Failing to build custom database for HBV #9
Comments
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Hi Wonseok, It looks like the file Please let me know if this didn't work for you. Best, |
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Hi, Sara, I ran Best, |
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Hi Wonseok, Do you get an error when running Best, |
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Hi, Sara. The Thank you, |
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Hi Wonseok, Did you try running the |
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Hi Javadzadeh, I have downloaded your suggested dataset for sample-level FastFiVi for the HPV virus: https://drive.google.com/file/d/1QYn5lDWjvhtIWCrwmzDc_1fy8ANrXWz1/view?usp=sharing. However, when I was attempting to extract it, it showed errors (tar -xzvf kraken_datasets.tar.gz). Could you please suggest to me how I can figure it out? |
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Hi Muhammod, Thanks for reaching out. |
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Hi Javadzadeh, Thank you so much for your response. I was getting the below errors. The downloaded file size is "15796400321" bytes. gzip: stdin: invalid compressed data--crc error
tar: Child returned status 1
tar: Error is not recoverable: exiting nowls -l kraken_datasets.tar.gz |
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Hi again, Thanks! Although the output to Did you try running By the way, the uncompressed should be about 60GB. Is that taken into consideration? Thanks, |
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Hi Javadzadeh, Yes, I have tried. However, it doesn't work out. gzip: kraken_datasets.tar.gz: invalid compressed data--crc error |
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Hi Javazadesh, could you please provide a different download link? |
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I can provide another link, it'll take a couple of hours to upload the database.
Sara |
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Yes, it shows errors. You can view the error by clicking the link. tar -tf kraken_datasets.tar.gz > errors-text.txtOutput: |
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Thanks for checking. Sara |
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Hi again, Here's a second link for the same Kraken databases: https://drive.google.com/file/d/1DrKgDE7fl5Tff2bV8K9XBxLYsbTeOcgh/view?usp=sharing I suspect this might be a tar library incompatibility rather than file problem. I was able to list the contents of Sara |
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Thank you, Ms. Javadzadeh. It helped me a lot. I used a Python script instead of import tarfile
sourcePATH = '/mnt/sdb1/kraken2/kraken_datasets.tar.gz'
destinationPATH = '/mnt/sdb1/kraken2/'
with tarfile.open(sourcePATH) as tar:
tar.extractall(destinationPATH)
tar.close() |
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Great! Thanks for letting me know.
The size of extracted files sound reasonable.
Sara
…On Wed, Jun 14, 2023 at 9:47 AM Rafsanjani, Muhammod < ***@***.***> wrote:
Thank you, Ms. Javadzadeh. It helped me a lot.
I used a Python script instead of tar, and this time, it has not shown
errors. After extracting, I got a 61.4 GB file size. Is it the correct file
size?
import tarfile
sourcePATH = '/mnt/sdb1/kraken2/kraken_datasets.tar.gz'destinationPATH = '/mnt/sdb1/kraken2/'
with tarfile.open(sourcePATH) as tar:
tar.extractall(destinationPATH)
tar.close()
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hi sara |
Hi Sara,
I've been trying to build custom databases by following FastViFi Readme. Building databases for HCV and EBV were successful, however, building the hbv databases for k=18, k-22 were unsuccessful. The following message was shown in the log file:
Is there a way to solve this problem?
Best,
Wonseok
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