killed error

[rsandean]

Hi, I was trying to use NucFreq as such:
python3 /gpfs01/home/mbars7/NucFreq/NucPlot.py -w 32 sorted_nosecondary_hifi.bam hap1_nucfreq.png

And I have an error which simply says killed, but I'm not sure why this error happened:
Using a font-size of 16
Packages loaded
Reading the whole bam becuase no region or bed argument was made.
Killed

Do I need to include a Bed file for this?

Any advice would be great, thank you! :)

[mrvollger]

Killed is most commonly an out of memory error from your computer. If this is indeed the case passing a bed file with a subset of regions is likely to help.

[rsandean]

Hi, thank you for the reply, It seems that I do have memory on my hpc, which is weird that it came up with a killed error. How much memory does it usually take? But having passed a bed file with only two regions, I now keep getting this error:

python3 /gpfs01/home/mbars7/NucFreq/NucPlot.py -w 32 sorted_nosecondary_hifi.bam --bed firsthap_reg2.bed hap3_reg2_nucfreq.png
Using a font-size of 16
Packages loaded
Reading in the region or bed argument(s).
Reading in NucFreq from region: RL_1:1000000-2000000
Reading in NucFreq from region: RL_1:3000000-4000000
Plotting 2 regions in hap3_reg2_nucfreq.png
RL_1:1000000-1999999
/gpfs01/home/mbars7/NucFreq/NucPlot.py:402: UserWarning: FixedFormatter should only be used together with FixedLocator
ax.set_xticklabels(xlabels)
RL_1:3000000-3999999

I noticed in the python script, that it's commented
# Including this causes some internal bug in matplotlib when the font-size changes
# ylabels = [format(label, ",.0f") for label in ax.get_yticks()]
# ax.set_yticklabels(ylabels)
ax.set_xticklabels(xlabels)

Should I just remove this section?

Thank you!