing for traversal 
INFO  21:57:10,142 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  21:57:10,143 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  21:57:10,143 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime 
INFO  21:57:10,501 ReadShardBalancer$1 - Loading BAM index data 
INFO  21:57:10,503 ReadShardBalancer$1 - Done loading BAM index data 
DEBUG   2016-08-10 21:57:12 BlockCompressedOutputStream Using deflater: Deflater
INFO  21:57:40,149 ProgressMeter -       2L:728929    455030.0    30.0 s      65.0 s        0.6%    77.0 m      76.5 m 
INFO  21:58:10,151 ProgressMeter -      2L:1623887    855037.0    60.0 s      70.0 s        1.2%    84.8 m      83.8 m 
INFO  21:58:40,152 ProgressMeter -      2L:2463104   1255041.0    90.0 s      71.0 s        1.7%    89.4 m      87.9 m 
INFO  21:59:10,154 ProgressMeter -      2L:3347264   1655045.0   120.0 s      72.0 s        2.2%    90.9 m      88.9 m 
INFO  21:59:40,155 ProgressMeter -      2L:4134152   2055049.0     2.5 m      72.0 s        2.7%    93.7 m      91.2 m 
INFO  22:00:10,157 ProgressMeter -      2L:4945810   2455055.0     3.0 m      73.0 s        3.1%    95.3 m      92.3 m 
INFO  22:00:40,158 ProgressMeter -      2L:5865193   2855060.0     3.5 m      73.0 s        3.7%    94.8 m      91.3 m 
INFO  22:01:10,160 ProgressMeter -      2L:6795176   3355071.0     4.0 m      71.0 s        4.2%    94.2 m      90.2 m 
INFO  22:01:40,161 ProgressMeter -      2L:7601397   3655075.0     4.5 m      73.0 s        4.7%    95.3 m      90.8 m 
INFO  22:02:10,163 ProgressMeter -      2L:8569552   4155081.0     5.0 m      72.0 s        5.3%    94.4 m      89.4 m 
INFO  22:02:40,165 ProgressMeter -      2L:9370591   4555088.0     5.5 m      72.0 s        5.8%    95.3 m      89.8 m 
INFO  22:03:10,166 ProgressMeter -     2L:10124859   4855091.0     6.0 m      74.0 s        6.2%    96.5 m      90.5 m 
INFO  22:03:40,168 ProgressMeter -     2L:11058329   5355098.0     6.5 m      72.0 s        6.8%    96.0 m      89.5 m 
INFO  22:04:10,172 ProgressMeter -     2L:11993100   5755102.0     7.0 m      72.0 s        7.3%    95.6 m      88.6 m 
INFO  22:04:40,174 ProgressMeter -     2L:12704630   6055105.0     7.5 m      74.0 s        7.7%    96.8 m      89.3 m 
INFO  22:05:10,187 ProgressMeter -     2L:13746201   6555111.0     8.0 m      73.0 s        8.4%    95.7 m      87.7 m 
INFO  22:05:40,189 ProgressMeter -     2L:14589852   7055118.0     8.5 m      72.0 s        8.9%    95.9 m      87.4 m 
INFO  22:06:10,190 ProgressMeter -     2L:15508925   7455124.0     9.0 m      72.0 s        9.4%    95.7 m      86.7 m 
INFO  22:06:40,191 ProgressMeter -     2L:16590582   7955129.0     9.5 m      71.0 s       10.0%    94.5 m      85.0 m 
INFO  22:07:10,193 ProgressMeter -     2L:17609520   8355133.0    10.0 m      71.0 s       10.7%    93.9 m      83.9 m 
INFO  22:07:40,195 ProgressMeter -     2L:18760574   8955139.0    10.5 m      70.0 s       11.3%    92.6 m      82.1 m 
INFO  22:08:10,196 ProgressMeter -     2L:19846296   9455144.0    11.0 m      69.0 s       12.0%    91.8 m      80.8 m 
INFO  22:08:40,198 ProgressMeter -     2L:20865001   9955150.0    11.5 m      69.0 s       12.6%    91.4 m      79.9 m 
INFO  22:09:10,200 ProgressMeter -     2L:22133130   1.0555159E7    12.0 m      68.0 s       13.3%    90.0 m      78.0 m 
