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 bernt@interactive.ghpc.dk 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 bernt@interactive.ghpc.dk 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