Good afternoon Nils.
I attach ouputs and log for ValidateSamFile from input BAM to
MarkDuplicates.
Thanks. Antonio M. Agraz
2014-11-24 15:28 GMT+01:00 Nils Homer <nho...@broadinstitute.org>:
> Hey Antonio,
>
> could you run ValidateSamFile on the input BAM to MarkDuplicates? If you
> have a small test case on which we can reproduce, please send it along,
>
> N
>
> On Mon, Nov 24, 2014 at 5:14 AM, antonio agraz <
> antonio.agraz.bio...@gmail.com> wrote:
>
>> Good afternoon. I send you this mail due to dubts using Picard.
>>
>> We use Picard/CleanSmar.jar:
>> java -Xmx4g -jar $Picard_jarFolder/CleanSam.jar INPUT=$sample
>> OUTPUT=$clean_picard VALIDATION_STRINGENCY=LENIENT 2>$log_clean_picard"
>>
>> Later we use fixmate a sort by samtools.
>> but when we use the next step:
>>
>> java -Xmx2g -jar $Picard_jarFolder/MarkDuplicates.jar
>> INPUT=$sorted1_samtools_bam OUTPUT=$sorted_picard_marked_bam TMP_DIR=./
>> METRICS_FILE=$log_duplicate_metrics REMOVE_DUPLICATES=false
>> ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
>> 2>$log_picard_marked_bam"
>>
>> We have the next problem and we dont know why, if we had used CleanSam
>> (which it is supposed to
>>
>> Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference
>> alignments and setting MAPQ to 0 for unmapped reads)
>>
>> [Thu Nov 13 12:43:12 CET 2014] net.sf.picard.sam.MarkDuplicates done.
>> Elapsed time: 10,13 minutes.
>> Runtime.totalMemory()=1691418624
>> Exception in thread "main" net.sf.samtools.SAMException: Exception when
>> processing alignment for BAM index HS12_10750:8:2310:1400:98064#42 1/2 75b
>> unmapped read.
>> at net.sf.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:112)
>> at net.sf.samtools
>> .SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:168)
>> at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:208)
>> at net.sf.picard
>> .cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
>> at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:106)
>> Caused by: net.sf.samtools.SAMException: Exception creating BAM index
>> for record HS12_10750:8:2310:1400:98064#42 1/2 75b unmapped read.
>> at net.sf.samtools.BAMIndexer.processAlignment(BAMIndexer.java:94)
>> at net.sf.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:109)
>> ... 4 more
>> Caused by: java.lang.ArrayIndexOutOfBoundsException: 8304
>> at net.sf.samtools
>> .BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:219)
>> at net.sf.samtools.BAMIndexer.processAlignment(BAMIndexer.java:92)
>> ... 5 more
>>
>> Previously, we have not reported this problem.
>>
>> Thanks. Best regards,
>>
>> Antonio M. Agraz
>>
>>
>> ------------------------------------------------------------------------------
>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
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>>
>>
>
ERROR: Record 25511221, Read name HS5_7045:4:1104:14021:172923#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 54696488, Read name HS5_7045:4:2206:1376:200265#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124105383, Read name HS5_7045:4:1108:5246:193120#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105384, Read name HS5_7045:4:2203:14182:125644#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105387, Read name HS5_7045:4:1306:5368:24950#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124105388, Read name HS5_7045:4:2107:20863:118643#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105390, Read name HS5_7045:4:2205:2833:147063#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105392, Read name HS5_7045:4:2103:17268:179167#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105394, Read name HS5_7045:4:1308:11627:2869#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124105395, Read name HS5_7045:4:1203:12926:44093#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105396, Read name HS5_7045:4:2206:17873:32130#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105398, Read name HS5_7045:4:2201:15410:32762#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105400, Read name HS5_7045:4:2202:14223:40562#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105403, Read name HS5_7045:4:2105:6522:19167#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124105405, Read name HS5_7045:4:1102:7426:47937#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124105407, Read name HS5_7045:4:1105:16142:187521#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105409, Read name HS5_7045:4:2202:16885:86629#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105410, Read name HS5_7045:4:1308:7128:188371#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105412, Read name HS5_7045:4:1306:7185:139800#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105414, Read name HS5_7045:4:1101:21350:2717#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124105416, Read name HS5_7045:4:2207:7006:141588#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105418, Read name HS5_7045:4:2202:4886:155778#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105419, Read name HS5_7045:4:1201:17324:39571#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105558, Read name HS5_7045:4:1101:16223:18951#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124105939, Read name HS5_7045:4:2108:7088:5074#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124105957, Read name HS5_7045:4:2205:12670:61454#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124106018, Read name HS5_7045:4:1104:7908:94824#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124106074, Read name HS5_7045:4:1206:16948:38663#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124106137, Read name HS5_7045:4:1207:15029:161940#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124106332, Read name HS5_7045:4:1304:6449:68548#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124106337, Read name HS5_7045:4:2301:20127:28795#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124106379, Read name HS5_7045:4:1301:20697:13237#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124106380, Read name HS5_7045:4:2106:17048:143334#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124106535, Read name HS5_7045:4:2303:3858:68433#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124106662, Read name HS5_7045:4:1208:13966:92525#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124106809, Read name HS5_7045:4:1101:12803:158952#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124106810, Read name HS5_7045:4:1208:17624:18466#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107011, Read name HS5_7045:4:2206:16605:71412#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107226, Read name HS5_7045:4:1307:1217:107676#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107384, Read name HS5_7045:4:1105:12710:46108#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107440, Read name HS5_7045:4:2306:13613:181266#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107497, Read name HS5_7045:4:2305:20641:83189#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107504, Read name HS5_7045:4:1102:16343:132621#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107505, Read