INFO  22:09:40,202 ProgressMeter -       X:1535118   1.1387818E7    12.5 m      65.0 s       14.8%    84.7 m      72.2 m 
INFO  22:10:10,203 ProgressMeter -       X:4360069   1.2087827E7    13.0 m      64.0 s       16.4%    79.1 m      66.1 m 
INFO  22:10:40,205 ProgressMeter -       X:7063127   1.2787834E7    13.5 m      63.0 s       18.0%    74.8 m      61.3 m 
INFO  22:11:10,207 ProgressMeter -      X:10005186   1.3387843E7    14.0 m      62.0 s       19.8%    70.8 m      56.8 m 
INFO  22:11:40,209 ProgressMeter -      X:12996735   1.408785E7    14.5 m      61.0 s       21.6%    67.3 m      52.8 m 
INFO  22:12:10,211 ProgressMeter -      X:16008065   1.4787858E7    15.0 m      60.0 s       23.3%    64.3 m      49.3 m 
INFO  22:12:40,213 ProgressMeter -      X:19013529   1.5487865E7    15.5 m      60.0 s       25.1%    61.7 m      46.2 m 
INFO  22:13:10,215 ProgressMeter -      X:21950101   1.6187873E7    16.0 m      59.0 s       26.9%    59.6 m      43.6 m 
INFO  22:13:40,217 ProgressMeter -       3L:953582   1.6811571E7    16.5 m      58.0 s       27.7%    59.5 m      43.0 m 
INFO  22:14:10,219 ProgressMeter -      3L:1727963   1.7111574E7    17.0 m      59.0 s       28.2%    60.4 m      43.4 m 
INFO  22:14:40,220 ProgressMeter -      3L:2592821   1.7611582E7    17.5 m      59.0 s       28.7%    61.0 m      43.5 m 
INFO  22:15:10,222 ProgressMeter -      3L:3533515   1.8011589E7    18.0 m      59.0 s       29.2%    61.6 m      43.6 m 
INFO  22:15:40,223 ProgressMeter -      3L:4386550   1.8411593E7    18.5 m      60.0 s       29.7%    62.2 m      43.7 m 
INFO  22:16:10,225 ProgressMeter -      3L:5290606   1.8811598E7    19.0 m      60.0 s       30.3%    62.8 m      43.8 m 
INFO  22:16:40,226 ProgressMeter -      3L:6132878   1.9211603E7    19.5 m      60.0 s       30.8%    63.4 m      43.9 m 
INFO  22:17:10,230 ProgressMeter -      3L:7076432   1.9611608E7    20.0 m      61.0 s       31.3%    63.8 m      43.8 m 
INFO  22:17:40,232 ProgressMeter -      3L:7878069   2.0011612E7    20.5 m      61.0 s       31.8%    64.4 m      43.9 m 
INFO  22:18:10,234 ProgressMeter -      3L:8757264   2.0411616E7    21.0 m      61.0 s       32.3%    64.9 m      43.9 m 
INFO  22:18:40,236 ProgressMeter -      3L:9509978   2.0811625E7    21.5 m      61.0 s       32.8%    65.6 m      44.1 m 
INFO  22:19:10,237 ProgressMeter -     3L:10325961   2.1111628E7    22.0 m      62.0 s       33.3%    66.1 m      44.1 m 
INFO  22:19:40,239 ProgressMeter -     3L:10993915   2.1411633E7    22.5 m      63.0 s       33.7%    66.8 m      44.3 m 
INFO  22:20:10,241 ProgressMeter -     3L:11833752   2.1811637E7    23.0 m      63.0 s       34.2%    67.3 m      44.3 m 
INFO  22:20:40,242 ProgressMeter -     3L:12670762   2.2211642E7    23.5 m      63.0 s       34.7%    67.8 m      44.3 m 
INFO  22:21:10,313 ProgressMeter -     3L:13606912   2.2611646E7    24.0 m      63.0 s       35.2%    68.2 m      44.2 m 
INFO  22:21:40,314 ProgressMeter -     3L:14576257   2.3111653E7    24.5 m      63.0 s       35.8%    68.5 m      44.0 m 
INFO  22:22:10,316 ProgressMeter -     3L:15708546   2.3611659E7    25.0 m      63.0 s       36.5%    68.6 m      43.6 m 
INFO  22:22:40,318 ProgressMeter -     3L:16764228   2.4111665E7    25.5 m      63.0 s       37.1%    68.8 m      43.3 m 
INFO  22:23:10,320 ProgressMeter -     3L:17924226   2.4711673E7    26.0 m      63.0 s       37.8%    68.8 m      42.8 m 
