search

TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
http://www.earlham.ac.uk/kat-tools
GNU General Public License v3.0
206 stars 52 forks source link

Using KAT to generate the k-mer spectrum #153

Closed Otis-chan closed 3 years ago

Otis-chan commented 3 years ago

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 script distanalysis.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.

jonwright99 commented 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.

bjclavijo commented 3 years ago

closing due to inactivity