Trying to run FIMO from Meme suite using command line

Question

[DormoD]

Hi everyone. I am trying to run FIMO. I have downloaded the motif databases and installed them. The prompt is: fimo [options] <motif file> <sequence file>. However, I typed the file name of the motif and it did not work. Can anyone tell me where I have gone wrong? Thanks a lot!!

[seidel]

Was there an error message? What did it say? What was your exact command? For instance, using non-existent files schmoo and nofile.fa, comments start with "#" :

fimo schmoo nofile.fa
FATAL: Failed to open motif file: schmoo

# schmoo does not exist (nor does nofile.fa)
# create a file called schmoo and try again:
touch schmoo
fimo schmoo nofile.fa
There were no convincing matches to any MEME Suite motif format.
FATAL: An error occurred reading the motif file.

# use a real meme motif database
fimo transfac/meme/transfac.vertebrate.meme nofile.fa
Error opening file nofile.fa.
FATAL: Couldn't open the file nofile.fa.

Did you get any of these errors?

[DormoD]

I get

fimo schmoo nofile.fa FATAL: Failed to open motif file: schmoo

while schmoo is my databases file

[seidel]

What this means, is that fimo is not able to find your database file. The first step is to prove (1) that your database file exists, and (2) that you know how to reference it (type its path) so that fimo can find it. You can see in my example above, that the name and location of my database file is: transfac/meme/transfac.vertebrate.meme. I can find out information about this file using ls -l (which means: list files, long format - all information about the file).

cws@pi ~$ ls -l transfac/meme/transfac.vertebrate.meme
lrw-rw----. 1 cws cws 69 Oct 17  2019 transfac/meme/transfac.vertebrate.meme

When I used ls, the system returned information about the file to me. You should do the same. If you can reference the file this way, and the system tells you about the file, then you should use the same path for fimo, and it should be able to find the file. List your results here Or if you get a novel error message, list that.

Answer 1

[Alex Reynolds]

On the Bioinformatics SE, I posted a walkthrough the commands to use to run FIMO with a JASPAR TF database and sequences-of-interest, at a typical threshold of sensitivity:

https://bioinformatics.stackexchange.com/questions/2467/where-to-download-jaspar-tfbs-motif-bed-file/2491#2491

[DormoD]

Thank you! I think I have downloaded the database from the meme suite's website. So it might be a different database. Still, your post is very helpful, I really appreciate it

[Alex Reynolds]

There may not be enough information in your question. Perhaps post the exact error message you get with the full description of file paths you are using. The schmoo database referred to elsewhere does not really exist, so perhaps this is about fimo not being able to find the files you are specifying, or some other problem with the exact options you are specifying.

[DormoD]

For example, I am using the ECOLI in motif_database, I am not sure how to use this database or others like JASPAR that exist in the /db category of the MEME suite. It often returns to me as file not found.

[Alex Reynolds]

It is very hard to debug this without more information. I would suggest that you copy and paste here: 1) the exact command you are running, 2) the error message returned, and 3) the path to where you downloaded the motif databases (where exactly on your system you downloaded files to).