INFO  22:23:40,322 ProgressMeter -     3L:18903953   2.5111681E7    26.5 m      63.0 s       38.3%    69.1 m      42.6 m 
INFO  22:24:10,323 ProgressMeter -     3L:20214584   2.5711688E7    27.0 m      63.0 s       39.1%    69.0 m      42.0 m 
INFO  22:24:40,325 ProgressMeter -     3L:21681493   2.6411697E7    27.5 m      62.0 s       40.0%    68.8 m      41.3 m 
INFO  22:25:10,327 ProgressMeter -     3L:23177358   2.7211707E7    28.0 m      61.0 s       40.9%    68.5 m      40.5 m 
INFO  22:25:40,328 ProgressMeter -        4:540715   2.8090923E7    28.5 m      60.0 s       42.0%    67.8 m      39.3 m 
INFO  22:26:10,330 ProgressMeter -       2R:923017   2.893589E7    29.0 m      60.0 s       43.0%    67.4 m      38.4 m 
INFO  22:26:40,332 ProgressMeter -      2R:2241392   2.9535897E7    29.5 m      59.0 s       43.8%    67.3 m      37.8 m 
INFO  22:27:10,333 ProgressMeter -      2R:3599671   3.0235904E7    30.0 m      59.0 s       44.6%    67.2 m      37.2 m 
INFO  22:27:40,484 ProgressMeter -      2R:4870781   3.0835911E7    30.5 m      59.0 s       45.4%    67.2 m      36.7 m 
INFO  22:28:10,486 ProgressMeter -      2R:6056583   3.1435917E7    31.0 m      59.0 s       46.1%    67.3 m      36.3 m 
INFO  22:28:40,487 ProgressMeter -      2R:6913677   3.1835921E7    31.5 m      59.0 s       46.6%    67.6 m      36.1 m 
INFO  22:29:10,489 ProgressMeter -      2R:7841241   3.2235926E7    32.0 m      59.0 s       47.1%    67.9 m      35.9 m 
INFO  22:29:40,491 ProgressMeter -      2R:8656457   3.2635934E7    32.5 m      59.0 s       47.6%    68.2 m      35.7 m 
INFO  22:30:10,492 ProgressMeter -      2R:9540841   3.3035938E7    33.0 m      59.0 s       48.1%    68.5 m      35.5 m 
INFO  22:30:40,494 ProgressMeter -     2R:10411988   3.3435944E7    33.5 m      60.0 s       48.7%    68.8 m      35.3 m 
INFO  22:31:10,496 ProgressMeter -     2R:11329361   3.3835957E7    34.0 m      60.0 s       49.2%    69.1 m      35.1 m 
INFO  22:31:40,497 ProgressMeter -     2R:12240767   3.4335964E7    34.5 m      60.0 s       49.7%    69.4 m      34.9 m 
INFO  22:32:10,499 ProgressMeter -     2R:13189186   3.473597E7    35.0 m      60.0 s       50.3%    69.6 m      34.6 m 
INFO  22:32:40,501 ProgressMeter -     2R:14074437   3.5235977E7    35.5 m      60.0 s       50.8%    69.8 m      34.3 m 
INFO  22:33:10,502 ProgressMeter -     2R:14919845   3.553598E7    36.0 m      60.0 s       51.3%    70.1 m      34.1 m 
INFO  22:33:40,503 ProgressMeter -     2R:15910242   3.6035987E7    36.5 m      60.0 s       51.9%    70.3 m      33.8 m 
INFO  22:34:10,505 ProgressMeter -     2R:16756187   3.6435992E7    37.0 m      60.0 s       52.4%    70.6 m      33.6 m 
INFO  22:34:40,507 ProgressMeter -     2R:17438564   3.6735995E7    37.5 m      61.0 s       52.8%    71.0 m      33.5 m 
INFO  22:35:10,509 ProgressMeter -     2R:18287221    3.7136E7    38.0 m      61.0 s       53.3%    71.3 m      33.3 m 
INFO  22:35:40,510 ProgressMeter -     2R:19152129   3.7536005E7    38.5 m      61.0 s       53.8%    71.5 m      33.0 m 
INFO  22:36:10,512 ProgressMeter -     2R:20133962   3.803601E7    39.0 m      61.0 s       54.4%    71.7 m      32.7 m 
INFO  22:36:40,513 ProgressMeter -       3R:369999   3.867342E7    39.5 m      61.0 s       55.2%    71.5 m      32.0 m 
INFO  22:37:10,514 ProgressMeter -      3R:1866919   3.9473432E7    40.0 m      60.0 s       56.1%    71.3 m      31.3 m 
