Picard: FixMateInformation crash

Hello,

I was asked to re-post this question here. It was originally posted in the Picard forum at GitHub at https://github.com/broadinstitute/picard/issues/161.

Regards,

Bernt


ORIGINAL POST (edited)

There seems to be a problems with FixMateInformation crashing with

Exception in thread "main" java.lang.``````NullPointerException``````
at htsjdk.samtools.SamPairUtil.setMateInformationOnSupplementalAlignment(SamPairUtil.java:300)
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.advance(SamPairUtil.java:442)
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.next(SamPairUtil.java:454)
at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.next(SamPairUtil.java:360)
at picard.sam.FixMateInformation.doWork(FixMateInformation.java:194)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:185)
at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:125)
at picard.sam.FixMateInformation.main(FixMateInformation.java:93)

The problem first appeared in version 1.121. It is present in version 1.128. Versions prior to 1.120 worked and continue to work fine. I am currently using Java 1.7.0_75, but I observed the same problem with earlier version of Java. The problem occurs under several different version of Fedora.

The command lines I am using are:

java -jar picard-1.128/picard.jar FixMateInformation INPUT=test.bam OUTPUT=fixed.bam
(fails)

java -jar picard-1.121/FixMateInformation.jar INPUT=test.bam OUTPUT=fixed.bam
(fails)

java -jar picard-1.120/FixMateInformation.jar INPUT=test.bam OUTPUT=fixed.bam
(succeeds)

I have observed the problem with various BAM files. This one is (a small subset of) the output of an indel realignment with GATK.


Later in the same thread:

ValidateSam produces:
java -jar /opt/ghpc/picard-1.121/ValidateSamFile.jar INPUT=test.bam OUTPUT=out.bam [Wed Feb 18 08:48:40 CET 2015] picard.sam.ValidateSamFile INPUT=test.bam OUTPUT=out.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 [Wed Feb 18 08:48:40 CET 2015] Executing as [email protected] on Linux 2.6.35.14-106.fc14.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_75-b13; Picard version: 1.121(da291b4d265f877808b216dce96eaeffd2f30bd3_1411396652) IntelDeflater [Wed Feb 18 08:48:41 CET 2015] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=505937920 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp


And later:

The problem also exists in the new version, 1.129.


New

Re-posted in GATK forum

Picard (1.129)'s ValidateSamFile complains about Mate not found - which was the reason for running FixMateInformation in the first place.

The output is:

java -jar /opt/ghpc/picard-current/picard.jar ValidateSamFile I=test.bam

[Thu Mar 26 16:44:49 CET 2015] picard.sam.ValidateSamFile INPUT=test.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
[Thu Mar 26 16:44:49 CET 2015] Executing as [email protected] on Linux 2.6.35.14-106.fc14.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_75-b13; Picard version: 1.129(b508b2885562a4e932d3a3a60b8ea283b7ec78e2_1424706677) IntelDeflater
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2215:5439:78978, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1216:7853:25411, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2301:9078:52020, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2104:18417:29553, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2310:18752:24451, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2310:6551:24766, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1105:9672:78339, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2112:20003:44801, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2213:8473:74864, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2306:11852:94726, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1110:11106:17369, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2215:12401:47072, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2312:13964:14859, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1312:3886:41184, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1206:12827:34659, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1107:18908:98983, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1313:7640:45146, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1306:1595:15034, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2209:2036:47281, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1201:6826:100382, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2213:4861:63517, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2204:10202:63100, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1207:7125:93640, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1101:9691:36089, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2211:1839:100174, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2312:7331:16518, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2303:13396:44533, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1103:15274:86897, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2110:1541:39614, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1206:10320:20874, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2104:12084:25830, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2115:6231:35664, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1106:5365:6728, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1201:5887:87680, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1204:9449:99890, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2207:6920:91927, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1113:17505:78862, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2311:19423:17546, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2303:6787:39570, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1116:6350:25293, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1305:15016:58323, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1116:10894:97830, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2306:13179:38191, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1301:11303:99731, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2102:13726:37821, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2312:11652:76919, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1208:4895:32748, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1106:9371:79983, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2111:1798:22917, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1107:1267:20231, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1109:15189:92031, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2302:9045:63944, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1102:14247:57062, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2305:7407:36655, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2204:12584:72228, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1111:18302:40904, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2316:8382:94789, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2109:12845:82338, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1206:10557:31568, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2210:14790:11210, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1303:7824:5423, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2111:9909:100689, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2202:16293:94205, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1102:16519:74708, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1305:10365:69588, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2102:8288:100810, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1311:17645:65928, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1109:17819:68329, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2206:3160:52730, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1112:18820:52584, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1108:4475:4687, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2205:7334:35631, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2106:9384:64665, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2316:12960:78271, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1104:3451:71528, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2211:21055:28695, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2202:13814:96357, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2111:17147:10853, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2106:20520:88043, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1214:2637:77724, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1109:9367:35640, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1215:11379:23758, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1304:17507:91188, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2204:12459:100042, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2216:8585:77239, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1313:12667:24591, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1316:10367:5281, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1315:15333:2359, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1206:5534:7650, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2102:4820:93659, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2104:6528:72676, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2305:7297:76200, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1315:5361:88165, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2305:17200:26640, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1302:2356:100479, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1101:3217:24975, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2314:1898:42432, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:1316:5424:4897, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2104:16620:81246, Mate not found for paired read
ERROR: Read name HWI-D00474:91:C62ARANXX:8:2102:15822:17446, Mate not found for paired read
Maximum output of [100] errors reached.
[Thu Mar 26 16:44:50 CET 2015] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=505937920
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

