Hi all,
I did a search of this forum and wasn't able to find a solution to my problem. Point me in a direction if this has already been addressed.
I'm getting the following error when running IndelRealigner:
ERROR MESSAGE: Error caching SAM record
HWI-ST632:9204NCACXX:2:1101:10620:83792, which is usually caused by malformed SAM/BAM files in which multiple identical copies of a read are
present.
The command I'm running is:
java -Xmx8g -Djava.io.tmpdir=/tmp/110809S10v1.2.9_zmzk -jar
GenomeAnalysisTK-1.1-26-g9f3328d/GenomeAnalysisTK.jar -T IndelRealigner -R human_g1k_v37.fasta -targetIntervals 110809S10_realn.intervals
-B:dbsnp,vcf dbsnp_134_b37.vcf -I 110809S10_tumor_dupRem.bam -o 110809S10_tumor_realign.bam
I checked the dupRem.bam file for the HWI-ST632:9204NCACXX:2:1101:10620:83792 record and found the following lines:
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16902900 0 77M835N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16902900 HI:i:0
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16902900 0 77M7112N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16902900 HI:i:1
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16902900 0 77M13417N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16909177 HI:i:2
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16909177 0 77M835N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16909177 HI:i:3
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16909177 0 77M7140N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16915482 HI:i:4
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16915482 0 77M835N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:147589993 HI:i:5
HWI-ST632:9204NCACXX:2:1101:10620:83792 153 1 147589993 0 77M7112N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:147596274 HI:i:6
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 147596274 0 77M831N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:148343732 HI:i:7
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 148343732 0 77M831N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 HI:i:8
Sorry for all the data, but I though it better to include everything. I ran picard MarkDuplicates in an earlier step in the pipeline but it didn't seem to get rid of the offending records. I tried running picard MarkDuplicates again on the dupRep.bam file to no avail. I'm relatively new at this game and appreciate any suggestions.
I did a search of this forum and wasn't able to find a solution to my problem. Point me in a direction if this has already been addressed.
I'm getting the following error when running IndelRealigner:
ERROR MESSAGE: Error caching SAM record
HWI-ST632:9204NCACXX:2:1101:10620:83792, which is usually caused by malformed SAM/BAM files in which multiple identical copies of a read are
present.
The command I'm running is:
java -Xmx8g -Djava.io.tmpdir=/tmp/110809S10v1.2.9_zmzk -jar
GenomeAnalysisTK-1.1-26-g9f3328d/GenomeAnalysisTK.jar -T IndelRealigner -R human_g1k_v37.fasta -targetIntervals 110809S10_realn.intervals
-B:dbsnp,vcf dbsnp_134_b37.vcf -I 110809S10_tumor_dupRem.bam -o 110809S10_tumor_realign.bam
I checked the dupRem.bam file for the HWI-ST632:9204NCACXX:2:1101:10620:83792 record and found the following lines:
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16902900 0 77M835N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16902900 HI:i:0
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16902900 0 77M7112N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16902900 HI:i:1
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16902900 0 77M13417N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16909177 HI:i:2
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16909177 0 77M835N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16909177 HI:i:3
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16909177 0 77M7140N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:16915482 HI:i:4
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 16915482 0 77M835N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:147589993 HI:i:5
HWI-ST632:9204NCACXX:2:1101:10620:83792 153 1 147589993 0 77M7112N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:147596274 HI:i:6
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 147596274 0 77M831N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 CC:Z:= CP:i:148343732 HI:i:7
HWI-ST632:9204NCACXX:2:1101:10620:83792 409 1 148343732 0 77M831N24M * 0 0 CATCTCTCCCTTCCCGTAACTTCTCCCTTAACTGGGTCAGCTCTCGTTCCTGAGAGTGAACCAGGACTTTATATTGCCTGAGCCCCTCAGCTTGCTTGAGC @:0@958@B?5588(>5(,?A>BB=@>@@>;???;.).)==5'-'88=).)8B4B8??*009*9:0**@DD:?)FC1112))3+:EA++FC?FDDA:F@BB RG:Z:110809S10_tumor NM:i:1 XS:A:- NH:i:9 HI:i:8
Sorry for all the data, but I though it better to include everything. I ran picard MarkDuplicates in an earlier step in the pipeline but it didn't seem to get rid of the offending records. I tried running picard MarkDuplicates again on the dupRep.bam file to no avail. I'm relatively new at this game and appreciate any suggestions.
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