FIMO outputs only xml file

[Waqasuddin Khan]

Hi Community,

I ran FIMO successfully:

fimo --oc . --verbosity 1 --bgfile /home/regmwkh/Scratch/databases_work/vcf_data/test_ref.fna.bfile --thresh 1.0E-4 /home/regmwkh/Scratch/databases_work/vcf_data/test_ref_meme.fasta /home/regmwkh/Scratch/databases_work/hg38.fasta

but the output folder is showing only xml file, no txt and html files are generated.

Is there any command line option missing, I read that, but didn't come to success.

Regards,

Waqas.

[CharlesEGrant]

HI Waqas,

FIMO should write status or error messages to the terminal as its running. These should indicate what the problem may have been. If you could forward those messages to us, that would help us troubleshoot the problem. I do notice that the name of the file that contains the motif to search for is

 /home/regmwkh/Scratch/databases_work/vcf_data/test_ref_meme.fasta

Is that actually a FASTA file? That files should be in the MEME motif format. If it was not in the correct format you would have seen an error message like:

There were no convincing matches to any MEME Suite motif format.
FATAL: No motifs could be read.

Charles

[Waqasuddin Khan]

Hi Charles,

Actually, the file test_ref_meme.fasta is the motif search file in meme format, I just forgot to rename it as test_ref_meme.txt.

So, now I changed test_ref_meme.fasta to test_ref_meme.txt.

Is it the right extension name? The job is running now.

Best,

Waqas.

[CharlesEGrant]

Hi Waqas,

FIMO doesn't pay any attention to the filename extension. I just wanted to make sure that you weren't trying to run FIMO on two FASTA files.

Charles

[Waqasuddin Khan]

Hi Cahrels,

I got fimo results. The problem is that I gave very less wall clock time to my pbs script. Before completing the job properly, the time ends with incomplete output.

All well now,

Best,

Waqas.