INFO  22:37:40,516 ProgressMeter -      3R:3263765   4.0073441E7    40.5 m      60.0 s       57.0%    71.1 m      30.6 m 
INFO  22:38:10,518 ProgressMeter -      3R:4565977   4.0773449E7    41.0 m      60.0 s       57.7%    71.0 m      30.0 m 
INFO  22:38:40,519 ProgressMeter -      3R:5794048   4.1373457E7    41.5 m      60.0 s       58.5%    71.0 m      29.5 m 
INFO  22:39:10,521 ProgressMeter -      3R:6977686   4.1873464E7    42.0 m      60.0 s       59.2%    71.0 m      29.0 m 
INFO  22:39:40,522 ProgressMeter -      3R:8164994   4.2473471E7    42.5 m      60.0 s       59.9%    71.0 m      28.5 m 
INFO  22:40:10,524 ProgressMeter -      3R:9342837   4.3073479E7    43.0 m      59.0 s       60.6%    71.0 m      28.0 m 
INFO  22:40:40,526 ProgressMeter -     3R:10261934   4.3473484E7    43.5 m      60.0 s       61.1%    71.2 m      27.7 m 
INFO  22:41:10,527 ProgressMeter -     3R:11268008   4.397349E7    44.0 m      60.0 s       61.7%    71.3 m      27.3 m 
INFO  22:41:40,529 ProgressMeter -     3R:12413521   4.4473497E7    44.5 m      60.0 s       62.4%    71.3 m      26.8 m 
INFO  22:42:10,530 ProgressMeter -     3R:13539491   4.5073506E7    45.0 m      59.0 s       63.0%    71.4 m      26.4 m 
INFO  22:42:40,532 ProgressMeter -     3R:14364248   4.5373509E7    45.5 m      60.0 s       63.5%    71.6 m      26.1 m 
INFO  22:43:10,534 ProgressMeter -     3R:15204883   4.5773513E7    46.0 m      60.0 s       64.0%    71.8 m      25.8 m 
INFO  22:43:40,535 ProgressMeter -     3R:16272001   4.6273518E7    46.5 m      60.0 s       64.7%    71.9 m      25.4 m 
INFO  22:44:10,537 ProgressMeter -     3R:17397757   4.6873525E7    47.0 m      60.0 s       65.3%    71.9 m      24.9 m 
INFO  22:44:40,538 ProgressMeter -     3R:18358177   4.7273533E7    47.5 m      60.0 s       65.9%    72.1 m      24.6 m 
INFO  22:45:10,540 ProgressMeter -     3R:19208810   4.7673538E7    48.0 m      60.0 s       66.4%    72.3 m      24.3 m 
INFO  22:45:40,542 ProgressMeter -     3R:20263460   4.8173546E7    48.5 m      60.0 s       67.0%    72.4 m      23.9 m 
INFO  22:46:10,543 ProgressMeter -     3R:21267189   4.8673551E7    49.0 m      60.0 s       67.6%    72.5 m      23.5 m 
INFO  22:46:40,544 ProgressMeter -     3R:22287808   4.9173557E7    49.5 m      60.0 s       68.2%    72.5 m      23.0 m 
INFO  22:47:10,546 ProgressMeter -     3R:23236245   4.9673563E7    50.0 m      60.0 s       68.8%    72.7 m      22.7 m 
INFO  22:47:40,631 ProgressMeter -     3R:24175550   5.0073568E7    50.5 m      60.0 s       69.3%    72.8 m      22.3 m 
INFO  22:48:10,633 ProgressMeter -     3R:25114552   5.0573573E7    51.0 m      60.0 s       69.9%    73.0 m      22.0 m 
INFO  22:48:40,635 ProgressMeter -     3R:25936420   5.0873577E7    51.5 m      60.0 s       70.4%    73.2 m      21.7 m 
INFO  22:49:10,636 ProgressMeter -     3R:26734649   5.1273582E7    52.0 m      60.0 s       70.9%    73.4 m      21.4 m 
INFO  22:49:40,638 ProgressMeter -     3R:27904511   5.1873589E7    52.5 m      60.0 s       71.6%    73.4 m      20.9 m 
INFO  22:50:10,640 ProgressMeter -  Uextra:2637715   5.2712308E7    53.0 m      60.0 s       73.1%    72.5 m      19.5 m 
INFO  22:50:24,438 IndelRealigner - Not attempting realignment in interval Uextra:3080831-3081283 because there are too many reads. 
