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Database problem #270

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ADelacuv opened this issue Feb 15, 2024 · 1 comment
Open

Database problem #270

ADelacuv opened this issue Feb 15, 2024 · 1 comment

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@ADelacuv
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I dowaloaded database sequences from https://genome-idx.s3.amazonaws.com/centrifuge/nt_2018_3_3.tar.gz with wget follow by tar -tvf. I have 4 files.cf (nt.1.cf, nt.2.cf, nt.3.cf, nt.4.cf) in "/home/users/a/d/adelacuv/Metagenomique/Sylvie/Centrifuge-database/".
When I execute:
centrifuge -x /home/users/a/d/adelacuv/Metagenomique/Sylvie/Centrifuge-database -U /home/users/a/d/adelacuv/Metagenomique/Sylvie/FAX68388_pass_barcode01_ef101f35_72d0bf9a_0.fastq -S /home/users/a/d/adelacuv/Metagenomique/Sylvie/output-centrifuge --host-taxids 9606

I have this error:
Could not locate a Centrifuge index corresponding to basename "/home/users/a/d/adelacuv/Metagenomique/Sylvie/Centrifuge-database"
Error: Encountered internal Centrifuge exception (#1)
Command: /home/umons/promicro/adelacuv/anaconda3/envs/centrifuge/bin/centrifuge-class --wrapper basic-0 -x /home/users/a/d/adelacuv/Metagenomique/Sylvie/Centrifuge-database -S /home/users/a/d/adelacuv/Metagenomique/Sylvie/output-centrifuge --host-taxids 9606 -U /home/users/a/d/adelacuv/Metagenomique/Sylvie/FAX68388_pass_barcode01_ef101f35_72d0bf9a_0.fastq
(ERR): centrifuge-class exited with value 1
Can you help me?

@nicolo-tellini
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Hi,

the option -x requires also the name of the index without the extension i.e. nt :

-x /home/users/a/d/adelacuv/Metagenomique/Sylvie/Centrifuge-database/nt

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