Fail to find the prebuilt database obj file! (But it is there!)

[raquelgarza]

Hi!

I followed the instructions to download all resources as the example you provided in the README (using mm10 instead of hg38):

~/COMPSRA$ java -jar COMPSRA.jar -tk -dr -ck miRNA_hg38,piRNA_hg38,tRNA_hg38,snoRNA_hg38,snRNA_hg38,circRNA_hg38

I got everything I need I think (see tree.txt for the listed content of bundle_v1). However, I get this error message when running the pipeline:

17:09:59.746 [pool-3-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - edu.harvard.channing.compass.entity.DBTree; local class incompatible: stream classdesc serialVersionUID = 1386352989058994328, local class serialVersionUID = 556476181312992002
17:09:59.747 [pool-3-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file!
17:09:59.747 [pool-3-thread-1] WARN  edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /Users/Documents/Projects/src/bundle_v1/prebuilt_db/miRBase_mm10.obj doesn't exist!
17:09:59.747 [pool-3-thread-1] INFO  edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /Users/Documents/Projects/src/bundle_v1/db/miRBase/miRBase_mm10.gff3 !
17:09:59.747 [pool-3-thread-1] INFO  edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /Users/Documents/Projects/src/bundle_v1/db/miRBase/miRBase_mm10.gff3.
17:09:59.748 [pool-3-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:85)
    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:78)
    at edu.harvard.channing.compass.core.ann.SAMAnnotator.call(SAMAnnotator.java:159)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
17:09:59.749 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException
17:09:59.749 [main] INFO  edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!

If I understand correctly, miRBase_mm10.gff3 is produced from the miRBase_mm10.obj, and for some reason this object can't be found (although the bundle_v1 directory is in the same directory I'm running COMPSRA at, and the file is looking it for does exist: /Users/Documents/Projects/src/bundle_v1/prebuilt_db/miRBase_mm10.obj).

Any ideas what could be going wrong?

Thanks,

tree.txt

[cougarlj]

Dear aquelgarza,

According to the error message, it seems that the version of COMPSRA doesn't match the bundle, because of the serialVersionUID. When this happen, COMPSRA will try to download the target files from UCSC/miRBase/some other databases and builds them into pre-built databases. So did you use the latest version of COMPSRA?

Best Wishes, Jiang Li

[SoManyPepople]

+++++++++++++++++++++++++++++++

• Module ---> Annotation + +++++++++++++++++++++++++++++++

DEBUG 2022-03-30 09:54:48 BlockCompressedOutputStream Using deflater: Deflater 09:54:48.270 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Not in GZIP format 09:54:48.270 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 09:54:48.270 [pool-2-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /public/home/huangp/software/COMPSRA/bundle_v1/prebuilt_db/miRBase_mm10.obj doesn't exist! 09:54:48.271 [pool-2-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /public/home/huangp/software/COMPSRA/bundle_v1/db/miRBase/miRBase_mm10.gff3 ! 09:54:48.271 [pool-2-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 09:54:48.271 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null 09:54:48.272 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /public/home/huangp/software/COMPSRA/bundle_v1/db/miRBase/miRBase_mm10.gff3. 09:54:48.272 [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:834) 09:54:48.273 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException 09:54:48.274 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!

Hi, Li Jiang, I just got the same problem. I downloaded the newest version of COMPSRA and obj files for mm10 via the link you provided in your reply to another issue. Do you have any idea about this error?

[raquelgarza]

Hi,

Thank you for your answer. But yes, I used the latest version of COMPSRA.

[cougarlj]

Dear SoManyPeople,

Another method to solve this problem is to let COMPSRA build the pre-built database by itself. Please directly download the file mm10.gff3 from miRBase and rename and put it in /public/home/huangp/software/COMPSRA/bundle_v1/db/miRBase/miRBase_mm10.gff3

Best Wishes, Jiang Li

[cougarlj]

Hi,

Thank you for your answer. But yes, I used the latest version of COMPSRA.

Dear raquelgarza,

Please download these files from GitHub manually and try it again.

Best Wishes, Jiang Li