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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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A BAM/CRAM ERROR #1632

Closed pengxiao78 closed 7 years ago

pengxiao78 commented 8 years ago

Hi Brad, I am running tumor-germline somatic variant calling pipeline. The bcbio-nextgen is 1.0.0 development version and all the --data have been updated into the newest in November 3rd including dbnsfp database. I am using the following yaml file,

details:

Could you help me with the debugging? Thanks.

[2016-11-05T02:52Z] **.edu: Unexpected error Traceback (most recent call last): File "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 50, in _setup_logging yield config File "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 193, in postprocess_alignment return ipython.zip_args(apply(sample.postprocess_alignment, args)) File "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 209, in postprocess_alignment data = _recal_no_markduplicates(data) File "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 215, in _recal_no_markduplicates data = recalibrate.prep_recal(data)[0][0] File "/path/to/anaconda/lib/python2.7/site-packages/bcbio/variation/recalibrate.py", line 44, in prep_recal platform, dbsnp_file, intervals, data) File "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/recalibrate.py", line 89, in _gatk_base_recalibrator broad_runner.run_gatk(params, tmp_dir) File "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/broad/init.py", line 311, in run_gatk log_error=log_error) File "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run _do_run(cmd, checks, log_stdout) File "/path/to/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; unset JAVA_HOME && export PATH=/path/to/bcbio/anaconda/bin:$PATH && /path/to/bcbio/anaconda/bin/gatk -Xms500m -Xmx25480m -XX:+UseSerialGC -Djava.io.tmpdir=/path/to/12th_s/work/tx/tmpaUNcQq -T BaseRecalibrator -o /path/to/12th_s/work/align/1126T/tx/tmpqL63Ut/1126T-sort.grp -I /path/to/12th_s/work/align/1126T/1126T-sort.bam -R /path/to/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --downsample_to_fraction 0.313230956739 --downsampling_type ALL_READS --knownSites /path/to/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp-147.vcf.gz -L /path/to/12th_s/work/bedprep/1126T-sort-callable_sample-callableblocks.bed --interval_set_rule INTERSECTION -nct 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment INFO 21:16:54,580 ProgressMeter - 10:102763801 4.1652958E7 82.3 m 118.0 s 57.5% 2.4 h 60.8 m INFO 21:17:24,584 ProgressMeter - 10:113924337 4.1952962E7 82.8 m 118.0 s 57.9% 2.4 h 60.3 m INFO 21:17:56,363 ProgressMeter - 10:121212132 4.2252968E7 83.3 m 118.0 s 58.1% 2.4 h 60.1 m INFO 21:18:24,998 ReadShardBalancer$1 - Loading BAM index data INFO 21:18:26,138 ReadShardBalancer$1 - Done loading BAM index data INFO 21:18:26,387 ProgressMeter - 10:134270207 4.245297E7 83.8 m 118.0 s 58.5% 2.4 h 59.4 m INFO 21:18:56,595 ProgressMeter - 11:1283168 4.2724879E7 84.3 m 118.0 s 58.6% 2.4 h 59.6 m INFO 21:19:27,115 ProgressMeter - 11:5602599 4.3024882E7 84.8 m 118.0 s 58.7% 2.4 h 59.6 m INFO 21:19:57,118 ProgressMeter - 11:10797004 4.3224888E7 85.3 