Getting a bowtie2 error when aligning reads

Question

[gina02]

I made index from my reference file and run command to align my data the command I used is bowtie2 -x <index_referance> -1 <single_end_read_path_1.fastq> -s <outputname.sam> the output im getting is Error: Must specify at least one read input with -U/-1/-2 (ERR): bowtie2-align exited with value 1

what is wrong in the command I used?

[GenoMax]

Can you post the actual command you used instead of posting inline help command?

[gina02]

 bowtie2 --very-fast-local -x /Users/ria/Desktop/bowtie_2/bowtie -1 /Volumes/elements/trim_tool/SRR12304924.trimmed.fastq -S /Users/ria/Desktop/SRR12304924.sam

Answer 1

[GenoMax]

Since you have single end reads you should use -U. Try following.

 bowtie2 --very-fast-local -x /Users/ria/Desktop/bowtie_2/bowtie -U /Volumes/elements/trim_tool/SRR12304924.trimmed.fastq -S /Users/ria/Desktop/SRR12304924.sam

Did you name your bowtie2 reference index bowtie?

[gina02]

I used the command bowtie2-build genome_assemblies_genome_fasta bowtie to build my ref index the out came out as (bowtie.3.bt2 and bowtie.4.bt2) is it wrong?

[GenoMax]

It is not wrong but unusual, assuming the command above is now working. Giving your reference indexes a basename already used for a different program has potential to cause confusion. e.g. if you were running bowtie v.1.x instead of bowtie2.

[gina02]

I've changes my reference index name to bowtie2 and I ran the code bowtie2 --very-fast-local -x /Users/ria/Desktop/bowtie_2/bowtie2 -U /Volumes/elements/trim_tool/SRR12304924.trimmed.fastq -S /Users/ria/Desktop/SRR12304924.sam

the error I got is Could not locate a Bowtie index corresponding to basename "/Users/ria/Desktop/bowtie_2/bowtie2" Error: Encountered internal Bowtie 2 exception (#1)

[GenoMax]

Yikes! This is what I was referring to above. Use a index basename that is NOT the name of a real program.

bowtie2-build genome_assemblies_genome_fasta my_index #something other than a program name

bowtie2 --very-fast-local -x /Users/ria/Desktop/bowtie_2/my_index -U /Volumes/elements/trim_tool/SRR12304924.trimmed.fastq -S /Users/ria/Desktop/SRR12304924.sam

[gina02]

I changed to my_index and ran the command bowtie2 --very-fast-local -x /Users/ria/Desktop/bowtie_2/my_index -U /Volumes/elements/trim_tool/SRR12304924.trimmed.fastq -S /Users/ria/Desktop/SRR12304924.sam

the output still is Could not locate a Bowtie index corresponding to basename "/Users/ria/Desktop/bowtie_2/my_index" Error: Encountered internal Bowtie 2 exception (#1) Command: /Users/ria/miniconda3/bin/bowtie2-align-s --wrapper basic-0 --very-fast-local -x /Users/ria/Desktop/bowtie_2/my_index -S /Users/ria/Desktop/SRR12304924.sam -U /Volumes/elements/trim_tool/SRR12304924.trimmed.fastq (ERR): bowtie2-align exited with value 1

[GenoMax]

Simply running commands is not the way to go here. Did you actually check to make sure if the appropriate set of index files with my_index as base name were created in whichever directory you are running the build command in?

I simply copied and pasted your command lines as illustrative examples. You would need to replace /Users/ria/Desktop/bowtie_2/ with correct directory name which contains the index files (assuming they are created).

[gina02]

I have created a directory and my index files were created in that directory(bowtie_2 from the command is the name of my directory) apparently my reference index were in a compressed format I extracted it and did the whole process again and now it works.