cougarlj
commented
1 year ago Dear kengjunglee,
Sorry for the late reply. It seems that COMPSRA couldn't find the obj file. The reason may be that the obj file was damaged inside. You can download the obj file again from GitHub. Another way is to download the miRBase_hg38.gff3 file from miRBase database and put this file in /home/ubuntu/COMPSRA/bundle_v1/db/miRBase/ . In this situation, COMPSRA will build the obj file automatically. If you have any questions, please let me know.
Best regards, Jiang Li
On Mon, Feb 20, 2023 at 10:48 PM kengjunglee @.***> wrote:
Hello,
I used the latest COMPSRA V1.0.3 version and I also confirm that I have miRBase_hg38.obj in the target file. But I still get this error. Could you kindly let me know how to solve it?
Thanks
+++++++++++++++++++++++++++++++
- Module ---> Annotation + +++++++++++++++++++++++++++++++
DEBUG 2023-02-20 14:41:19 BlockCompressedOutputStream Using deflater: Deflater 14:41:19.302 [pool-4-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Not in GZIP format 14:41:19.303 [pool-4-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 14:41:19.303 [pool-4-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! 14:41:19.303 [pool-4-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 ! 14:41:19.303 [pool-4-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 14:41:19.303 [pool-4-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null 14:41:19.304 [pool-4-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. 14:41:19.304 [pool-4-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:829) 14:41:19.305 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation
- java.lang.NullPointerException 14:41:19.305 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!
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Hello,
I used the latest COMPSRA V1.0.3 version and I also confirm that I have miRBase_hg38.obj in the target file. But I still get this error. Could you kindly let me know how to solve it?
Thanks
+++++++++++++++++++++++++++++++
DEBUG 2023-02-20 14:41:19 BlockCompressedOutputStream Using deflater: Deflater 14:41:19.302 [pool-4-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Not in GZIP format 14:41:19.303 [pool-4-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 14:41:19.303 [pool-4-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! 14:41:19.303 [pool-4-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 ! 14:41:19.303 [pool-4-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 14:41:19.303 [pool-4-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null 14:41:19.304 [pool-4-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. 14:41:19.304 [pool-4-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:829) 14:41:19.305 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException 14:41:19.305 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!