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centrifuge not working- index error

hi, I am trying to run centrifuge but I am getting some error listed below. I would really appreciate your help if you could help me to troubleshoot this error.

**(centrifuge) ncim@ncim-Super-Server:~/softwares/centrifuge_db/p+h+v$ centrifuge -x p+h+v.1.cf -U 1KO.fastq -S centrifuge_out --report-file centrifuge_1ko --threads 30 
Could not locate a Centrifuge index corresponding to basename "p+h+v.1.cf"
Error: Encountered internal Centrifuge exception (#1)
Command: /home/ncim/anaconda3/envs/centrifuge/bin/centrifuge-class --wrapper basic-0 -x p+h+v.1.cf -S centrifuge_out --report-file centrifuge_1ko --threads 30 -U 1KO.fastq 
(ERR): centrifuge-class exited with value 1**
next-gen sequence sequencing software error
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updated by h.mon h.mon • written by srm.vinay0005 • srm.vinay0005

Using + in unix names is likely not a good idea. Try renaming the files (you may need to recreate the index if simple renaming of all index files does not work).

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written by GenoMax GenoMax

1 answer

You are passing the full name of a file from the index, centrifuge wants just the prefix of the index name (minus trailing .X.cf):

  centrifuge [options]* -x <cf-idx> {-1 <m1> -2 <m2> | -U <r> | --sample-sheet <s> } [-S <filename>] [--report-file <report>]

 <cf-idx>   Index filename prefix (minus trailing .X.cf).

Try with:

centrifuge -x p+h+v [...]
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written by h.mon h.mon

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