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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: local class incompatible: stream classdesc serialVersionUID #12

Open Paula-V-IPT opened 3 years ago

Paula-V-IPT commented 3 years ago

Dear COMPSRA team, I am following your tutorial and the modules Quality Control and Alignment were successful both for an example datafile from yours and for an actual sample. Now I am having trouble with the Annotation Module: I copy your code: 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 and I get the following: `+++++++++++++++++++++++++++++++

Working Directory: /home/ipt/Documents/COMPSRA Bundle Directory: /home/ipt/Documents/COMPSRA/bundle_v1 Configuration Directory: /home/ipt/Documents/COMPSRA/bundle_v1/configuration Plug Directory: /home/ipt/Documents/COMPSRA/bundle_v1/plug N_CPU: 48

Configuration Info: The endogenous database configuration has been set! Configuration Info: 37 databases are set! 13:29:09.683 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed!

The hg38 reference genome was set. QC module will not be performed. Alignment module will not be performed. Microbe module will not be performed. Function module will not be performed.

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

DEBUG 2021-01-27 13:29:09 BlockCompressedOutputStream Using deflater: Deflater 13:29:09.729 [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 13:29:09.730 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 13:29:09.730 [pool-2-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /home/ipt/Documents/COMPSRA/bundle_v1/prebuilt_db/miRBase_hg38.obj doesn't exist! 13:29:09.730 [pool-2-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /home/ipt/Documents/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3 ! 13:29:09.730 [pool-2-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 13:29:09.730 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null 13:29:09.730 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /home/ipt/Documents/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3. 13:29:09.730 [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:1130) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630) at java.base/java.lang.Thread.run(Thread.java:832) 13:29:09.731 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException 13:29:09.731 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!

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

I do not think the problem are the prebuilt databases (The prebuilt database file ....obj doesn't exist!) because the objects do exist and are in the mentioned directory. I downloaded them through the commands and also through the html links.

Could you help to get this step running?

I am not a java user, I only followed your tutorial for the specific purpose of small RNA-Seq, and when googling for answers I ended up "loster".

cougarlj commented 3 years ago

Dear Paula-V-IPT,

The reason is that the COMPSRA version is not consist with the pre-built database version. Because our server is not robust, please download COMPSRA (https://github.com/cougarlj/COMPSRA/blob/master/COMPSRA_V1.0.3.zip) and pre-built database (https://github.com/cougarlj/COMPSRA/tree/master/bundle_v1/prebuilt_db) directly from GitHub.

Best Wishes, Jiang Li

Paula-V-IPT commented 3 years ago

Dear Jiang Li, thank you for your quick answer! I will try that. Best, Paula

YoonheeJ commented 3 years ago

Hi Jiang Li,

I can't find the piRBase_mm10.obj in (https://github.com/cougarlj/COMPSRA/tree/master/bundle_v1/prebuilt_db). Could you please upload it? I keep having error of annotation to piRNA. Thank you, YH

cougarlj commented 3 years ago

Do you mean https://github.com/cougarlj/COMPSRA/blob/master/bundle_v1/prebuilt_db/piRBase_hg38.obj ?

On Thu, Feb 4, 2021 at 4:28 PM YoonheeJ notifications@github.com wrote:

Hi Jiang Li,

I can't find the piRBase_hg38.obj in ( https://github.com/cougarlj/COMPSRA/tree/master/bundle_v1/prebuilt_db). Could you please upload it? I keep having error of annotation to piRNA. Thank you, YH

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YoonheeJ commented 3 years ago

I mean mm10.

cougarlj commented 3 years ago

Dear YoonheeJ,

There are huge number of items of mouse piRNAs in piRBase. I'm not sure the reason and they don't respond to me. If you could, you can download from https://regepi.bwh.harvard.edu/circurna/bundle_v1/prebuilt_db/piRBase_mm10.obj .

Best Wishes, Jiang

YoonheeJ commented 3 years ago

Hi Jiang,

Thanks for the information, I tried to download the piRBase_mm10.obj from that link, but it failed (only failed with mm9 and mm10). Is there any other place I could download? Thanks again. YH

cougarlj commented 3 years ago

Hi, YoonheeJ,

The file is too large to upload to GitHub. I suggest that you could use piRBank_mm10.obj.

Best Wishes, Jiang Li

YoonheeJ commented 3 years ago

OK, Thank you!!

