Hi,
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
Try
Edit* Checked previous times I have used mapper.pl and nope, that's not it. Maybe provide the path like:
Hi, Ty for the suggestion!
I tried
Then, out of mild desperation...
Anything else I might try?
Going back to look at PATH..? To see if that might be the issue.
Give it a shot with the full path to the index files, or the relative path (try make a folder for em).
You forgot to try -p ./genome which would be another take on the relative path. If this doesn't work then I'm not sure what to do, except to do the trimming manually (which I have had success with)..
Hey,
Thank you for the suggestions. Still hasn't worked. Frustratingly, I have copies that have been trimmed already, I was just trying to do an all in one alignment. Is this what you use for alignment? Back to the drawing board.
bw,
L
Did you make the bowtie v.1 indexes yourself or downloaded them from somewhere? Are they known to work?
Have figured it out. I missed a full stop when I linked the bowtie sequences. It was looking through the root directory rather than from the current directory I was in.
I learned that black highlight of anything that you ls is not a good thing!
Great! Put up the fixed code, just as a future reference for anyone else coming across the same issue