kSNP Activity
kSNP4 does SNP discovery and SNP annotation from whole genomes
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barryghall,
shea0
Activity for kSNP
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hansen wang posted a comment on discussion General Discussion
the error you encounter is the same as me. Do you get some response for this, how do you resolve this?
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Hi, When I execute kSNP4 -in A.in -outdir phylo -k 11 |tee Run1Log.txt, it is paused in the second step, and then it is interruptted, so I could not get the tree file, how could I resolve it?
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Barry G. Hall posted a comment on discussion General Discussion
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...
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James Doonan posted a comment on discussion General Discussion
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 from kmers.fsplit0 to /home/kSNP/FilteredKmersCache/f9a0efc6f8d763224331f8087822612a86bd118219e4e5f8c001320bc2265537.17. DEBUG:Cached filtered kmers from kmers.fsplit1...
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Rita modified a comment on discussion General Discussion
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It was the RAM on those samples and I was able to fix it and have it run. However, those were on assembled genomes and now I am trying to run with raw (quality checked and trimmed) paired-end combined Illumina fasta files and it hangs on the second step. I have attached the log file describing the error.
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It was the RAM on those samples and I was able to fix it and have it run. However, those were on assembled genomes and now I am trying to run with raw (quality checked and trimmed) paired-end combined Illumina fasta files and it hangs on the second step. I have attached the log file describing the error.
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Kenny OBERLE modified a comment on discussion General Discussion
Hi, I am also running kSNP4.1 and I got the same issue for the SNPs count (0 is indicated in tree) but also to use the parseNCBIcsv command. The message was as follow: "Error loading Python lib '/tmp/_MEIoPrYG7/libpython3.10.so.1.0': dlopen: /lib64/libm.so.6: version `GLIBC_2.35' not found (required by /tmp/_MEIoPrYG7/libpython3.10.so.1.0)" Currently, ldd (GNU libdc) 2.28 is intalled on our server.** It seems that there is no source to compile in the repertoire /usr/local/src/kSNP4/kSNP4.1_source/...
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Hi, I am also running kSNP4.1 and I got the same issue for the SNPs count (0 is indicated in tree) but also to use the parseNCBIcsv command. The message were as follow: "Error loading Python lib '/tmp/_MEIoPrYG7/libpython3.10.so.1.0': dlopen: /lib64/libm.so.6: version `GLIBC_2.35' not found (required by /tmp/_MEIoPrYG7/libpython3.10.so.1.0)" Currently, ldd (GNU libdc) 2.28 is intalled on our server.** It seems that there is no source to compile in the repertoire /usr/local/src/kSNP4/kSNP4.1_source/...
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Hi I am looking to use kSNP4 using raw read data. I have been able to use short reads that I mapped to a reference, called variants on, generated a consensus seqeunce and used that as the input for kSNP4 and it worked very well. However, I want to use the raw short read data now to compare the results and see if I can obtain a similar tree without the bias of the reference. I know the first step to using this tool is to MakeKSNP4infile but I wanted to know if it made sense to include both read sets...
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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...
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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 to account for more memory or CPU?
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pmhgrt posted a comment on discussion General Discussion
Dear @barryghall & @shea0, We just tried to use some Candida auris assemblies using kSNP4.1. We have multiple contigs in each files. We tried to run the program but we got a early termination in step 2. (base) pmh@pmh-Alienware-Aurora-R13:~/program/kSNP4.1/Test/CAUR$ /home/pmh/program/kSNP4.1/kSNP4.1_Linux_package/kSNP4.1_Linux_package/kSNP4.1pkg/kSNP4 -in Test01.in -outdir Run1 -k 11 | tee Run3Log fasta_list: /home/pmh/program/kSNP4.1/Test/CAUR/Test01.in Output directory: /home/pmh/program/kSNP4.1/Test/CAUR/Run1...
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kSNP updated /Download history.txt
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wenao hu posted a comment on discussion General Discussion
I'm very anxious, could you please reply as soon as possible?
