addGeneAnnotation.pl: not found

Question

[aminearmich40]

hey community, I am facing a problem related to the quantification step of RNAseq analysis: I have run this command '

/home/aarmich/Documents/000TOOLS/homer/bin/analyzeRepeats.pl rna hg38 -count genes -d /home/aarmich/Documents/000TOOLS/homer/A549ctrl_RNAseq_hg38 /home/aarmich/Documents/000TOOLS/homer/A549TGFB_RNAseq_hg38 -noadj > lastt.txt 

and terminal is responding like this:

missing NM_003718...
missing NM_152604...
missing NM_001114132...
missing NR_149079...
missing NM_138286...
missing NM_001040431...
missing NM_001320100...
missing NM_173602...
missing NR_046366...
missing NM_001330283...
missing NM_001282444...
missing NM_001317096...
missing NM_000084...
missing NM_207012...
missing NM_001352956...
missing NM_031303...
missing NM_052987...
missing NM_021907...
missing NR_046325...
missing NR_135499...
    Printing output
sh: 1: addGeneAnnotation.pl: not found
        Printed 4344 of 70507 repeats (expression >= -1e+20)

did any one faced the same problem? thanks.

Answer 1

[ATpoint]

Add the folder with these Perl scripts to PATH.

[aminearmich40]

i already added the folder path but its giving the same error

[Mensur Dlakic]

addGeneAnnotation.pl: not found

There are only two possibilities with this kind of error: either you didn't install the required script, or you did install it but the system doesn't know how to find it. ATpoint gave you a suggestion for the latter possibility. If you can find addGeneAnnotation.pl somewhere in that folder (/home/aarmich/Documents/000TOOLS/homer/bin) but typing which addGeneAnnotation.pl still says the script can't be found, then the PATH variable hasn't been set correctly to include /home/aarmich/Documents/000TOOLS/homer/bin.