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Old 09-10-2020, 08:04 AM   #1
Location: NJ

Join Date: Oct 2012
Posts: 97
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 , which was included in bbtools package.

Unfortunately we are receiving the following error:

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(
    at tax.RenameGiToTaxid.updateHeadersFromServer_fasta(
    at tax.RenameGiToTaxid.updateHeadersFromServer(
    at tax.RenameGiToTaxid.processInner_server(
    at tax.RenameGiToTaxid.process(
    at tax.RenameGiToTaxid.main(

Is there any way to fix this issue/error?

Thank you for the help.
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