Open palakela opened 1 year ago
Hi! Sorry you're running into this problem. We are aware of the existence of this sort of database locking problem, and have been looking into it. Long story short, we are evaluating a couple of different ways to address the issue but have not made any final decisions yet.
Interestingly, we have not seen this problem specifically in plot_enrichment
. We aren't surprised it can happen there, we just haven't seen it ourselves yet.
Some thoughts:
plot_enrichment
?Some strategies we have had some success with for getting around this issue:
I am working locally on Linux CentOS 8 with 128 cores, trying to analyze modbam files generated by Megalogon v2.3.4
with Guppy v5.0.16
, they are around 8 GB each.
I am using the default parameters of plot_enrichment
and your bed file for ctcf motif+peak.
I have tried to use a subset of the files (1.24 GB) but I run into the same issue. plot_enrichment
only works when I reduce the analysis to a single chromosome (445 MB), but plot_enrichment_profile
still doesn't work.
The last thing I'd try in the short term is to reduce the number of cores (even possibly to a single core, if necessary). Theoretically you shouldn't be able to run into the database locking error if there is only one core. I know that's not a great long term solution, but right now that's the best idea I have.
Sorry I don't have anything better! We're working on this error.
Hi,
I am trying to analyse a megalodon output bam file using your python package. I am able to correctly generate the qc report using the
qc_report
function, but when I try to useplot_enrichment
orplot_enrichment_profile
functions, I run into this error:Can you please someone help me to figure out what is happening?