m 118.0 s 58.9% 2.4 h 59.6 m INFO 21:20:30,258 ProgressMeter - 11:20649623 4.3524894E7 85.9 m 118.0 s 59.2% 2.4 h 59.2 m INFO 21:21:00,262 ProgressMeter - 11:34670672 4.3724897E7 86.4 m 118.0 s 59.7% 2.4 h 58.4 m INFO 21:21:30,621 ProgressMeter - 11:47772553 4.4024904E7 86.9 m 118.0 s 60.1% 2.4 h 57.7 m INFO 21:22:00,626 ProgressMeter - 11:59260027 4.4324908E7 87.4 m 118.0 s 60.5% 2.4 h 57.1 m INFO 21:22:33,202 ProgressMeter - 11:63979134 4.4624911E7 87.9 m 118.0 s 60.6% 2.4 h 57.1 m INFO 21:23:03,487 ProgressMeter - 11:67012937 4.5024916E7 88.4 m 117.0 s 60.7% 2.4 h 57.2 m INFO 21:23:33,578 ProgressMeter - 11:71944030 4.532492E7 88.9 m 117.0 s 60.9% 2.4 h 57.2 m INFO 21:24:05,943 ProgressMeter - 11:78780766 4.5524925E7 89.5 m 117.0 s 61.1% 2.4 h 57.0 m INFO 21:24:38,423 ProgressMeter - 11:93464822 4.5724927E7 90.0 m 118.0 s 61.6% 2.4 h 56.2 m INFO 21:25:08,923 ProgressMeter - 11:108063061 4.602493E7 90.5 m 118.0 s 62.0% 2.4 h 55.4 m INFO 21:25:41,049 ProgressMeter - 11:115760132 4.6324936E7 91.1 m 117.0 s 62.3% 2.4 h 55.2 m INFO 21:26:12,877 ProgressMeter - 11:121414874 4.6624943E7 91.6 m 117.0 s 62.5% 2.4 h 55.0 m INFO 21:26:36,618 ReadShardBalancer$1 - Loading BAM index data INFO 21:26:37,869 ReadShardBalancer$1 - Done loading BAM index data INFO 21:26:43,193 ProgressMeter - 11:130773140 4.6824945E7 92.1 m 118.0 s 62.8% 2.4 h 54.6 m INFO 21:27:13,196 ProgressMeter - 12:4737198 4.708522E7 92.6 m 118.0 s 63.1% 2.4 h 54.3 m INFO 21:27:43,200 ProgressMeter - 12:9144877 4.7385225E7 93.1 m 117.0 s 63.2% 2.5 h 54.2 m INFO 21:28:13,516 ProgressMeter - 12:18891897 4.7685234E7 93.6 m 117.0 s 63.5% 2.5 h 53.8 m INFO 21:28:44,402 ProgressMeter - 12:28544401 4.7885237E7 94.1 m 117.0 s 63.8% 2.5 h 53.3 m INFO 21:29:14,721 ProgressMeter - 12:40922106 4.8085239E7 94.6 m 118.0 s 64.2% 2.5 h 52.7 m INFO 21:29:44,826 ProgressMeter - 12:50821723 4.8485247E7 95.1 m 117.0 s 64.5% 2.5 h 52.3 m INFO 21:30:17,469 ProgressMeter - 12:54765488 4.8785253E7 95.7 m 117.0 s 64.7% 2.5 h 52.3 m INFO 21:30:47,633 ProgressMeter - 12:57892432 4.9085261E7 96.2 m 117.0 s 64.8% 2.5 h 52.3 m INFO 21:31:17,828 ProgressMeter - 12:70760914 4.9385265E7 96.7 m 117.0 s 65.2% 2.5 h 51.6 m INFO 21:31:47,850 ProgressMeter - 12:81688980 4.9585268E7 97.2 m 117.0 s 65.5% 2.5 h 51.1 m INFO 21:32:17,855 ProgressMeter - 12:100646366 4.9885277E7 97.7 m 117.0 s 66.1% 2.5 h 50.0 m INFO 21:32:48,459 ProgressMeter - 12:106901574 5.0185282E7 98.2 m 117.0 s 66.3% 2.5 h 49.8 m INFO 21:33:20,059 ProgressMeter - 12:114395710 5.0485288E7 98.7 m 117.0 s 66.6% 2.5 h 49.5 m INFO 21:33:52,052 ProgressMeter - 12:121766326 5.0785296E7 99.3 m 117.0 s 66.8% 2.5 h 49.3 m INFO 21:34:24,784 ProgressMeter - 12:133225675 5.10853E7 99.8 m 117.0 s 67.2% 2.5 h 48.7 m INFO 21:34:25,566 ReadShardBalancer$1 - Loading BAM index data INFO 21:34:26,559 ReadShardBalancer$1 - Done loading BAM index data INFO 21:34:57,435 ProgressMeter - 13:26154110 5.1302494E7 100.3 m 117.0 s 68.1% 2.5 h 47.1 m INFO 21:35:27,443 ProgressMeter - 13:35756614 5.16025E7 100.8 m 117.0 s 68.4% 2.5 h 46.6 m INFO 21:35:57,561 ProgressMeter - 13:46725011 5.1802506E7 101.3 m 117.0 s 68.7% 2.5 h 46.1 m INFO 21:36:27,572 ProgressMeter - 13:60566363 5.2002508E7 101.8 m 