Downloading files from https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt

[brianherb]

Hi,

Thank you for this tool. I get errors when trying to download files from https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt - for example:

java -jar COMPSRA.jar -tk -dr -ck blast_bacteria

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

•        COMPSRA          +
  

• (V1.0.2 2020-07-03)     +
  

• rejia@channing.harvard.edu +
  +++++++++++++++++++++++++++++++

Working Directory: /autofs/burnsfs/projects-t3/idea/amentlab_software/COMPSRA
Bundle Directory: /autofs/burnsfs/projects-t3/idea/amentlab_software/COMPSRA/bundle_v1
Configuration Directory: /autofs/burnsfs/projects-t3/idea/amentlab_software/COMPSRA/bundle_v1/configuration
Plug Directory: /autofs/burnsfs/projects-t3/idea/amentlab_software/COMPSRA/bundle_v1/plug
N_CPU: 48

Configuration Info: The endogenous database configuration has been set!
Configuration Info: 37 databases are set!
09:49:32.259 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed!

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

•  COMPASS ---> ToolKit   +
  

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

09:49:32.267 [main] INFO edu.harvard.channing.compass.utility.Download - Start to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_bacteria.fasta.gz
09:49:33.093 [main] INFO edu.harvard.channing.compass.utility.Download - Finish to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_bacteria.fasta.gz
09:49:33.105 [main] ERROR edu.harvard.channing.compass.core.Factory - Not in GZIP format
Exception in thread "main" java.lang.NullPointerException
at edu.harvard.channing.compass.utility.DeCompress.UnGZipFile(DeCompress.java:54)
at edu.harvard.channing.compass.utility.Download.download(Download.java:66)
at edu.harvard.channing.compass.toolkit.DownloadResource.downloadResource(DownloadResource.java:221)
at edu.harvard.channing.compass.toolkit.DownloadResource.runKit(DownloadResource.java:45)
at edu.harvard.channing.compass.toolkit.ProduceTK.Dispatch(ProduceTK.java:41)
at edu.harvard.channing.compass.core.COMPSRA.main(COMPSRA.java:54)

[cougarlj]

Dear Brain, Currently, our server is not open for downloading resource files. I'm afraid that the microbiome module is not available now. Or you can download nt database directly from UCSC and extract bacterial sequences by yourself. I'm sorry for the inconvenience. We will try to move the resource to another server in COMPSRA2 this year. Best regards, Jiang Li

…

On Fri, Jan 5, 2024 at 11:04 PM Brian Herb ***@***.***> wrote: Hi, Thank you for this tool. I get errors when trying to download files from https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt - for example: java -jar COMPSRA.jar -tk -dr -ck blast_bacteria +++++++++++++++++++++++++++++++ - COMPSRA + - (V1.0.2 2020-07-03) + - ***@***.*** + +++++++++++++++++++++++++++++++ Working Directory: /autofs/burnsfs/projects-t3/idea/amentlab_software/COMPSRA Bundle Directory: /autofs/burnsfs/projects-t3/idea/amentlab_software/COMPSRA/bundle_v1 Configuration Directory: /autofs/burnsfs/projects-t3/idea/amentlab_software/COMPSRA/bundle_v1/configuration Plug Directory: /autofs/burnsfs/projects-t3/idea/amentlab_software/COMPSRA/bundle_v1/plug N_CPU: 48 Configuration Info: The endogenous database configuration has been set! Configuration Info: 37 databases are set! 09:49:32.259 [main] INFO edu.harvard.channing.compass.core.Configuration - The Configuration was completed! +++++++++++++++++++++++++++++++ - COMPASS ---> ToolKit + +++++++++++++++++++++++++++++++ 09:49:32.267 [main] INFO edu.harvard.channing.compass.utility.Download - Start to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_bacteria.fasta.gz 09:49:33.093 [main] INFO edu.harvard.channing.compass.utility.Download - Finish to download the resource: https://regepi.bwh.harvard.edu/circurna/bundle_v1/db/nt/nt_bacteria.fasta.gz *09:49:33.105 [main] ERROR edu.harvard.channing.compass.core.Factory - Not in GZIP format* Exception in thread "main" java.lang.NullPointerException at edu.harvard.channing.compass.utility.DeCompress.UnGZipFile(DeCompress.java:54) at edu.harvard.channing.compass.utility.Download.download(Download.java:66) at edu.harvard.channing.compass.toolkit.DownloadResource.downloadResource(DownloadResource.java:221) at edu.harvard.channing.compass.toolkit.DownloadResource.runKit(DownloadResource.java:45) at edu.harvard.channing.compass.toolkit.ProduceTK.Dispatch(ProduceTK.java:41) at edu.harvard.channing.compass.core.COMPSRA.main(COMPSRA.java:54) — Reply to this email directly, view it on GitHub <#57>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABGMAD4LQ4MD3UBGCAVV4G3YNAI6HAVCNFSM6AAAAABBORVYKKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DONJQGI2TGMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>