I have no idea what I've done wrong. I'm trying to run miRDeep2 on some miRNA seq runs. I have linked the bowtie (1) index files to the current directory, and (attempted) to save a path to the originals anyway, I kep getting an error message saying it can't find them.
Below is the script showing what I have in the working directory, the line I tried to execute and everything I got in response.
I then show my path, and that the path I think I used gets me to the files... Any help would be greatly appreciated. Apologies, I'm very new to this so have thrown everything I can think of at it (hence the directory is a pigstye).
-bash-4.2$ ls anaconda3 hairpin_hsa_dna.fa miRNA_analysis Homo_sapiens data-shell.zip genome.fa genome.1.ebwt genome.2.ebwt genome.3.ebwt genome.4.ebwt genome.rev.1.ebwt genome.rev.2.ebwt Test_1.fq dir_mapper_seq_Test_1.fq_3398472581_09_12_2019_t_09_31_42 dir_mapper_seq_Test_1.fq_8799825770_03_12_2019_t_16_37_29 index.html GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.tar mature_hsa_dna.fa shellex -bash-4.2$ mapper.pl Test_1.fq -e -j -k AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -l 18 -m -h -p genome -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -o 4 -v parsing fastq to fasta format discarding sequences with non-canonical letters clipping 3' adapters discarding short reads collapsing reads mapping reads to genome index Could not locate a Bowtie index corresponding to basename "genome" Please make sure you used bowtie version 1 to build the index. Usual index files have suffix .ebwt -bash-4.2$ echo $PATH /rds/general/user/lah17/home/anaconda3/bin:/usr/lib64/qt-3.3/bin:/rds/general/user/lah17/home/perl5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/opt/pbs/bin:/apps/anaconda3/4.5.12/install:/rds/general/user/lah17/home/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/ -bash-4.2$ -bash-4.2$ #checking the path to the index... -bash-4.2$ cd /rds/general/user/lah17/home/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/ -bash-4.2$ ls genome.1.ebwt genome.2.ebwt genome.3.ebwt genome.4.ebwt genome.fa genome.rev.1.ebwt genome.rev.2.ebwt