ps_scan pfscan: Syntax error: "(" unexpected

Question

[rachid.fermi]

hello all

I'm using ltr_finder with ps_scan,

I'm using this command

ltr_finder organis_name.fa  -s tRNA_file.fa -a $ps_scan -w2 -E -C > organis_name.table

where $ps_scan is the path to ps_scan folder(/mnt/c/Users/hp/Desktop/BioinformaticsProject/LTR_Database/LTR_FINDER/ps_scan)

ltr_finder was installed via conda install -c bioconda ltr_finder

i got this error

/ps_scan/pfscan: 1: Syntax error: "(" unexpected

I've been stuck in this error for almost three days

[Mensur Dlakic]

What do you get when you type:

echo $ps_scan

Try inserting full directory name /mnt/c/Users/hp/Desktop/BioinformaticsProject/LTR_Database/LTR_FINDER/ps_scan instead of $ps_scan.

[rachid.fermi]

hello sir

thank you for replying, about the paths I'm sure of them

here's the full command

ltr_finder /mnt/c/Users/hp/Desktop/BioinformaticsProject/LTR_Database/Files/Data/organis_name.fa \
        -s /mnt/c/Users/hp/Desktop/BioinformaticsProject/LTR_Database/Files/tRNA/organis_name.fa \
        -a /mnt/c/Users/hp/Desktop/BioinformaticsProject/LTR_Database/LTR_FINDER/ps_scan \
        -w2 -E \
        -C > /mnt/c/Users/hp/Desktop/BioinformaticsProject/LTR_Database/Arabidopsis_thaliana/LTR_finder/organis_name.table

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.