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Old 09-10-2020, 08:04 AM   #1
Zapages
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Default BBtool's Fetchnt Error

Hi Everyone,

I hope to test bbtool's sketch tool our bioinformatics needs. Before we proceed to doing any tests, we are having issues with retrieving the pre made/indexed NT database.

We ran the fetchNT.sh , which was included in bbtools package.


Unfortunately we are receiving the following error:

Code:
java -ea -Xmx1g -Xms1g -cp /opt/conda/opt/bbmap-38.86-0/current/ tax.RenameGiToTaxid -Xmx1g in=stdin.fa.gz out=renamed.fa.gz pigz=32 unpigz bgzip zl=8 server ow shrinknames maxbadheaders=5000 badheaders=badHeaders.txt taxpath=/BBSketch/taxonomy
Executing tax.RenameGiToTaxid [-Xmx1g, in=stdin.fa.gz, out=renamed.fa.gz, pigz=32, unpigz, bgzip, zl=8, server, ow, shrinknames, maxbadheaders=5000, badheaders=badHeaders.txt, taxpath=/BBSketch/taxonomy]

 

java.lang.Exception: Maximum bad headers exceeded: 5000
    at shared.KillSwitch.kill(KillSwitch.java:96)
    at tax.RenameGiToTaxid.updateHeadersFromServer_fasta(RenameGiToTaxid.java:629)
    at tax.RenameGiToTaxid.updateHeadersFromServer(RenameGiToTaxid.java:527)
    at tax.RenameGiToTaxid.processInner_server(RenameGiToTaxid.java:737)
    at tax.RenameGiToTaxid.process(RenameGiToTaxid.java:249)
    at tax.RenameGiToTaxid.main(RenameGiToTaxid.java:38)

Is there any way to fix this issue/error?

Thank you for the help.
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Old 09-10-2020, 11:37 AM   #2
GenoMax
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NCBI's FTP site appears to be offline today. So that may be one reason why this is not working.
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Old 09-17-2020, 08:29 AM   #3
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Thank you, unfortunately we are still experiencing the issue...
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Old 09-17-2020, 09:42 AM   #4
GenoMax
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I just tried the script and was able to get it to work (did not let it finish). It started making two files. renamed.fa.gz (which has fasta sequences) and badHeaders.txt.

Check to see if you are able to directly access NCBI FTP server from machine you are running this on.
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Old 09-18-2020, 07:24 AM   #5
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Quote:
Originally Posted by GenoMax View Post
I just tried the script and was able to get it to work (did not let it finish). It started making two files. renamed.fa.gz (which has fasta sequences) and badHeaders.txt.

Check to see if you are able to directly access NCBI FTP server from machine you are running this on.
It works for me too, but it will eventually error out when the bad headers exceed more than 5000...
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Old 09-19-2020, 05:44 AM   #6
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Create a ticket via BBMap's repo so Brian is aware of the problem.
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