I would love to try out kSNP, it looks very promising. However I'm experiencing some problems running it.
I'm running the most basic setting of kSNP v3 (no annotations) for 42 microbial strains (fasta files containing multiple contigs) however it goes very slowly.
It has been counting k-mers with Jellyfish for 3 days now. The fsplit files are present in the output folder, but in the terminal it says that it only made fsplit0,1 and 10.
Is it normal that the program takes this much time to run jellyfish? Or am I doing something wrong that is causing the program to slow down?
Please let me know if any extra information is necessairy to solve the problem.
Kind regards,
Vincent
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No, this is not normal.
Please email me at barryghall@gmail.com barryghall@gmail.com so we can try to figure out the problem together. Once we have the solution you can post it to the kSNP discussion group.
Barry G. Hall
I would love to try out kSNP, it looks very promising. However I'm experiencing some problems running it.
I'm running the most basic setting of kSNP v3 (no annotations) for 42 microbial strains (fasta files containing multiple contigs) however it goes very slowly.
It has been counting k-mers with Jellyfish for 3 days now. The fsplit files are present in the output folder, but in the terminal it says that it only made fsplit0,1 and 10.
Is it normal that the program takes this much time to run jellyfish? Or am I doing something wrong that is causing the program to slow down?
Please let me know if any extra information is necessairy to solve the problem.
Dear Prof. Hall,
I would love to try out kSNP, it looks very promising. However I'm experiencing some problems running it.
I'm running the most basic setting of kSNP v3 (no annotations) for 42 microbial strains (fasta files containing multiple contigs) however it goes very slowly.
It has been counting k-mers with Jellyfish for 3 days now. The fsplit files are present in the output folder, but in the terminal it says that it only made fsplit0,1 and 10.
Is it normal that the program takes this much time to run jellyfish? Or am I doing something wrong that is causing the program to slow down?
Please let me know if any extra information is necessairy to solve the problem.
Kind regards,
Vincent
No, this is not normal.
Please email me at barryghall@gmail.com barryghall@gmail.com so we can try to figure out the problem together. Once we have the solution you can post it to the kSNP discussion group.
Barry G. Hall