How to download BBTools sketch databases using fetchRefSeq?
Does anyone know how to download these databases properly for BBTools?
I got it to work back in 2019 but can’t seem to get it to work with the newest version. Here’s the error I’ve gotten with the fetch scripts:
Version: BBMap version 38.93
RefSeq
(bbmap_env) -bash-4.2$ /usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/bbmap_env/opt/bbmap-38.93-0/pipelines/fetch/fetchRefSeq.sh
java -ea -Xmx1g -Xms1g -cp /usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/bbmap_env/opt/bbmap-38.93-0/current/ tax.RenameGiToTaxid -Xmx1g in=stdin.fa.gz out=renamed.fa.gz pigz=16 unpigz zl=9 server ow maxbadheaders=5000 badheaders=badHeaders.txt bgzip
Executing tax.RenameGiToTaxid [-Xmx1g, in=stdin.fa.gz, out=renamed.fa.gz, pigz=16, unpigz, zl=9, server, ow, maxbadheaders=5000, badheaders=badHeaders.txt, bgzip]
Time: 488.852 seconds.
Reads Processed: 39175 0.08k reads/sec
Bases Processed: 1273m 2.61m bases/sec
Valid Sequences: 39175
Valid Bases: 1273716988
Invalid Sequences: 0
Invalid Bases: 0
Exception in thread "main" java.lang.RuntimeException: tax.RenameGiToTaxid terminated in an error state; the output may be corrupt.
at tax.RenameGiToTaxid.process(RenameGiToTaxid.java:307)
at tax.RenameGiToTaxid.main(RenameGiToTaxid.java:39)
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