Florian411
commented
7 years ago Hey, Thanks for using the tool! If you could provide me with a set of regions (a bed file, can be a subset of the full set, but should still cover all chromosomes), and a link to the reference genome and the annotation file you are using, I will have a look as well.
Did you ensure that you are using the latest version of TEPIC?
CRoberto1926
Hello, I'm using the software on Drosophila with a custom set of PWMs, that I converted using PSCM_to_PSEM.cpp I'm interested in using DREM, so I need to run TEPIC.sh with the -r option. However, when I do so, I get the following:
Preprocessing region file: Removing chr prefix, sorting regions and removing duplicats Generating random genomic regions Results from chrom 4 saved Traceback (most recent call last): File "/home/roberto/Dropbox/phd_project_data/Ecdysone_timecourse_data/TEPIC_INVOKE_DYNAMITE_DREM/TEPIC/Code/findBackground.py", line 284, in find_background_regions │
matched = start_relaxed_search(kdtree, chrom_seq, taken, idxmap, data_limits, params) │
File "/home/roberto/Dropbox/phd_project_data/Ecdysone_timecourse_data/TEPIC_INVOKE_DYNAMITE_DREM/TEPIC/Code/findBackground.py", line 206, in start_relaxed_search │
cand_feat = compfeat(cand_seq) │
File "/home/roberto/Dropbox/phd_project_data/Ecdysone_timecourse_data/TEPIC_INVOKE_DYNAMITE_DREM/TEPIC/Code/findBackground.py", line 168, in compute_seq_features │
ft_pct_gc = np.round((num_g + num_c) / seq_len * 100., 2) │
ZeroDivisionError: float division by zero │
Error processing chromosome 2LResults from chrom 2R saved │
Results from chrom 3R saved │
Results from chrom 3L saved │
Results from chrom X saved │
Runnig bedtools │
Converting invalid characters │
Starting TRAP │
Discretising TF affinities │
Error in x/y : non-numeric argument to binary operator │
Calls: apply -> FUN │
Execution halted
I will try to narrow down the problem, meanwhile I'm opening the issue. Also, let me know if you need data for a reproducible example.
Best, Roberto