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I have set that the argument '-cachedir', but the folder still be made in the home directory
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Hi, recently when I was using the kSNP4, I found that the directory "FilteredKmerCache" had been made in the home dir. However, there is not enough storage in the home folder on our server. Could you please tell me how to solve that? Such as changing the FilteredKmerCache folder path and so on. Thanks
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Eric Fournier posted a comment on discussion General Discussion
Hi Abed, do you receive a response regarding your problem. I got exactly the same error. Best, Eric Fournier Bioinformatician, LSPQ
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Hi, I am running kSNP4.1 on a CentOS Linux release 7.9.2009 and I get the following error at the final step of Placing SNPs on nodes SNPs_all tree; [36019] Error loading Python lib '/archives/tmp_eric2/_MEIvd5yJI/libpython3.10.so.1.0': dlopen: /lib64/libm.so.6: version `GLIBC_2.35' not found (required by /archives/tmp_eric2/_MEIvd5yJI/libpython3.10.so.1.0) As result, all tip SNPs count in tree_tipAlleleCounts.parsimony.tre are 0. Currently ldd (GNU libc) 2.17 is installed on our server. I think the...
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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...
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Abed Kurdi posted a comment on discussion General Discussion
Dear Barry, I tried to run it again without the backslash and it did not work.
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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/...
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Hello there, I am facing a problem while trying to run kSNP4. I am using the following command: kSNP4 -k 11 -outdir kSNP_output/ -in input_for_kSNP.in -vcf -NJ -core -ML -CPU 50 The program reaches (2/10) Running jellyfish to get kmer counts for few seconds and it stops. It is throwing the following error: DEBUG:Waiting for dumpers and frequency checkers to finish Traceback (most recent call last): File "inline_frequency_check.py", line 97, in <module> File "inline_frequency_check.py", line 79, in...
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Hello there, I am facing a problem while trying to run kSNP4. I am using the following command: kSNP4 -k 11 -outdir kSNP_output/ -in input_for_kSNP.in -vcf -NJ -core -ML -CPU 50 The program reaches (2/10) Running jellyfish to get kmer counts for few seconds and it stops. It is throwing the following error: DEBUG:Waiting for dumpers and frequency checkers to finish Traceback (most recent call last): File "inline_frequency_check.py", line 97, in <module> File "inline_frequency_check.py", line 79, in...
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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...
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Brad Yang posted a comment on discussion General Discussion
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 kSNP3 generated the following: headers.annotate_list: headers.annotate_list annotate_list: annotate_list genbank files: genbank_from_NCBI.gbk $all_snps_file: SNPs_all $redundant_annotations 0 SNP_annotations file: SNP_annotations SNPs_all_annotated: SNPs_all_annotated SNPs_all Finished...
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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...
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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...
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Arancha posted a comment on discussion General Discussion
Hi, I have the same problem and I can not find the solution. I will appreciate some help. Arancha
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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
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I have not seen this particular error, but since it references fsplit357 the number of genomes in your input must be at least 357. That is a pretty big data set, so you may just be running out of RAM. Barry G. Hall Director, Bellingham Research Institute barryghall@gmail.com http://www.bellinghamresearch.com http://www.bellinghamresearch.com/ On Aug 1, 2022, at 4:00 AM, Neelam neel7400@users.sourceforge.net wrote: Hi, I am trying to run Ksnp3 and it give following error terminate called after throwing...
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Neelam posted a comment on discussion General Discussion
Hi, I am trying to run Ksnp3 and it give following error terminate called after throwing an instance of 'jellyfish::file_parser::FileParserError' what(): Empty input file 'fsplit357' Abort (core dumped) foreach: No match. Thank you!
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Aminah posted a comment on discussion General Discussion
I am using Ubuntu 20.4 When I tried to run kSNP3 it gives me this message kSNP3: command not found What is the problem ?
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Hanna posted a comment on discussion General Discussion
This helped me, thank you for posting attaching the script.
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Iowa modified a comment on discussion General Discussion
I have the same proglem, ~1300 genomes, more than 800GB of data generated on hard drive. Is there a solution? SOLUTION: I used a dedicated high capacity SSD I ran into a second problem: Now it runs smoothly, jellyfish runs but then there is a step where it has to write into dedicated directoryies. It runs ok the first 600 genomes than it reports for every other genomes "awk: write failure (File too large) awk: close failed on file /dev/stdout (File too large)" until the last one. It generates a fasta...
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I have the same proglem, ~1300 genomes, more than 800GB of data generated on hard drive. Is there a solution? SOLUTION: I used a dedicated high capacity SSD I ran into a second problem: Now it runs smoothly, jellyfish runs but then there is a step where it has to write into dedicated directoryies. It runs ok the first 600 genomes than it reports for every other genomes "awk: write failure (File too large) awk: close failed on file /dev/stdout (File too large)" until the last one. It generates a fasta...