Best, YH

ANDdna1991 commented 3 years ago

Hello,

I'm just starting in the smallRNA seq world and I would like to use COMPSRA. I followed the manual but I'm finding the same issue. I'm just using the example datafile. The Quality Control and Alignment were fine, however, when I try to run the Annotation modules it crashes. I have already downloaded the prebuild databases from here but the problem persist.

I don't know which exactly is the problem, it reports miRBase_hg38.obj doesn't exist! but it exists:

prebuilt_db]$ ls | grep "miRBase_hg38.obj" miRBase_hg38.obj

I let the complete output. Basically, I'm just submitting the codes from the manual.

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

Configuration Info: The endogenous database configuration has been set! Configuration Info: 37 databases are set! 18:46:42.310 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed!

The hg38 reference genome was set. QC module will not be performed. Alignment module will not be performed. Microbe module will not be performed. Function module will not be performed.

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

18:46:42.377 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Not in GZIP format 18:46:42.377 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 18:46:42.377 [pool-2-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/prebuilt_db/miRBase_hg38.obj doesn't exist! 18:46:42.378 [pool-2-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3 ! 18:46:42.378 [pool-2-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 18:46:42.378 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null 18:46:42.379 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3. 18:46:42.380 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - null 18:46:42.381 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException 18:46:42.381 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!

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

Any input is more than welcome! Thanks, And

cougarlj commented 3 years ago

Dear ANDdna1991,

According to the error message, it seems that COMPSRA couldn't download the pre-built database by itself. Because our server is not robust, please download COMPSRA (https://github.com/cougarlj/COMPSRA/blob/master/COMPSRA_V1.0.3.zip) and pre-built database (https://github.com/cougarlj/COMPSRA/tree/master/bundle_v1/prebuilt_db) directly from GitHub. After that, please put these obj files in .../bundle_v1/prebuilt_db/ .

Best Wishes, Jiang Li

ANDdna1991 commented 3 years ago

Dear Jiang Li,

I've uninstalled and reinstalled COMPSRA as you suggest directly from GitHub. I also have downloaded the pre-built database directly from GitHub.

!# here you can see the files are in prebuilt_db folder.

prebuilt_db]$ ls circBase_hg38.obj gencode_snoRNA_hg38.obj GtRNAdb_hg38.obj piRBase_hg38.obj piRNACluster_hg38.obj gencode_lncRNA_hg38.obj gencode_snRNA_hg38.obj miRBase_hg38.obj piRNABank_hg38.obj

However, the problem persists, the error is the same. The annotation module fails to find the database obj files. Could you give me some clue to solve this?

16:07:55.922 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Not in GZIP format 16:07:55.922 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 16:07:55.922 [pool-2-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/prebuilt_db/miRBase_hg38.obj doesn't exist! 16:07:55.922 [pool-2-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3 ! 16:07:55.923 [pool-2-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 16:07:55.923 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null 16:07:55.924 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3. 16:07:55.924 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - null 16:07:55.925 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException 16:07:55.925 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!

kind Regards, Andres

cougarlj commented 2 years ago

Dear ANDdna1991,

Please also make sure the directory prebuilt_db is located in bundle_v1.

Best regards, Jiang

On Mon, Jul 5, 2021 at 11:15 PM ANDdna1991 @.***> wrote:

Dear Jiang Li,

I've uninstalled and reinstalled COMPSRA as you suggest directly from GitHub. I also have downloaded the pre-built database directly from GitHub.

!# here you can see the files are in prebuilt_db folder.

prebuilt_db]$ ls circBase_hg38.obj gencode_snoRNA_hg38.obj GtRNAdb_hg38.obj piRBase_hg38.obj piRNACluster_hg38.obj gencode_lncRNA_hg38.obj gencode_snRNA_hg38.obj miRBase_hg38.obj piRNABank_hg38.obj

However, the problem persist, the error is the same. The annotation module fails to fin the database obj files. Could you give me some clue to solve this?

16:07:55.922 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Not in GZIP format 16:07:55.922 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt database obj file! 16:07:55.922 [pool-2-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/prebuilt_db/miRBase_hg38.obj doesn't exist! 16:07:55.922 [pool-2-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3 ! 16:07:55.923 [pool-2-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21 16:07:55.923 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null 16:07:55.924 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /rds/project/rds-XUr6B1Jhndg/ah2192_backup/projects/small_rna_seq/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3. 16:07:55.924 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.ann.SAMAnnotator - null 16:07:55.925 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation

  • java.lang.NullPointerException 16:07:55.925 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!

kind Regards, Andres

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