Barry G. Hall

No I dea. I have no experience with external servers Barry G. Hall barryghall@gmail.com  On Sep 6, 2024, at 12:49 AM, James Doonan jamdoo@users.sourceforge.net wrote: I installed kSNP4 on an external server. When the program runs it places cached output in my home directory which fills up fast. I have a large space allowance on another directory (data_dir). Is there an easy way to redirect the FilteredKmersCache to data_dir? I don't have sudo rights. This is the error: DEBUG:Cached filtered kmers...

You are probably running out of RAM. Barry G. Hall barryghall@gmail.com  On Feb 12, 2024, at 11:39 AM, Rita rimo2@users.sourceforge.net wrote: This is happening to me as well. I don't think it's due to only handling one contig per file as I was previously able to successfully run over 150 samples each with 16 contigs in the individual files. However, now I have about 172 samples (each with 16 contigs) and now it hangs and crashes on that step. Is there something I can add to the command I am using...

Please email me directly at the address in the “Troubleshooting kSNP4.1 (or kSNP4)” document that was included in the package you downloaded. Answer All of the questions in that document or I will ignore your request for support. Barry G. Hall Director, Bellingham Research Institute barryghall@gmail.com http://www.bellinghamresearch.com http://www.bellinghamresearch.com/  On Aug 19, 2023, at 6:55 AM, Abed Kurdi abedkurdi@users.sourceforge.net wrote: Dear Barry, I tried to run it again without the...

File names may contain only A-Z a-Z 0-1 _ and - characters. Your output file name kSNP_output/ contains the / character. Try getting rid of the / character. Barry G. Hall Director, Bellingham Research Institute barryghall@gmail.com http://www.bellinghamresearch.com http://www.bellinghamresearch.com/  On Aug 18, 2023, at 2:41 AM, Abed Kurdi abedkurdi@users.sourceforge.net wrote: Hello there, I am facing a problem while trying to run kSNP4. I am using the following command: kSNP4 -k 11 -outdir kSNP_output/...

Brad, Email me directly at barryghall@gmail.com for assistance. Barry G. Hall Director, Bellingham Research Institute barryghall@gmail.com http://www.bellinghamresearch.com http://www.bellinghamresearch.com/ On May 31, 2023, at 3:01 PM, Brad Yang ly276@users.sourceforge.net wrote: Hi all, I have tried to use kSNP3/kSNP4 to annotate SNP but both fail to do so. The annotation summary in kSNP3 is empty while it shows those core SNPs are not in annotated . kSNP4 doesn't give me any error message and...

Whenever you have a problem and ask for help be SURE to provide sufficient information for someone to actually help you. In this case you should have stated how many species you included in your input file. If it was fewer than 4 species it is impossible to make a phylogenetic tree. kSNP3 has been replaced by kSNP4. Download kSNP4 from source forge and read the ENTIRE User Guide - including FAQ - before installing or trying to use kSNP4. If you still have problems follow all the instructions for...

kSNP3 has been replaced by kSNP4. Get kSNP4 from SourceForge and install it according to the kSNP4 User Guide. Barry G. Hall Director, Bellingham Research Institute barryghall@gmail.com http://www.bellinghamresearch.com http://www.bellinghamresearch.com/ On Mar 1, 2023, at 7:20 AM, Arancha arancha@users.sourceforge.net wrote: Hi, I have the same problem and I can not find the solution. I will appreciate some help. Arancha cannot get ksnp3 to complete TOO FEW SPECIES https://sourceforge.net/p/ksnp/discussion/general/thread/d7980673/?limit=25#f277...

kSNP4, a major revision and upgrade of kSNP3 was released on Oct. 26, 2022. It is about 2.5 x faster than kSNP3. To the experienced kSNP3 user it will look about the same and the same commands do the same thing. Barry Hall