(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...

Question

[eimanpharmacist]

Hi,

I am new to using trinity tool, and I went through a tutorial to run and assess the assembly.

I already generated Trinity.fasta file, then # Build Index using this:

bowtie2-build ~/workdir/trinity/trinity_out_dir/Trinity.fasta index/Trinity.fa

This generated multiple Trinity.fa files in the index folder

bowtie2_assessment/index$ ls
Trinity.fa.1.bt2  Trinity.fa.3.bt2  Trinity.fa.rev.1.bt2
Trinity.fa.2.bt2  Trinity.fa.4.bt2  Trinity.fa.rev.2.bt2

So, when I ran

R1="$HOME/workdir/sample_data/sample1-ErccTranscripts-chr22.read1.fastq.gz"
R2="$HOME/workdir/sample_data/sample2-ErccTranscripts-chr22.read2.fastq.gz"

bowtie2 -p 1 -q --no-unal -k 20 -x index/Trinity.fa -1 $R1 -2 $R2 2> align_stats.txt| samtools view -Sb -o bowtie2.bam

# View align_stats.txt

cat align_stats.txt

I got this error message:

(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...

since I do not have Trinity.fa, but multiple Trinity.fa files.

I do not understand what is wrong here. Your help is much appreciated!

[GenoMax]

This generated multiple Trinity.fa files in the index folder

Did the process complete successfully?

[eimanpharmacist]

It is completed but I can not find any bam files, as you see above, I should get a bowtie2.bam file as an output but I did not.

[eimanpharmacist]

I think the problem in bowtie2 installation. it was installed using this: conda install -c bioconda bowtie2 I removed it then re-installed using

conda install -c "bioconda/label/broken" bowtie2

But now, it generates a new error (command bowtie2 does not exit. I also tried sudo apt install bowtie2 Same output