Picard Tools Markduplicates 'No Group 1' Error

Question

[bruce.moran]

Hi all,

I am getting a funny error and can't figure out what the issue is:

[Mon Jun 24 17:29:31 IST 2013] Executing as bmoran@compute04 on Linux 2.6.32.59-0.7-default amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_02-b13; Picard version: 1.93(1476)
INFO    2013-06-24 17:29:31     MarkDuplicates  Start of doWork freeMemory: 1133547176; totalMemory: 1140457472; maxMemory: 16924540928
INFO    2013-06-24 17:29:31     MarkDuplicates  Reading input file and constructing read end information.
INFO    2013-06-24 17:29:31     MarkDuplicates  Will retain up to 67160876 data points before spilling to disk.
[Mon Jun 24 17:29:32 IST 2013] net.sf.picard.sam.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1140457472
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.IndexOutOfBoundsException: No group 1
        at java.util.regex.Matcher.group(Matcher.java:487)
        at net.sf.picard.sam.AbstractDuplicateFindingAlgorithm.addLocationInformation(AbstractDuplicateFindingAlgorithm.java:94)
        at net.sf.picard.sam.MarkDuplicates.buildReadEnds(MarkDuplicates.java:488)
        at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:413)
        at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:161)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
        at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:145)

I have no idea about Java so help appreciated. Seems to be a find/replace error in general (from Google) but I do not see where that is happening in markDuplicates. I give it a regex for the read names (format= HWI-ST0988:234:C1MAUXR:3:1131:7638:2239), but that is validated and correct (AFAIK!). I am using output from the latest stable version of STAR (2.3.0) which is apparently importable to Picard.

java -jar ~/bin/picard-tools-1.93/MarkDuplicates.jar I=./Aligned.out.sam O=./Aligned.rmdup.sam M=./pic.met REMOVE_DUPLICATES=TRUE AS=TRUE READ_NAME_REGEX="[a-zA-Z0-9-]+:[0-9]+:[a-zA-Z0-9]+:[0-9]+:[0-9]+:[0-9]+:[0-9]+" VALIDATION_STRINGENCY=LENIENT

Thanks,
Bruce.

Answer 1

[Pierre Lindenbaum]

you need to specify a regular expression group (= specify the parenthesis) in your parameter: READ_NAME_REGEX

Example:

"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*

[bruce.moran]

Hi Pierre, thanks for the answer, thought it was something horrendously complicated, had tried all combinations of the REGEX I give above but the parentheses caught me out. Need them around numeric ([0-9]+) but not on the alphanumeric. Appreciate your response. Bruce.