Command

[sabah150170]

Hi,

I am confused about how I can run the program. I have a fastq file and I want to get frequency for k = 20 just for this fastq file. I tried this,

"./cuCLARK -k 20 -T /home/sabah/Desktop/bitirme-kmers/file.txt -D /home/sabah/Desktop/bitirme-kmers -O /home/sabah/Desktop/bitirme-kmers/SAMPLE.fastq -R output -n 4 -t 1"

and also this is the output of file.txt,
cat file.txt
"/home/user_x/Desktop/bitirme-kmers/SAMPLE.fastq T1"

is this correct command, if yes. I got this error,
"CuCLARK version 1.1 (Copyright 2016 Robin Kobus, rkobus@students.uni-mainz.de)
Based on CLARK version 1.1.3 (UCR CS&E. Copyright 2013-2016 Rachid Ounit, rouni001@cs.ucr.edu)
Minimum k-mers occurences in Targets is set to 1
Starting the creation of the database of targets specific 20-mers from input files...
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)"

Could you please help me how I can run the program?

[Funatiq]

Honestly, it's been years since I last used the program and I'm not sure how to help you. I don't know what your goal is, but I would suggest to take a look at MetaCache(-GPU), which is in the same domain and offers higher accuracy and speed compared to cuCLARK.