name HS5_7045:4:1305:4952:44501#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124107506, Read name HS5_7045:4:1105:20498:7223#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124107558, Read name HS5_7045:4:2208:11188:68414#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107664, Read name HS5_7045:4:1201:17807:10128#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107832, Read name HS5_7045:4:2208:5763:162489#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107948, Read name HS5_7045:4:2107:16332:163579#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124107983, Read name HS5_7045:4:2301:6932:151079#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108109, Read name HS5_7045:4:2305:12002:118218#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108140, Read name HS5_7045:4:2208:19842:94373#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108534, Read name HS5_7045:4:1206:19144:81398#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108535, Read name HS5_7045:4:1302:16508:131219#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108536, Read name HS5_7045:4:2203:16646:124396#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108697, Read name HS5_7045:4:1205:12006:22412#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108818, Read name HS5_7045:4:1108:9771:169132#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108819, Read name HS5_7045:4:2204:18842:161947#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124108868, Read name HS5_7045:4:2204:1187:2297#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124108999, Read name HS5_7045:4:1201:15491:90067#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109042, Read name HS5_7045:4:1204:10498:174842#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109095, Read name HS5_7045:4:2206:4867:155276#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109131, Read name HS5_7045:4:1105:5776:83938#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124109150, Read name HS5_7045:4:2203:13310:148273#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109151, Read name HS5_7045:4:2301:18567:35321#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109189, Read name HS5_7045:4:1207:1138:104867#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109195, Read name HS5_7045:4:2302:10966:96841#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109227, Read name HS5_7045:4:2105:1594:72974#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124109233, Read name HS5_7045:4:1201:11423:72833#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109234, Read name HS5_7045:4:1201:1293:68537#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124109348, Read name HS5_7045:4:1207:21088:6778#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124109412, Read name HS5_7045:4:1302:15570:63300#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109618, Read name HS5_7045:4:2308:20392:98051#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109638, Read name HS5_7045:4:1103:12775:117638#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109681, Read name HS5_7045:4:1308:2703:48063#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124109721, Read name HS5_7045:4:1202:18920:174027#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109725, Read name HS5_7045:4:2305:6405:142602#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109806, Read name HS5_7045:4:1101:6249:184156#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109807, Read name HS5_7045:4:1202:19614:12736#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109808, Read name HS5_7045:4:2301:7583:82697#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124109809, Read name HS5_7045:4:1206:17744:78420#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109982, Read name HS5_7045:4:1304:2689:148571#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124109983, Read name HS5_7045:4:2104:7178:76429#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124110018, Read name HS5_7045:4:2201:3225:79115#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124110049, Read name HS5_7045:4:1204:14155:74337#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110050, Read name HS5_7045:4:1205:9884:53551#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124110053, Read name HS5_7045:4:1108:5588:102297#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110073, Read name HS5_7045:4:2102:6869:56367#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124110137, Read name HS5_7045:4:1108:13603:115629#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110216, Read name HS5_7045:4:1306:4187:148272#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110219, Read name HS5_7045:4:1302:8748:58885#8, MAPQ should be
0 for unmapped read.
ERROR: Record 124110241, Read name HS5_7045:4:1102:17329:133501#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110293, Read name HS5_7045:4:1306:6045:180348#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110425, Read name HS5_7045:4:1108:16236:198442#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110459, Read name HS5_7045:4:2107:11632:93856#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110463, Read name HS5_7045:4:2102:16001:166446#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110497, Read name HS5_7045:4:2102:19322:90335#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110532, Read name HS5_7045:4:2102:18428:17524#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110533, Read name HS5_7045:4:2201:9474:150810#8, MAPQ should
be 0 for unmapped read.
ERROR: Record 124110750, Read name HS5_7045:4:1102:13576:167153#8, MAPQ should
be 0 for unmapped read.
Maximum output of [100] errors reached.
[Mon Nov 24 16:03:40 CET 2014] net.sf.picard.sam.ValidateSamFile INPUT=BPRV1_2d_tail_sort2_sort1.bam OUTPUT=output.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Nov 24 16:03:40 CET 2014] Executing as agr...@ibbtecpc62.ibbtec.unican.es on Linux 2.6.32-358.23.2.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; Picard version: 1.61(1094)
INFO 2014-11-24 16:04:13 SamFileValidator 10000000 reads validated.
INFO 2014-11-24 16:04:45 SamFileValidator 20000000 reads validated.
INFO 2014-11-24 16:05:17 SamFileValidator 30000000 reads validated.
INFO 2014-11-24 16:05:49 SamFileValidator 40000000 reads validated.
INFO 2014-11-24 16:06:20 SamFileValidator 50000000 reads validated.
INFO 2014-11-24 16:06:51 SamFileValidator 60000000 reads validated.
INFO 2014-11-24 16:07:23 SamFileValidator 70000000 reads validated.
INFO 2014-11-24 16:07:54 SamFileValidator 80000000 reads validated.
INFO 2014-11-24 16:08:25 SamFileValidator 90000000 reads validated.
INFO 2014-11-24 16:08:57 SamFileValidator 100000000 reads validated.
INFO 2014-11-24 16:09:27 SamFileValidator 110000000 reads validated.
INFO 2014-11-24 16:09:57 SamFileValidator 120000000 reads validated.
[Mon Nov 24 16:10:10 CET 2014] net.sf.picard.sam.ValidateSamFile done. Elapsed time: 6,50 minutes.
Runtime.totalMemory()=432865280
------------------------------------------------------------------------------
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