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tianshilu / QBRC-Somatic-Pipeline

QBRC Somatic Mutation Calling Pipeline
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About LocatIt_ #18

Open SuqinYang opened 2 years ago

SuqinYang commented 2 years ago

Hi, Professor Wang@wtwt5237 Sorry to bother you. thank you for doing such an excellent job! I am trying to use the "QBRC-Somatic-Pipeline" in my deep exome sequencing data.I see that the software LocatIt_v4.0.1.jar is used here, and I get an error in the "mark duplicates" step when I use this software. I don't know why this is. By the way I would like to ask what is the difference between it and picard in the "mark duplicates" step? Errors: Saving /tumor/tmp/_login01_fccf7c70-7e84-4817-83b3-3f6c7c576376_041.bam, #reads: 800000 (0), 703822 amplicons written to file. java.lang.OutOfMemoryError: GC overhead limit exceeded at java.lang.StringCoding$StringEncoder.encode(StringCoding.java:300) at java.lang.StringCoding.encode(StringCoding.java:344) at java.lang.StringCoding.encode(StringCoding.java:387) at java.lang.String.getBytes(String.java:958) at com.agilent.locatit.main.SequencingRead.readBarcode(SequencingRead.java:485) at com.agilent.locatit.main.MolecularBarcodePairedEndProcess.createSequencingReadsFromSAMRecs(MolecularBarcodePairedEndProcess.java:295) at com.agilent.locatit.main.MolecularBarcodePairedEndProcess.processRestOfCache(MolecularBarcodePairedEndProcess.java:580) at com.agilent.locatit.main.MolecularBarcodePairedEndProcess.locate(MolecularBarcodePairedEndProcess.java:678) at com.agilent.locatit.main.LocatIt.main(LocatIt.java:665)

Internal Error caught: 30.

1664112213862
wtwt5237 commented 1 year ago

Hi @SuqinYang

Are you trying to apply our pipeline on deep sequencing data? There is a flag in our pipeline to inform the pipeline that it is accepting agilent deep sequencing data. If you are not using deep sequencing data, you should not use that flag, and our pipeline will be using the picard software to do de-dup. Picard is used for regular exome-seq data

Thanks!

Tao