error in bowtie2 alignment

Question

[zizigolu]

Hey friends,

For months I'm working with bowtie2 but today I am getting error

My reference genome fasta is in bowtie2 folder, I indexed the genome and the rRNA.1.bt2 and so on built already but when alignment this is my error:

[izadi@lbox161 angel]$ $BT2/bowtie2 -x rRNA --un SRR1944936_trimmed_unmapped.fastq -U SRR1944936_trimmed.fastq -S mapped_and_unmapped.sam
Could not locate a Bowtie index corresponding to basename "rRNA"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/people/home/izadi/fereshteh/bowtie2-2.2.5/bowtie2-align-s --wrapper basic-0 -x rRNA --passthrough -U SRR1944936_trimmed.fastq
(ERR): bowtie2-align exited with value 1

Help me please as already

Thank you

Answer 1

[Brice Sarver]

Could not locate a Bowtie index corresponding to basename "rRNA"

The argument you are passing as the name of your reference is not the same as what you named it when you indexed it. Alternatively, you are not executing in the correct directory (i.e., providing the incorrect path).

Usage:
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.

Usage: bowtie2-build [options]* <reference_in> <bt2_index_base>
    reference_in            comma-separated list of files with ref sequences
    bt2_index_base          write bt2 data to files with this dir/basename
 Bowtie 2 indexes work only with v2 (not v1).  Likewise for v1 indexes.

[zizigolu]

Thank you for your complete definition. Monday I will try