INFO  22:50:40,641 ProgressMeter -  Uextra:3081230   5.2912312E7    53.5 m      60.0 s       73.4%    72.9 m      19.4 m 
INFO  22:51:09,225 IndelRealigner - Not attempting realignment in interval Uextra:3204726-3204888 because there are too many reads. 
INFO  22:51:10,643 ProgressMeter -  Uextra:3212676   5.3012315E7    54.0 m      61.0 s       73.5%    73.5 m      19.5 m 
INFO  22:51:40,645 ProgressMeter -  Uextra:3430793   5.3112318E7    54.5 m      61.0 s       73.6%    74.1 m      19.6 m 
INFO  22:52:10,647 ProgressMeter -  Uextra:3430793   5.3112318E7    55.0 m      62.0 s       73.6%    74.7 m      19.7 m 
INFO  22:52:40,648 ProgressMeter -  Uextra:3431109   5.3112318E7    55.5 m      62.0 s       73.6%    75.4 m      19.9 m 
INFO  22:53:10,650 ProgressMeter -  Uextra:4484209   5.3412321E7    56.0 m      62.0 s       74.2%    75.5 m      19.5 m 
INFO  22:53:26,600 IndelRealigner - Not attempting realignment in interval Uextra:4935949-4936092 because there are too many reads. 
INFO  22:53:40,651 ProgressMeter -  Uextra:5064499   5.3712325E7    56.5 m      63.0 s       74.6%    75.8 m      19.3 m 
INFO  22:54:10,653 ProgressMeter -  Uextra:5465022   5.3912327E7    57.0 m      63.0 s       74.8%    76.2 m      19.2 m 
INFO  22:54:39,728 IndelRealigner - Not attempting realignment in interval Uextra:6346415-6346720 because there are too many reads. 
INFO  22:54:40,655 ProgressMeter -  Uextra:6346600   5.4212332E7    57.5 m      63.0 s       75.3%    76.3 m      18.8 m 
INFO  22:54:47,185 IndelRealigner - Not attempting realignment in interval Uextra:6550395-6550567 because there are too many reads. 
INFO  22:55:00,753 IndelRealigner - Not attempting realignment in interval Uextra:6950174-6950351 because there are too many reads. 
INFO  22:55:10,656 ProgressMeter -  Uextra:6952576   5.4512739E7    58.0 m      63.0 s       75.7%    76.6 m      18.6 m 
INFO  22:55:33,795 IndelRealigner - Not attempting realignment in interval Uextra:8045498-8045602 because there are too many reads. 
INFO  22:55:40,658 ProgressMeter -  Uextra:8146281   5.4912766E7    58.5 m      63.0 s       76.4%    76.6 m      18.1 m 
INFO  22:55:41,820 IndelRealigner - Not attempting realignment in interval Uextra:8147743-8147834 because there are too many reads. 
INFO  22:55:48,996 IndelRealigner - Not attempting realignment in interval Uextra:8372106-8372317 because there are too many reads. 
INFO  22:55:58,262 IndelRealigner - Not attempting realignment in interval Uextra:8459350-8459458 because there are too many reads. 
INFO  22:56:07,571 IndelRealigner - Not attempting realignment in interval Uextra:8511091-8511348 because there are too many reads. 
INFO  22:56:10,659 ProgressMeter -  Uextra:8511234   5.5212769E7    59.0 m      64.0 s       76.6%    77.0 m      18.0 m 
INFO  22:56:40,660 ProgressMeter -  Uextra:9743712   5.5612775E7    59.5 m      64.0 s       77.3%    76.9 m      17.4 m 
INFO  22:56:44,005 IndelRealigner - Not attempting realignment in interval Uextra:9834791-9834880 because there are too many reads. 
INFO  22:56:46,659 IndelRealigner - Not attempting realignment in interval Uextra:9930145-9930146 because there are too many reads. 
INFO  22:56:52,981 IndelRealigner - Not attempting realignment in interval Uextra:10241463-10241641 because there are too many reads. 
INFO  22:57:10,662 ProgressMeter - Uextra:10274884   5.5812778E7    60.0 m      64.0 s       77.6%    77.3 m      17.3 m 
INFO  22:57:28,073 IndelRealigner - Not attempting realignment in interval Uextra:10890896-10891044 because there are too many reads. 
INFO  22:57:40,664 ProgressMeter - Uextra:10891021   5.6112781E7    60.5 m      64.0 s       78.0%    77.5 m      17.0 m 
INFO  22:57:50,627 IndelRealigner - Not attempting realignment in interval Uextra:11781259-11781310 because there are too many reads. 
