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cougarlj / COMPSRA

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis
https://regepi.bwh.harvard.edu/circurna/
GNU General Public License v3.0
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Annotation module error #45

Closed Ben7124 closed 1 year ago

Ben7124 commented 1 year ago

Hello, I used the example command:

java -jar COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 -in ./example_out/sample01/sample01_17to50_FitRead_STAR_Aligned.out.bam -out ./example_out/sample01/sample01_17to50_FitRead_STAR_Aligned

But I get the below error: Fail to find the prebuilt database obj file! , but I even redownloaded the obj files and they are there. Can you please help me to fix this issue? Thanks!

DEBUG 2022-07-14 21:06:32 BlockCompressedOutputStream Using deflater: Deflater 21:06:32.939 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - edu.harvard.channing.compass.entity.DBTree; local class incompatible: stream classdesc serialVersionUID = 556476181312992002, local class serialVersionUID = 1386352989058994328 21:06:32.940 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 21:06:32.940 [pool-2-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /home/ubu/COMPSRA/bundle_v1/prebuilt_db/miRBase_hg38.obj doesn't exist! 21:06:32.940 [pool-2-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /home/ubu/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3 ! 21:06:32.941 [pool-2-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 21:06:32.941 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null 21:06:32.941 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /home/ubu/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3. 21:06:32.941 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - null java.lang.NullPointerException at edu.harvard.channing.compass.utility.ReadFile.readGFF3(ReadFile.java:384) at edu.harvard.channing.compass.db.DB_miRBase.getForest(DB_miRBase.java:102) at edu.harvard.channing.compass.core.ann.IPTR_miRNA.buildForest(IPTR_miRNA.java:51) at edu.harvard.channing.compass.core.ann.SAMAnnotator.Annotate(SAMAnnotator.java:79) at edu.harvard.channing.compass.core.ann.SAMAnnotator.call(SAMAnnotator.java:160) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:830) 21:06:32.942 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException 21:06:32.942 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!

Ben7124 commented 1 year ago

Ok thank you I figured out the issue. When you unzip the zip file, unzip into a separate directory and copy it into the main COMPSRA directory. I skipped the downloading of the databases via the command line and just used the ones in the bundle_v1 directory. It looks like it's working now.