117.0 s 69.2% 2.5 h 45.4 m INFO 21:36:57,582 ProgressMeter - 13:93922401 5.2202511E7 102.3 m 117.0 s 70.2% 2.4 h 43.3 m INFO 21:37:27,793 ProgressMeter - 13:103387886 5.2402514E7 102.8 m 117.0 s 70.6% 2.4 h 42.9 m INFO 21:37:44,727 ReadShardBalancer$1 - Loading BAM index data INFO 21:37:45,741 ReadShardBalancer$1 - Done loading BAM index data INFO 21:37:57,813 ProgressMeter - 13:115091817 5.2702517E7 103.3 m 117.0 s 70.9% 2.4 h 42.4 m INFO 21:38:27,956 ProgressMeter - 14:24034984 5.3049218E7 103.9 m 117.0 s 71.7% 2.4 h 41.0 m INFO 21:38:58,403 ProgressMeter - 14:33290904 5.3249221E7 104.4 m 117.0 s 72.0% 2.4 h 40.6 m INFO 21:39:30,671 ProgressMeter - 14:50088440 5.3449226E7 104.9 m 117.0 s 72.5% 2.4 h 39.7 m INFO 21:40:00,687 ProgressMeter - 14:60622009 5.3749229E7 105.4 m 117.0 s 72.9% 2.4 h 39.2 m INFO 21:40:30,691 ProgressMeter - 14:69795338 5.4049233E7 105.9 m 117.0 s 73.2% 2.4 h 38.8 m INFO 21:41:02,270 ProgressMeter - 14:75325228 5.4349238E7 106.4 m 117.0 s 73.4% 2.4 h 38.6 m INFO 21:41:32,273 ProgressMeter - 14:89039432 5.454924E7 106.9 m 117.0 s 73.8% 2.4 h 38.0 m INFO 21:42:02,483 ProgressMeter - 14:95598000 5.4749242E7 107.4 m 117.0 s 74.0% 2.4 h 37.7 m INFO 21:42:36,699 ProgressMeter - 14:105615774 5.5149252E7 108.0 m 117.0 s 74.3% 2.4 h 37.3 m INFO 21:42:37,191 ReadShardBalancer$1 - Loading BAM index data INFO 21:42:37,873 ReadShardBalancer$1 - Done loading BAM index data INFO 21:43:06,729 ProgressMeter - 15:25322377 5.5314904E7 108.5 m 117.0 s 75.2% 2.4 h 35.8 m INFO 21:43:37,374 ProgressMeter - 15:38786815 5.5614907E7 109.0 m 117.0 s 75.6% 2.4 h 35.1 m INFO 21:44:07,379 ProgressMeter - 15:42985034 5.591492E7 109.5 m 117.0 s 75.8% 2.4 h 35.0 m INFO 21:44:37,639 ProgressMeter - 15:48786354 5.6214928E7 110.0 m 117.0 s 76.0% 2.4 h 34.8 m INFO 21:45:08,108 ProgressMeter - 15:58044460 5.6514932E7 110.5 m 117.0 s 76.3% 2.4 h 34.4 m INFO 21:45:38,174 ProgressMeter - 15:66193445 5.6814935E7 111.0 m 117.0 s 76.5% 2.4 h 34.1 m INFO 21:46:08,217 ProgressMeter - 15:74364261 5.7114939E7 111.5 m 117.0 s 76.8% 2.4 h 33.7 m INFO 21:46:38,879 ProgressMeter - 15:80672525 5.7414946E7 112.0 m 117.0 s 77.0% 2.4 h 33.5 m INFO 21:47:14,348 ProgressMeter - 15:90758294 5.7614948E7 112.6 m 117.0 s 77.3% 2.4 h 33.0 m INFO 21:47:29,041 ReadShardBalancer$1 - Loading BAM index data INFO 21:47:29,880 ReadShardBalancer$1 - Done loading BAM index data INFO 21:47:44,487 ProgressMeter - 15:102517835 5.7914954E7 113.1 m 117.0 s 77.7% 2.4 h 32.5 m INFO 21:48:14,823 ProgressMeter - 16:2505495 5.8277864E7 113.6 m 116.0 s 77.8% 2.4 h 32.5 m INFO 21:48:46,398 ProgressMeter - 16:4940809 5.8477867E7 114.2 m 117.0 s 77.9% 2.4 h 32.5 m INFO 21:49:18,450 ProgressMeter - 16:17432072 5.8777874E7 114.7 m 117.0 s 78.3% 2.4 h 31.9 m INFO 21:49:48,979 ProgressMeter - 16:22192803 5.907788E7 115.2 m 116.0 s 78.4% 2.4 h 31.7 m INFO 21:50:20,959 ProgressMeter - 16:30734340 5.9377884E7 115.7 m 116.0 s 78.7% 2.5 h 31.3 m INFO 21:50:50,963 ProgressMeter - 16:48596053 5.9677888E7 116.2 m 116.0 s 79.3% 2.4 h 30.4 m INFO 21:51:23,006 ProgressMeter - 16:57089106 5.9977891E7 116.8 m 116.0 s 79.5% 2.4 h 30.0 m INFO 21:51:53,130 ProgressMeter - 16:67768911 6.0177893E7 117.3 m 116.0 s 79.9% 2.4 h 29.5 m

