Annotation error for mm10 based run #11
Comments
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Dear Murakami, Please unzip the attached miRBase_mm10.obj.zip file and put it in the directory /Volumes/NGS_1/NGS_tools/COMPSRA_mm/bundle_v1/prebuilt_db/ . Best Wishes, |
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Thank you for your reply. But, the error could not be prevented. All the best, #Error mm10# #Error hg38# |
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I also met the same problem in the annotation step for hg38 |
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Dear Murakami Please unzip the zip file and get miRBase_mm10.obj to use. All the problems you meet is the version problem. I think, maybe, you can download the latest version of COMPSRA. I will try to put these pre-built database in GitHub, because our server is not stable for downloading files. Best Wishes, |
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Dear Jiang Thank you for updating the files. All the best, DEBUG 2020-12-25 11:53:22 BlockCompressedOutputStream Using deflater: Deflater 11:53:23.420 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Lift Over Error: Fail to read the liftover file: /Volumes/NGS_1/NGS_tools/COMPSRA-master/bundle_v1/db/chain/mm8ToMm10.over.chain.gz |
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Dear Murakami, I have updated the prebuilt databases for mm9 and mm10 and please download them directly from GitHub. Best Wishes, |
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Please download the obj files from GitHub.
…On Wed, Dec 23, 2020 at 6:56 AM wei-course ***@***.***> wrote:
I also met the same problem in the annotation step for hg38
DEBUG 2020-12-23 11:06:55 BlockCompressedOutputStream Using deflater:
Deflater
11:06:55.171 [pool-4-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
11:06:55.172 [pool-4-thread-1] ERROR
edu.harvard.channing.compass.utility.ReadFile - Fail to find the prebuilt
database obj file!
11:06:55.172 [pool-4-thread-1] WARN
edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file
/STORAGE/wzhang/RNA-seq/COMPSRA/bundle_v1/prebuilt_db/miRBase_hg38.obj
doesn't exist!
11:06:55.172 [pool-4-thread-1] INFO
edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from
local files
/STORAGE/wzhang/RNA-seq/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3 !
11:06:55.173 [pool-4-thread-1] INFO
edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read
file: miRBase_v21
11:06:55.173 [pool-4-thread-1] ERROR
edu.harvard.channing.compass.utility.ReadFile - null
11:06:55.173 [pool-4-thread-1] INFO
edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to
read file:
/STORAGE/wzhang/RNA-seq/COMPSRA/bundle_v1/db/miRBase/miRBase_hg38.gff3.
11:06:55.177 [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:834)
11:06:55.179 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation
- java.lang.NullPointerException
11:06:55.179 [main] INFO edu.harvard.channing.compass.core.Produce -
Error: Annotation module fails!
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Dear Jiang, Thank you for upload of the files. DEBUG 2021-01-06 13:55:55 BlockCompressedOutputStream Using deflater: Deflater All the best, |
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Dear Murakami, Sorry to reply late. According to the message output, it's the problem of piRNA in mouse. We do have the pre-built database for piRNA in mouse, but the size is huge and couldn't upload to GitHub. Also, we still suspect the annotated piRNAs of mouse in piRBase, because there are too many piRNAs. So, the best solution is to ignore piRNA in your analysis, I think. Best Wishes, |
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Dear Jiang, Thank you for your supports. All the best, |
Hello. I am getting the following error for annotation using mm10.
All the best,
Murakami
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DEBUG 2020-12-19 15:18:28 BlockCompressedOutputStream Using deflater: Deflater
15:18:28.029 [pool-2-thread-1] WARN edu.harvard.channing.compass.db.DB_miRBase - The prebuilt database file /Volumes/NGS_1/NGS_tools/COMPSRA_mm/bundle_v1/prebuilt_db/miRBase_mm10.obj doesn't exist!
15:18:28.029 [pool-2-thread-1] INFO edu.harvard.channing.compass.db.DB_miRBase - Try to build the database from local files /Volumes/NGS_1/NGS_tools/COMPSRA_mm/bundle_v1/db/miRBase/miRBase_mm10.gff3 !
15:18:28.030 [pool-2-thread-1] INFO edu.harvard.channing.compass.core.Factory - Read File Error: Fail to read file: miRBase_v21
15:18:28.030 [pool-2-thread-1] ERROR edu.harvard.channing.compass.utility.ReadFile - null
15:18:28.031 [pool-2-thread-1] INFO edu.harvard.channing.compass.utility.ReadFile - Read File Error: Fail to read file: /Volumes/NGS_1/NGS_tools/COMPSRA_mm/bundle_v1/db/miRBase/miRBase_mm10.gff3.
15:18:28.031 [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.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
15:18:28.042 [main] ERROR edu.harvard.channing.compass.core.ann.Annotation - java.lang.NullPointerException
15:18:28.042 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Annotation module fails!
+++++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++
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