I am running KAT too in compute Canada to get some kmer estimations.
I use "comp" to compare two of my raw data files (R1 and R2) and the assembly file.
However, I end up getting the following error. It produces the .mx file but the file is empty.
My slurm output is like the following.
Could you please help me to understand the problem?
Lmod is automatically replacing "intel/2020.1.217" with "gcc/9.3.0".
Due to MODULEPATH changes, the following have been reloaded:
1) openmpi/4.0.3
/home/ksenevir/.local/easybuild/software/2020/avx2/Compiler/gcc9/kat/2.4.2/share/kat/scripts/kat/plot/spectra_cn.py:86: UserWarning: loadtxt: Empty input file: "<_io.TextIOWrapper name='kat_out-main.mx' mode='r' encoding='UTF-8'>"
matrix = np.loadtxt(input_file)
Traceback (most recent call last):
File "/home/ksenevir/.local/easybuild/software/2020/avx2/Compiler/gcc9/kat/2.4.2/share/kat/scripts/kat/plot/spectra_cn.py", line 227, in
main()
File "/home/ksenevir/.local/easybuild/software/2020/avx2/Compiler/gcc9/kat/2.4.2/share/kat/scripts/kat/plot/spectra_cn.py", line 130, in main
nm = np.zeros((len(bands),len(matrix[0])))
IndexError: index 0 is out of bounds for axis 0 with size 0
Time taken: 1.0s
Hi There,
I am running KAT too in compute Canada to get some kmer estimations. I use "comp" to compare two of my raw data files (R1 and R2) and the assembly file. However, I end up getting the following error. It produces the .mx file but the file is empty. My slurm output is like the following. Could you please help me to understand the problem?
Due to MODULEPATH changes, the following have been reloaded: 1) openmpi/4.0.3
Kmer Analysis Toolkit (KAT) V2.4.2
Running KAT in COMP mode
Input Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... success! success! success! success! success! success! success! success!
Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... success! success! success! success! success! success! success! success!
Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... success! success! success! success! success! success! success! success!
Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... success! success! success! success! success! success! success! success!
Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... success! success! success! success! success! success! success! success!
Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... success! success! success! success! success! success! success! success!
Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... success! success! success! success! success! success! success! success! Time taken: 5610.2s
Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... Warning: Specified hash size insufficent - attempting to double hash size... success! success! success! success! success! success! success! success! Time taken: 17.6s
Time taken: 1101.7s
Time taken: 1.9s
Time taken: 0.3s
/home/ksenevir/.local/easybuild/software/2020/avx2/Compiler/gcc9/kat/2.4.2/share/kat/scripts/kat/plot/spectra_cn.py:86: UserWarning: loadtxt: Empty input file: "<_io.TextIOWrapper name='kat_out-main.mx' mode='r' encoding='UTF-8'>" matrix = np.loadtxt(input_file) Traceback (most recent call last): File "/home/ksenevir/.local/easybuild/software/2020/avx2/Compiler/gcc9/kat/2.4.2/share/kat/scripts/kat/plot/spectra_cn.py", line 227, in
main()
File "/home/ksenevir/.local/easybuild/software/2020/avx2/Compiler/gcc9/kat/2.4.2/share/kat/scripts/kat/plot/spectra_cn.py", line 130, in main
nm = np.zeros((len(bands),len(matrix[0])))
IndexError: index 0 is out of bounds for axis 0 with size 0
Time taken: 1.0s
KAT COMP completed. Total runtime: 6733.4s
../lib/include/kat/pyhelper.hpp([kat::KatPythonError*] = Unexpected python error
Thank you in advance. Kanishka