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Daniel-Liu-c0deb0t / UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
MIT License
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Problem executing umicollapse.jar #8

Open osvaldogc opened 3 years ago

osvaldogc commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

@osvaldogc Any updates?