Problem executing umicollapse.jar

[osvaldogc]

Hi Daniel,

I am trying to execute UMIcollapse on my samples, but I am facing problems during the execution. Any suggestion, please?

/usr/bin/java -server -Xms16G -Xmx16G -Xss32M -jar /home/ograna/SOFTWARE/UMICollapse/umicollapse.jar -i YCX00009.CLEAN_sorted.bam -o YCX00009.dedup.bam
Arguments [-i, YCX00009.CLEAN_sorted.bam, -o, YCX00009.dedup.bam]
Exception in thread "main" java.lang.NullPointerException
at umicollapse.main.Main.main(Main.java:32)

My version of java
/usr/bin/java -version
openjdk version "11.0.9.1" 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04)
OpenJDK 64-Bit Server VM (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04, mixed mode, sharing)

[osvaldogc]

I've just tried another possibility, adding 'bam' as a first argument:

/usr/bin/java -server -Xms16G -Xmx16G -Xss32M -jar /home/ograna/SOFTWARE/UMICollapse/umicollapse.jar bam -i YCX00009.CLEAN_sorted.bam -o YCX00009.dedup.bam
Arguments [bam, -i, YCX00009.CLEAN_sorted.bam, -o, YCX00009.dedup.bam]
Exception in thread "main" java.lang.IllegalStateException: No match found
at java.base/java.util.regex.Matcher.group(Matcher.java:645)
at umicollapse.util.SAMRead.getUMI(SAMRead.java:36)
at umicollapse.main.DeduplicateSAM.deduplicateAndMerge(DeduplicateSAM.java:106)
at umicollapse.main.Main.main(Main.java:212)

[Daniel-Liu-c0deb0t]

Yeah, you will need to explicitly specify sam/bam or fastq as the first argument to let UMICollapse know which mode is being used.

It seems like UMIs are not being found in the read headers of your BAM records. Either the UMI separator in your read header is not _ (you will need to specify --umi-sep with another separator), or you haven't extracted UMIs with UMI-tools before alignment. If you paste one of your BAM records here, perhaps I can try to see what's missing.

[Daniel-Liu-c0deb0t]

@osvaldogc Any updates?