ERROR ------------------------------------------------------------------------------------------
ERROR A BAM/CRAM ERROR has occurred (version 3.6-0-g89b7209):
ERROR
ERROR This means that there is something wrong with the BAM/CRAM file(s) you provided.
ERROR The error message below tells you what is the problem.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum until you have followed these instructions:
ERROR - Make sure that your BAM file is well-formed by running Picard's validator on it
ERROR (see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile for details)
ERROR - Ensure that your BAM index is not corrupted: delete the current one and regenerate it with 'samtools index'
ERROR - Ensure that your CRAM index is not corrupted: delete the current one and regenerate it with
ERROR 'java -jar cramtools-3.0.jar index --bam-style-index --input-file --reference-fasta-file '
ERROR (see https://github.com/enasequence/cramtools/tree/v3.0 for details)
ERROR
ERROR MESSAGE: Premature end of file
ERROR ------------------------------------------------------------------------------------------

' returned non-zero exit status 1

pengxiao78 commented 8 years ago

Can anybody answer my question? Urgent to solve the problem. Thanks!

chapmanb commented 8 years ago

Sorry about the delay and the issue. I'm not sure what is going on exactly, GATK is reporting that it thinks the BAM file is truncated, which you could check with:

picard ValidateSamFile I=/path/to/12th_s/work/align/1126T/1126T-sort.bam

If the file looks okay, we ran into a similar issue that was due to a problematic dbSNP file:

https://github.com/chapmanb/bcbio-nextgen/issues/1546#issuecomment-248328884

I still don't understand what happened (or why it gives this error) but you could check dbSNP and removing and re-downloading with bcbio if it's problematic.

Finally, if you don't need realignment and recalibration you can set:

realign: false
recalibrate: false

in your configuration to skip these steps in case there is an issue there. Hope one of these ideas helps.

pengxiao78 commented 8 years ago

Hi Brad,

When I run picard ValidateSamFile I=/path/to/12th_s/work/align/1126T/1126T-sort.bam, I did find the following errors. Any suggestion?

