Open aaronphillips7493 opened 2 years ago
Hi Aaron, that looks like a problem in your python/matplotlib installation. Typical case is matplotlib is trying to use the wrong locale, you should get the same problem by just opening a python interpreter and doing "import matplotlib". It may just be the case that you need to set the LC variables to sort it.
Best,
bj
I've had this before and it's a matplotlib problem not a problem with KAT. Unfortunately I can't remember how I fixed it but I found some suggestions here - https://stackoverflow.com/questions/34771191/matplotlib-taking-time-when-being-imported.
The messages you are seeing in the KAT log indicate that you should be asking for a larger hash size for the computation so you probably want to increase this using the -H parameter (default is 100000000). However, once you have fixed the matplotlib problem you shouldn't need to rerun the whole process as the matrix file has already been generated (called SRs_vs_contigs), all you need to do is plot it using kat plot spectra-cn -o plot SRs_vs_contigs
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Best, Jon
Hey,
I am trying to make some k-mer comparison plots using some short reads and a genome assembly I have done.
I ran the following command on my universities HPC with 8 threads and 20G memory:
kat comp -t 8 -m 17 -o SRs_vs_contigs reads.fastq contigs.fasta
And it seems to run fine, but it has been stalled at the following step for ~15 hours now:
Creating plot(s) ...Matplotlib is building the font cache; this may take a moment.
I am wondering: how long is 'a moment'? Is it reasonable to be waiting this long for the plots? Could this be a memory issue?
Thanks for making a great tool, Aaron :)
p.s. I have attached the job log file here slurm-12441689.txt