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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 error for hg19 based run #10

Closed drumair closed 3 years ago

drumair commented 3 years ago

Hi I am getting the following error for hg19 based run, though hg38 based run works smoothly

DEBUG 2020-12-17 13:58:33 BlockCompressedOutputStream Using deflater: Deflater 13:58:33.605 [pool-4-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - edu.harvard.channing.compass.entity.DBTree; local class incompatible: stream classdesc serialVersionUID = 1208565614191564338, local class serialVersionUID = 556476181312992002 13:58:33.605 [pool-4-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 13:58:33.606 [pool-4-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /home/COMPSRA/bundle_v1/prebuilt_db/miRBase_hg19.obj doesn't exist! 13:58:33.606 [pool-4-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /home/COMPSRA/bundle_v1/db/miRBase/miRBase_hg19.gff3 ! 13:58:33.606 [pool-4-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /home/COMPSRA/bundle_v1/db/miRBase/miRBase_hg19.gff3. 13:58:33.606 [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: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.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) 13:58:33.607 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException 13:58:33.607 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!

cougarlj commented 3 years ago

It's the version problem that the prebuilt database version is not fit for COMPSRA version. We haven't update hg19 for a long time, because few people used hg19. Let me build miRBase_hg19.obj for you. miRBase_hg19.zip

Some users response that there is a bug in building STAR genome index. So please download the reference genome and build it by yourself. I can provide some commands as reference.

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz gunzip hg19.fa.gz /your/own/path/bundle_v1/plug/star/STAR-2.5.3a/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 4 --genomeDir /your/own/path/bundle_v1/db/star/hg19 --genomeFastaFiles /your/own/path/bundle_v1/db/star/hg19/hg19.fa

If you have built this index by yourself, please delete the parameter "-mbi" in the command line.

Best Wishes, Jiang Li

drumair commented 3 years ago

It still gives the same error

cougarlj commented 3 years ago

Dear drumair,

Can you download and try the latest COMPSRA that I have updated to GitHub today?

Best Regards, Jiang LI

On Wed, Dec 23, 2020 at 12:42 PM drumair notifications@github.com wrote:

It still gives the same error

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