KenjiKamimoto-ac
commented
3 years ago HI gav-strum,
It seems that gimmemotifs crushed during the scanning process. gimmemotifs is one of the python package used in the celloracle. As you suspected, I think "Segmentation fault: 11" is a basic memory error. However I cannot identify the cause of this problem. The possible reasons are below.
- memory shortage
- gimmemotifs compile error
- os environment error
If possible, can you please try to use celloracle in a different PC? I guess a computer with larger memory will help.
While running tfi.scan I am running into the following error which seems to be related to (https://kb.iu.edu/d/aqsj). Any ideas what could be causing this? I am using human, hg38, reference genome and using 14000 peaks from ATACseq data. I have run it with the default motifs and the program still crashes.
Here is the output: Checking your motifs... Motifs format looks good.
Initiating scanner...
Calculating FPR-based threshold. This step may take substantial time when you load a new ref-genome. It will be done quicker on the second time.
Convert peak info into DNA sequences ...
Scanning motifs ... It may take several hours if you proccess many peaks.
HBox(children=(HTML(value=''), FloatProgress(value=1.0, bar_style='info', layout=Layout(width='20px'), max=1.0), HTML(value=''))) Segmentation fault: 11