Hi,
I am running BiasAway in a human dataset. tes_background_hsapeins.fa is coming from random fragments of 1000bp (done with bedtools). The TE_set_reference_hg38.fa is a compendium of 4million transposable elements. I get a weird error after quite a while of computation.
time python /home/jl/soft/bias_away/BiasAway.py c -b /projects/TE_stress_project/chip_seq_data/background_seqs/tes_background_hsapiens.fa -f /projects/TE_stress_project/humans/TE_set_reference_hg38.fa -r background_te_hsapiens/ > te_background_gc_matched_hsapiens.fa
/home/jl/soft/bias_away/GC_window_compo_matching.py:37: RuntimeWarning: invalid value encountered in double_scalars
return gc, min(tmp_gc), max(tmp_gc), sd, 100 sd / gc
/home/jl/soft/bias_away/GC_window_compo_matching.py:37: RuntimeWarning: divide by zero encountered in double_scalars
return gc, min(tmp_gc), max(tmp_gc), sd, 100 sd / gc
Killed
amathelier
commented
6 years ago
Hi, I am running BiasAway in a human dataset. tes_background_hsapeins.fa is coming from random fragments of 1000bp (done with bedtools). The TE_set_reference_hg38.fa is a compendium of 4million transposable elements. I get a weird error after quite a while of computation.
time python /home/jl/soft/bias_away/BiasAway.py c -b /projects/TE_stress_project/chip_seq_data/background_seqs/tes_background_hsapiens.fa -f /projects/TE_stress_project/humans/TE_set_reference_hg38.fa -r background_te_hsapiens/ > te_background_gc_matched_hsapiens.fa
/home/jl/soft/bias_away/GC_window_compo_matching.py:37: RuntimeWarning: invalid value encountered in double_scalars return gc, min(tmp_gc), max(tmp_gc), sd, 100 sd / gc /home/jl/soft/bias_away/GC_window_compo_matching.py:37: RuntimeWarning: divide by zero encountered in double_scalars return gc, min(tmp_gc), max(tmp_gc), sd, 100 sd / gc Killed
real 726m6.471s user 704m29.162s sys 4m44.320s