Thanks,

Peng

Linux 2.6.32-642.6.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 2.5.0(2c370988aefe41f579920c8a6a678a201c5261c1_1466708365) ERROR: Record 3709, Read name D00195:196:C9VUYANXX:1:1207:21262:59387, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 3709, Read name D00195:196:C9VUYANXX:1:1207:21262:59387, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 7180, Read name D00195:196:C9VUYANXX:2:2211:21295:62001, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 7180, Read name D00195:196:C9VUYANXX:2:2211:21295:62001, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 8607, Read name D00195:196:C9VUYANXX:7:1304:19203:36496, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 8607, Read name D00195:196:C9VUYANXX:7:1304:19203:36496, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 9168, Read name D00195:196:C9VUYANXX:2:1101:2004:90403, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 9168, Read name D00195:196:C9VUYANXX:2:1101:2004:90403, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 9421, Read name D00195:196:C9VUYANXX:6:1108:7516:70688, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 9421, Read name D00195:196:C9VUYANXX:6:1108:7516:70688, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 11017, Read name D00195:196:C9VUYANXX:8:2104:20312:51148, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 11017, Read name D00195:196:C9VUYANXX:8:2104:20312:51148, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 14530, Read name D00195:196:C9VUYANXX:2:1206:13809:51611, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 14530, Read name D00195:196:C9VUYANXX:2:1206:13809:51611, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 15224, Read name D00195:196:C9VUYANXX:4:1116:1639:68487, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 15224, Read name D00195:196:C9VUYANXX:4:1116:1639:68487, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 17226, Read name D00195:196:C9VUYANXX:2:2307:17035:13804, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 17226, Read name D00195:196:C9VUYANXX:2:2307:17035:13804, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 18988, Read name D00195:196:C9VUYANXX:7:1208:3257:46404, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 18988, Read name D00195:196:C9VUYANXX:7:1208:3257:46404, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 26139, Read name D00195:196:C9VUYANXX:7:1301:5115:3251, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 26139, Read name D00195:196:C9VUYANXX:7:1301:5115:3251, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 27360, Read name D00195:196:C9VUYANXX:4:2304:10154:86989, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 27360, Read name D00195:196:C9VUYANXX:4:2304:10154:86989, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 29302, Read name D00195:196:C9VUYANXX:3:2312:21296:67962, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 29302, Read name D00195:196:C9VUYANXX:3:2312:21296:67962, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 37297, Read name D00195:196:C9VUYANXX:2:1101:4929:70349, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 37297, Read name D00195:196:C9VUYANXX:2:1101:4929:70349, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 39568, Read name D00195:196:C9VUYANXX:1:1214:13318:47958, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 39568, Read name D00195:196:C9VUYANXX:1:1214:13318:47958, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 41105, Read name D00195:196:C9VUYANXX:8:1216:8068:73244, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 41105, Read name D00195:196:C9VUYANXX:8:1216:8068:73244, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 45339, Read name D00195:196:C9VUYANXX:8:2105:11850:68440, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 45339, Read name D00195:196:C9VUYANXX:8:2105:11850:68440, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 51300, Read name D00195:196:C9VUYANXX:1:1110:21260:100517, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 51300, Read name D00195:196:C9VUYANXX:1:1110:21260:100517, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 54649, Read name D00195:196:C9VUYANXX:1:2112:21284:43679, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 54649, Read name D00195:196:C9VUYANXX:1:2112:21284:43679, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 54679, Read name D00195:196:C9VUYANXX:7:2302:16845:94116, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 54679, Read name D00195:196:C9VUYANXX:7:2302:16845:94116, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55654, Read name D00195:196:C9VUYANXX:1:2115:13039:79747, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55654, Read name D00195:196:C9VUYANXX:1:2115:13039:79747, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55661, Read name D00195:196:C9VUYANXX:7:2315:5226:22337, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55661, Read name D00195:196:C9VUYANXX:7:2315:5226:22337, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55683, Read name D00195:196:C9VUYANXX:3:1207:1795:49121, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55683, Read name D00195:196:C9VUYANXX:3:1207:1795:49121, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55685, Read name D00195:196:C9VUYANXX:3:2113:3035:9209, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55685, Read name D00195:196:C9VUYANXX:3:2113:3035:9209, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55696, Read name D00195:196:C9VUYANXX:7:2304:16822:62096, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55696, Read name D00195:196:C9VUYANXX:7:2304:16822:62096, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55697, Read name D00195:196:C9VUYANXX:1:2308:3192:42862, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55697, Read name D00195:196:C9VUYANXX:1:2308:3192:42862, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55699, Read name D00195:196:C9VUYANXX:3:2211:18204:27633, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55699, Read name