Closed Otis-chan closed 3 years ago
Can you tell me which version of KAT you are using? I'm running 2.1.1 and the following command works for me;
kat hist -o prefix -t 16 -m 21 reads_R?.fastq
Maybe try putting the FASTQ files as the final argument.
closing due to inactivity
Hi, I have a questions about using the KAT to generate k-mer spectrum from the fastq data. The command is
kat hist fq1 fq2 -t 16 -m 21 -o prefix
.And I just want to get the spectrum for further analysis, but the error poped out which is :
ERROR
Traceback (most recent call last):
File "/home/chphl/biosoft/miniconda3/envs/KAT/lib/python3.6/local/kat/distanalysis.py", line 440, in main
a.plot(xmax=args.freq_cutoff, to_screen=args.plot, file_prefix=args.output_prefix)
File "/home/chphl/biosoft/miniconda3/envs/KAT/lib/python3.6/local/kat/distanalysis.py", line 67, in plot
if len(self.spectra.peaks) == 0:
TypeError: object of type 'NoneType' has no len()
but I check the scriptdistanalysis.py
, I think it told about some errors in the k-mer plotting process. I am not sure whether I'm right or not and whether it could affect the k-mer generation process. I'll really appreciate it, if you could give me a hint.