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ps_scan pfscan: Syntax error: "(" unexpected

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

gene sequence genome assembly rna
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updated by Ram Ram • written by rachid.fermi • rachid.fermi

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.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

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
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written by rachid.fermi • rachid.fermi

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.
code_formatting

• 0 views • link
written by Ram Ram

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