INFO  22:58:10,665 ProgressMeter - Uextra:11781383   5.6412784E7    61.0 m      64.0 s       78.5%    77.7 m      16.7 m 
INFO  22:58:40,667 ProgressMeter - Uextra:11781398   5.6412784E7    61.5 m      65.0 s       78.5%    78.3 m      16.8 m 
INFO  22:59:00,444 IndelRealigner - Not attempting realignment in interval Uextra:12699010-12699068 because there are too many reads. 
INFO  22:59:10,668 ProgressMeter - Uextra:12867518   5.681279E7    62.0 m      65.0 s       79.2%    78.3 m      16.3 m 
INFO  22:59:16,310 IndelRealigner - Not attempting realignment in interval Uextra:13495196-13495291 because there are too many reads. 
INFO  22:59:34,308 IndelRealigner - Not attempting realignment in interval Uextra:13785445-13785570 because there are too many reads. 
INFO  22:59:40,670 ProgressMeter - Uextra:13785556   5.7212798E7    62.5 m      65.0 s       79.7%    78.4 m      15.9 m 
INFO  22:59:56,468 IndelRealigner - Not attempting realignment in interval Uextra:13809123-13809309 because there are too many reads. 
INFO  23:00:06,013 IndelRealigner - Not attempting realignment in interval Uextra:14369329-14369448 because there are too many reads. 
INFO  23:00:10,672 ProgressMeter - Uextra:14369436   5.7512802E7    63.0 m      65.0 s       80.1%    78.7 m      15.7 m 
INFO  23:00:27,713 IndelRealigner - Not attempting realignment in interval Uextra:14420112-14420134 because there are too many reads. 
INFO  23:00:40,673 ProgressMeter - Uextra:14420121   5.7612803E7    63.5 m      66.0 s       80.1%    79.3 m      15.8 m 
INFO  23:01:10,688 ProgressMeter - Uextra:14844700   5.7812806E7    64.0 m      66.0 s       80.4%    79.6 m      15.6 m 
INFO  23:01:14,502 IndelRealigner - Not attempting realignment in interval Uextra:14983444-14983620 because there are too many reads. 
INFO  23:01:40,690 ProgressMeter - Uextra:15146304   5.7912807E7    64.5 m      66.0 s       80.5%    80.1 m      15.6 m 
INFO  23:01:50,249 IndelRealigner - Not attempting realignment in interval Uextra:16317685-16317818 because there are too many reads. 
INFO  23:02:08,163 IndelRealigner - Not attempting realignment in interval Uextra:17210543-17210741 because there are too many reads. 
INFO  23:02:10,691 ProgressMeter - Uextra:17297462   5.8612817E7    65.0 m      66.0 s       81.8%    79.5 m      14.5 m 
INFO  23:02:19,433 IndelRealigner - Not attempting realignment in interval Uextra:17373747-17373953 because there are too many reads. 
INFO  23:02:22,667 IndelRealigner - Not attempting realignment in interval Uextra:17507462-17507578 because there are too many reads. 
INFO  23:02:40,692 ProgressMeter - Uextra:17507578   5.8812821E7    65.5 m      66.0 s       81.9%    79.9 m      14.4 m 
INFO  23:03:06,679 IndelRealigner - Not attempting realignment in interval Uextra:18119591-18119676 because there are too many reads. 
INFO  23:03:10,694 ProgressMeter - Uextra:18411953   5.9112824E7    66.0 m      66.0 s       82.5%    80.0 m      14.0 m 
INFO  23:03:17,800 IndelRealigner - Not attempting realignment in interval Uextra:19169658-19170000 because there are too many reads. 
INFO  23:03:32,177 IndelRealigner - Not attempting realignment in interval Uextra:20415987-20416102 because there are too many reads. 
INFO  23:03:40,696 ProgressMeter - Uextra:20416087   5.971283E7    66.5 m      66.0 s       83.7%    79.5 m      13.0 m 
INFO  23:03:58,522 IndelRealigner - Not attempting realignment in interval Uextra:20872503-20872642 because there are too many reads. 
