Failings in BadCigarFilter, BadMateFilter, and others

mufernandomufernando São PauloMember

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 [email protected] 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 [email protected] 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

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