D00195:196:C9VUYANXX:3:2211:18204:27633, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55713, Read name D00195:196:C9VUYANXX:5:2212:2256:57699, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55713, Read name D00195:196:C9VUYANXX:5:2212:2256:57699, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55722, Read name D00195:196:C9VUYANXX:1:1210:17366:100768, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55722, Read name D00195:196:C9VUYANXX:1:1210:17366:100768, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55728, Read name D00195:196:C9VUYANXX:1:2109:19416:47232, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55728, Read name D00195:196:C9VUYANXX:1:2109:19416:47232, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55731, Read name D00195:196:C9VUYANXX:7:2315:6778:97238, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55731, Read name D00195:196:C9VUYANXX:7:2315:6778:97238, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55764, Read name D00195:196:C9VUYANXX:1:1109:3084:47925, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55764, Read name D00195:196:C9VUYANXX:1:1109:3084:47925, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55832, Read name D00195:196:C9VUYANXX:3:2106:17573:77823, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55832, Read name D00195:196:C9VUYANXX:3:2106:17573:77823, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55861, Read name D00195:196:C9VUYANXX:3:2104:5889:48475, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55861, Read name D00195:196:C9VUYANXX:3:2104:5889:48475, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55866, Read name D00195:196:C9VUYANXX:5:2102:19378:20316, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55866, Read name D00195:196:C9VUYANXX:5:2102:19378:20316, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55920, Read name D00195:196:C9VUYANXX:4:2113:14572:69285, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55920, Read name D00195:196:C9VUYANXX:4:2113:14572:69285, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55940, Read name D00195:196:C9VUYANXX:4:1209:7003:20298, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55940, Read name D00195:196:C9VUYANXX:4:1209:7003:20298, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 55987, Read name D00195:196:C9VUYANXX:2:2202:18275:6927, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 55987, Read name D00195:196:C9VUYANXX:2:2202:18275:6927, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56050, Read name D00195:196:C9VUYANXX:7:1212:14544:25212, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56050, Read name D00195:196:C9VUYANXX:7:1212:14544:25212, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56096, Read name D00195:196:C9VUYANXX:4:1110:2439:13403, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56096, Read name D00195:196:C9VUYANXX:4:1110:2439:13403, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56123, Read name D00195:196:C9VUYANXX:3:1106:17322:84913, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56123, Read name D00195:196:C9VUYANXX:3:1106:17322:84913, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56125, Read name D00195:196:C9VUYANXX:1:1115:5163:6796, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56125, Read name D00195:196:C9VUYANXX:1:1115:5163:6796, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56130, Read name D00195:196:C9VUYANXX:4:1307:4420:99391, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56130, Read name D00195:196:C9VUYANXX:4:1307:4420:99391, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56192, Read name D00195:196:C9VUYANXX:8:2110:4894:24611, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56192, Read name D00195:196:C9VUYANXX:8:2110:4894:24611, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56222, Read name D00195:196:C9VUYANXX:6:2113:10674:60906, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56222, Read name D00195:196:C9VUYANXX:6:2113:10674:60906, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56278, Read name D00195:196:C9VUYANXX:4:1303:17694:38818, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56278, Read name D00195:196:C9VUYANXX:4:1303:17694:38818, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56285, Read name D00195:196:C9VUYANXX:3:1306:14564:78703, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56285, Read name D00195:196:C9VUYANXX:3:1306:14564:78703, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56393, Read name D00195:196:C9VUYANXX:5:2214:17487:12566, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56393, Read name D00195:196:C9VUYANXX:5:2214:17487:12566, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56437, Read name D00195:196:C9VUYANXX:1:2208:13137:54602, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56437, Read name D00195:196:C9VUYANXX:1:2208:13137:54602, Mate CIGAR string does not match CIGAR string of mate ERROR: Record 56490, Read name D00195:196:C9VUYANXX:5:1301:5797:13143, Mate CIGAR String (MC Attribute) present for a read whose mate is unmapped ERROR: Record 56490, Read name D00195:196:C9VUYANXX:5:1301:5797:13143, Mate CIGAR string does not match CIGAR string of mate Maximum output of [100] errors reached.

chapmanb commented 8 years ago

Peng; Those errors/warnings aren't relevant to the problem you have (GATK is complaining about a truncated file). picard is pretty picky and the MC issue doesn't cause problems with other software (although is resolved with recent versions of samblaster and biobambam). You might need to use samtools instead to check the BAM file:

samtools quickcheck /path/to/12th_s/work/align/1126T/1126T-sort.bam

If that looks good I'd proceed to the other suggestions for debugging. Hope this helps.

pengxiao78 commented 8 years ago

Hi Brad, I just further updated the dbSNP. The running is going and does not show any error until now. Thank you!

lpantano commented 7 years ago

Hi @pengxiao78

I will close this guessing you got it working. Let us know if you find more issues.

Thanks!