Genomic landscape error

[lkulandaivelu]

Dear colleague,

We do not manage to perform the genome landscape analysis on the Arabidopsis exemple that you provided.

We tried on two different HPC.

Here is the error message:

[gdroc@core-login1 jcvi]$ singularity exec jcvi.sif python -m jcvi.graphics.landscape stack TAIR10_chr_all.fas --stacks=Repeats --window=250000 --shift=50000
[07/08/24 10:08:31] INFO latex not found. latex use is disabled. base.py:614
INFO lp not found. latex use is disabled. base.py:616
INFO Set text.usetex=False. Font styles may be inconsistent. base.py:453
DEBUG Line/stack-plot options: window=250000 shift=50000 subtract=None landscape.py:567
DEBUG Load file Repeats.bed.50000.span.bins base.py:36
DEBUG Load file TAIR10_chr_all.fas.sizes base.py:36
Traceback (most recent call last):
File "/usr/local/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/local/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/usr/local/lib/python3.8/site-packages/jcvi/graphics/landscape.py", line 1221, in
main()
File "/usr/local/lib/python3.8/site-packages/jcvi/graphics/landscape.py", line 139, in main
p.dispatch(globals())
File "/usr/local/lib/python3.8/site-packages/jcvi/apps/base.py", line 131, in dispatch
globalsaction
File "/usr/local/lib/python3.8/site-packages/jcvi/graphics/landscape.py", line 1201, in stack
draw_stacks(
File "/usr/local/lib/python3.8/site-packages/jcvi/graphics/landscape.py", line 1147, in draw_stacks
stackplot(ax, binfiles, nbins, palette, chr, window, shift)
File "/usr/local/lib/python3.8/site-packages/jcvi/graphics/landscape.py", line 1089, in stackplot
m += s
ValueError: operands could not be broadcast together with shapes (4,) (5,) (4,)

Thanking you in advance for your help

Letizia Kulandaivelu

[tanghaibao]

@lkulandaivelu

This is a bug that I failed to spot. Many thanks for reporting it.
It turns out ChrC (organelle) in the input genome has a length less than 250000, leading to the error.

This has been fixed in the commit above and new version.

Haibao