INFO  23:04:10,697 ProgressMeter - Uextra:20872615   5.9912835E7    67.0 m      67.0 s       83.9%    79.8 m      12.8 m 
INFO  23:04:40,699 ProgressMeter - Uextra:20872634   6.0012836E7    67.5 m      67.0 s       83.9%    80.4 m      12.9 m 
INFO  23:05:10,701 ProgressMeter - Uextra:20873770   6.0012836E7    68.0 m      67.0 s       83.9%    81.0 m      13.0 m 
INFO  23:05:40,703 ProgressMeter - Uextra:22179022   6.0512845E7    68.5 m      67.0 s       84.7%    80.9 m      12.4 m 
INFO  23:06:10,704 ProgressMeter - Uextra:23015524   6.0712848E7    69.0 m      68.0 s       85.2%    81.0 m      12.0 m 
INFO  23:06:40,705 ProgressMeter - Uextra:24525067   6.1212862E7    69.5 m      68.0 s       86.1%    80.7 m      11.2 m 
INFO  23:06:47,783 IndelRealigner - Not attempting realignment in interval Uextra:25030390-25030580 because there are too many reads. 
INFO  23:06:55,484 IndelRealigner - Not attempting realignment in interval Uextra:25184412-25184653 because there are too many reads. 
INFO  23:07:10,707 ProgressMeter - Uextra:25531695   6.1712871E7    70.0 m      68.0 s       86.7%    80.7 m      10.7 m 
INFO  23:07:21,235 IndelRealigner - Not attempting realignment in interval Uextra:26138404-26138520 because there are too many reads. 
INFO  23:07:32,607 IndelRealigner - Not attempting realignment in interval Uextra:26185609-26186059 because there are too many reads. 
INFO  23:07:40,708 ProgressMeter - Uextra:26311344   6.2012875E7    70.5 m      68.0 s       87.2%    80.9 m      10.4 m 
INFO  23:08:10,710 ProgressMeter - Uextra:27044494   6.2412881E7    71.0 m      68.0 s       87.6%    81.1 m      10.1 m 
INFO  23:08:39,140 IndelRealigner - Not attempting realignment in interval Uextra:27904124-27904531 because there are too many reads. 
INFO  23:08:40,711 ProgressMeter - Uextra:27904452   6.2812888E7    71.5 m      68.0 s       88.1%    81.2 m       9.7 m 
INFO  23:09:10,713 ProgressMeter - Uextra:27976827   6.3012941E7    72.0 m      68.0 s       88.1%    81.7 m       9.7 m 
INFO  23:09:19,445 IndelRealigner - Not attempting realignment in interval Uextra:28090560-28090703 because there are too many reads. 
INFO  23:09:30,079 IndelRealigner - Not attempting realignment in interval Uextra:28116584-28116692 because there are too many reads. 
INFO  23:09:40,714 ProgressMeter - Uextra:28137223   6.3212944E7    72.5 m      68.0 s       88.2%    82.2 m       9.7 m 
INFO  23:10:10,716 ProgressMeter - Uextra:28234952   6.3312945E7    73.0 m      69.0 s       88.3%    82.7 m       9.7 m 
INFO  23:10:16,260 IndelRealigner - Not attempting realignment in interval Uextra:28284670-28284866 because there are too many reads. 
INFO  23:10:40,717 ProgressMeter - Uextra:28423783   6.3612972E7    73.5 m      69.0 s       88.4%    83.1 m       9.6 m 
INFO  23:11:00,503 IndelRealigner - Not attempting realignment in interval Uextra:28501867-28501952 because there are too many reads. 
INFO  23:11:10,827 ProgressMeter - Uextra:28501958   6.3712973E7    74.0 m      69.0 s       88.5%    83.7 m       9.7 m 
INFO  23:11:40,829 ProgressMeter - Uextra:28570886   6.4012979E7    74.5 m      69.0 s       88.5%    84.2 m       9.7 m 
INFO  23:12:01,575 IndelRealigner - Not attempting realignment in interval Uextra:28597225-28597602 because there are too many reads. 
INFO  23:12:10,830 ProgressMeter - Uextra:28598553   6.4112981E7    75.0 m      70.0 s       88.5%    84.7 m       9.7 m 
INFO  23:12:24,747 IndelRealigner - Not attempting realignment in interval Uextra:28615554-28615595 because there are too many reads. 
INFO  23:12:40,832 ProgressMeter - Uextra:28615663   6.4312984E7    75.5 m      70.0 s       88.5%    85.3 m       9.8 m 
INFO  23:12:47,723 IndelRealigner - Not attempting realignment in interval Uextra:28615670-28615717 because there are too many reads. 
