cougarlj
commented
2 years ago Dear hafizmtalha,
According to the error message, COMPSRA couldn't import the pre-built databases. This may be the version problem. Please download the latest version of COMPSRA and pre-built databases from Github.
COMPSRA (https://github.com/cougarlj/COMPSRA/blob/master/COMPSRA_V1.0.3.zip) pre-built database (https://github.com/cougarlj/COMPSRA/tree/master/bundle_v1/prebuilt_db)
Best Wishes, Jiang Li
hafizmtalha
I have installed the COMPSRA and did the alignment module.. now when I run the annotation module it gives me following error.
022-01-21 05:56:56.937 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed!
2022-01-21 05:56:56.991 [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 2022-01-21 05:56:56.991 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 2022-01-21 05:56:56.991 [pool-2-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /home/ubuntu/COMPSRA/bundle_v1/prebuilt_db/miRBase_hg38.obj doesn't exist! 2022-01-21 05:56:56.992 [pool-2-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /home/ubuntu/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3 ! 2022-01-21 05:56:56.992 [pool-2-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 2022-01-21 05:56:56.992 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Cannot invoke "java.io.BufferedReader.readLine()" because "br" is null 2022-01-21 05:56:56.993 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /home/ubuntu/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3. 2022-01-21 05:56:56.993 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - Cannot invoke "java.util.HashMap.values()" because "dbt.hmpStart" is null 2022-01-21 05:56:56.994 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException: Cannot invoke "edu.harvard.channing.compass.core.ann.IPTR.getReport()" because "this.iptr[i]" is null 2022-01-21 05:56:56.995 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!
I have checked manually and the database object is present there, in mentioned place. But it still gives me errors. although, the local files database is not present. may be they no longer comes with the github package.