Please let me know where to send the test BAM file.

Regards,

Bernt

test.7z 443.4K

Issue · Github
by Geraldine_VdAuwera

Issue Number
201
State
closed
Last Updated
Closed By
vdauwera

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Thanks for posting this here, Bernt. See this FAQ for bug report upload instructions.

  • bgubgu Member

    The information has been uploaded to your webserver. The zip archive is named FixMateInformationException.zip.

    Regards,

    Bernt

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Thanks Bernt @bgu,

    I've reproduced your issue and it does look like there might be some faulty logic in the handling of supplemental alignments when mates are missing. We'll try to get this fixed.

    Note that FixMateInformation won't solve the problem of missing mates, it only ensures that information is consistent between mates that are present.

  • I got this huge error:

    picard.sam.FixMateInformation INPUT=[outBAM_sorted_marked_realigned.bam] OUTPUT=outBAM_sorted_marked_realigned_fixed.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
    [Tue Jan 30 16:28:36 CST 2018] Executing as [email protected] on Linux 2.6.32-573.8.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-mockbuild_2015_10_21_19_56-b00; Picard version: 1.140(a81bc82e781dae05c922d1dbcee737334612399f_1444244284) IntelDeflater
    INFO 2018-01-30 16:28:36 FixMateInformation Sorting input into queryname order.
    INFO 2018-01-30 17:01:29 FixMateInformation Sorting by queryname complete.
    INFO 2018-01-30 17:01:29 FixMateInformation Output will be sorted by coordinate
    INFO 2018-01-30 17:01:29 FixMateInformation Traversing query name sorted records and fixing up mate pair information.
    [Tue Jan 30 17:01:29 CST 2018] picard.sam.FixMateInformation done. Elapsed time: 32.88 minutes.
    Runtime.totalMemory()=2962751488
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" java.lang.NullPointerException
    at htsjdk.samtools.SamPairUtil.setMateInformationOnSupplementalAlignment(SamPairUtil.java:300)
    at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.advance(SamPairUtil.java:445)
    at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.next(SamPairUtil.java:454)
    at htsjdk.samtools.SamPairUtil$SetMateInfoIterator.next(SamPairUtil.java:360)
    at picard.sam.FixMateInformation.doWork(FixMateInformation.java:195)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @csmatyi
    Hi,

    Can you confirm you are using the latest version of Picard? If so, can you submit a bug report? Instructions are here.

    Thanks,
    Sheila

  • @Sheila said:
    @csmatyi
    Hi,

    Can you confirm you are using the latest version of Picard? If so, can you submit a bug report? Instructions are here.

    Thanks,
    Sheila

    Hello Sheila,
    Yes, it is version 1.14.
    I will leave a report.
    Thanks, Matt

  • SkyWarriorSkyWarrior TurkeyMember

    Version 1.14? That version is supposed to be ages old. The latest version is 2.17.6. Your error log is also not consistent. You seem to have 1.14 version of Picard with IntelDeflaters?? You are also using OpenJDK1.7.

    None of these add up on its own. Can you try your command with OracleJDK 1.8 and latest picard version 2.17.6?

  • Hi,
    I used version 2.17.8 of picard and I still had the same issue as csmatyi
    Should I also submit a bug report?
    Thanks

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @joanabs
    Hi,

    Yes, that would be great.

    Thanks,
    Sheila

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