INFO  23:13:10,833 ProgressMeter - Uextra:28615680   6.4312984E7    76.0 m      70.0 s       88.5%    85.9 m       9.9 m 
INFO  23:13:40,835 ProgressMeter - Uextra:28615694   6.4312984E7    76.5 m      71.0 s       88.5%    86.4 m       9.9 m 
INFO  23:14:10,836 ProgressMeter - Uextra:28647492   6.4512986E7    77.0 m      71.0 s       88.5%    87.0 m      10.0 m 
INFO  23:14:39,275 IndelRealigner - Not attempting realignment in interval Uextra:28714728-28714950 because there are too many reads. 
INFO  23:14:40,837 ProgressMeter - Uextra:28714929   6.4712989E7    77.5 m      71.0 s       88.6%    87.5 m      10.0 m 
INFO  23:14:46,673 IndelRealigner - Not attempting realignment in interval Uextra:28725252-28725527 because there are too many reads. 
INFO  23:15:10,839 ProgressMeter - Uextra:28726821   6.4813005E7    78.0 m      72.0 s       88.6%    88.1 m      10.1 m 
INFO  23:15:38,912 IndelRealigner - Not attempting realignment in interval Uextra:28776143-28776462 because there are too many reads. 
INFO  23:15:40,840 ProgressMeter - Uextra:28778101   6.5113008E7    78.5 m      72.0 s       88.6%    88.6 m      10.1 m 
INFO  23:15:57,299 IndelRealigner - Not attempting realignment in interval Uextra:28812354-28812460 because there are too many reads. 
INFO  23:16:00,754 IndelRealigner - Not attempting realignment in interval Uextra:28813460-28813719 because there are too many reads. 
INFO  23:16:10,843 ProgressMeter - Uextra:28814934   6.5313011E7    79.0 m      72.0 s       88.6%    89.1 m      10.1 m 
INFO  23:16:40,845 ProgressMeter - Uextra:28860786   6.5513015E7    79.5 m      72.0 s       88.7%    89.7 m      10.2 m 
INFO  23:17:10,846 ProgressMeter - Uextra:28933592   6.5813024E7    80.0 m      72.0 s       88.7%    90.2 m      10.2 m 
INFO  23:17:40,848 ProgressMeter - Uextra:28991448   6.601305E7    80.5 m      73.0 s       88.7%    90.7 m      10.2 m 
INFO  23:18:10,849 ProgressMeter -   2RHet:1633184   6.6763455E7    81.0 m      72.0 s       89.7%    90.3 m       9.3 m 
INFO  23:18:40,857 ProgressMeter -    3LHet:209530   6.7613584E7    81.5 m      72.0 s       91.0%    89.5 m       8.0 m 
INFO  23:19:10,859 ProgressMeter -   3LHet:2423178   6.8613596E7    82.0 m      71.0 s       92.4%    88.8 m       6.8 m 
INFO  23:19:40,860 ProgressMeter -   3RHet:2309509   6.9594065E7    82.5 m      71.0 s       93.8%    88.0 m       5.5 m 
INFO  23:20:10,862 ProgressMeter -       U:1969138   7.03779E7    83.0 m      70.0 s       95.1%    87.3 m       4.3 m 
INFO  23:20:40,863 ProgressMeter -       U:5290517   7.1177919E7    83.5 m      70.0 s       97.1%    86.0 m       2.5 m 
INFO  23:21:10,864 ProgressMeter -       U:6293372   7.1677943E7    84.0 m      70.0 s       97.7%    86.0 m       2.0 m 
INFO  23:21:25,163 IndelRealigner - Not attempting realignment in interval U:7316199-7316313 because there are too many reads. 
INFO  23:21:40,866 ProgressMeter -       U:8600252   7.2377954E7    84.5 m      70.0 s       99.0%    85.3 m      50.0 s 
INFO  23:21:52,256 IndelRealigner - Not attempting realignment in interval U:9151211-9151655 because there are too many reads. 
INFO  23:22:03,538 IndelRealigner - Not attempting realignment in interval U:10021896-10022113 because there are too many reads. 
INFO  23:22:07,323 ProgressMeter -            done   7.2936166E7    85.0 m      69.0 s      100.0%    85.0 m       0.0 s 
INFO  23:22:07,324 ProgressMeter - Total runtime 5097.18 secs, 84.95 min, 1.42 hours 
INFO  23:22:07,328 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 72936166 total reads (0.00%) 
INFO  23:22:07,328 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter 
INFO  23:22:07,328 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 

Can anybody help me out?

Best Answer

Answers

Sign In or Register to comment.