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I have the same proglem, ~1300 genomes, more than 800GB of data generated on hard drive. Is there a solution? SOLUTION: I used a dedicated high capacity SSD I ran into a second problem: Now it runs smoothly, jellyfish runs but then there is a step where it has to write into dedicated directoryies. It runs ok the first 600 genomes than it reports for every other genomes "awk: write failure (File too large) awk: close failed on file /dev/stdout (File too large)" until the last one. It generates a fasta...
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I have the same proglem, 1300 genomes, more than 800GB of data generated on hard drive. Is there a solution?
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Orson posted a comment on discussion General Discussion
Dear team ksnp3 I chosse to use these program KNSP3 because I need find SNP of 1550 genomes. I have experience using parsnp but with it is not possible analized my data. PD: I use a machine with 30 cores, 128 RAM. 950GB of hard disk. I have few question: My input files are draft genome assemblys,. not reads. 5Mb each file. 1. I run ksnp3 and I can see that it generated a lot of intermed files, for my data was more of 900GB of intermed files. Exist a option for remove the intermed files that the program...
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Be sure you are using kSNP v 3.1, the latest version. After NCBI discontinued use of GI numbers annotation would not work at all with earlier versions. The -genbank option doesn’t work at all. See the attached Troubleshooting file. Barry G. Hall On May 14, 2018, at 2:35 AM, Magnus Jespersen magnusjespersen@users.sourceforge.net wrote: I'm trying to compare some genomes of Listeria to identify SNPs. My problem is that I cannot get kSNP to annotate the SNPs identified. I have tried the following commands:...
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Magnus Jespersen posted a comment on discussion General Discussion
I'm trying to compare some genomes of Listeria to identify SNPs. My problem is that I cannot get kSNP to annotate the SNPs identified. I have tried the following commands: $ kSNP3 -in in_file.txt -outdir results_20 -k 20 -CPU 4 -vcf -annotate annotation_genome.txt -all_annotations $ kSNP3 -in in_file.txt -outdir results_20 -k 20 -CPU 4 -vcf -annotate annotation_genome.txt -genbank GCF_0001960351_ASM19603v1_genomic.gbff The in_file contains 9 fasta files containing the raw reads of my strains and...
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Alexander Banguela Castillo posted a comment on discussion General Discussion
This is my command line to excec ksnp3: ./kSNP3 -in CoryInFile -outdir K_result2 -k 15 My parsimony tree is file is always empty (I runned it two times). Interesting I have this "consensus tree" (?), but never the parsimony tree. I am analyzing genomes of fungi from the same species. Kspn3 runned for more than 30 h and use 150 Gbytes of my hdisk.... I will appreciate any help with this issue, This is the las part of the log: Consensus tree written to file "outtree" Consensus tree program, version...
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Min_frac will run just for the parsimony tree. All the trees in your outputs that include majority0.75 are parsimony trees. Barry G. Hall On Mar 5, 2018, at 4:22 AM, Cristina Kraemer Zimpel criskzimpel@users.sourceforge.net wrote: Hi, I am running kSNP with with the parameters of "-ML" and "-min_frac 0.75", and my doubt is related about this minimum fraction of genomes. The maximum likelihood output trees with be constructed with the amount genomes that I have selected (75%)? Our the min_frac command...
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Cristina Kraemer Zimpel posted a comment on discussion General Discussion
Hi, I am running kSNP with with the parameters of "-ML" and "-min_frac 0.75", and my doubt is related about this minimum fraction of genomes. The maximum likelihood output trees with be constructed with the amount genomes that I have selected (75%)? Our the min_frac command will run just for parsimony trees? As outputs I have: tree_AlleleCounts.majority0.75.NodeLabel.tre tree_AlleleCounts.majority0.75.tre tree_AlleleCounts.ML.NodeLabel.tre tree_AlleleCounts.ML.tre tree_AlleleCounts.parsimony.NodeLabel.tre...
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Jay Worley posted a comment on discussion General Discussion
I had the same issue and resolved it by forcing the kSNP bin folder to the front of the PATH variable. export PATH=/path/to/your/kSNP3:$PATH should work for people who have this reference/version issue, and is a simple fix. Worked with v.3.1, hope it's more widely applicable.
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Contact me directly at barryghall@gmail.com
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David Cleary posted a comment on discussion General Discussion
Hi, I am new to using ksnp, it is great and doing everything I need...apart from the labelling of nodes with significant snps step. When I run NodeChiSquare2tree3 I first get an error message that tree_nodeLabel.ML.tre doesnt exist - fair enough it doesnt, when I try and use one of the other other output trees it works but I get 0 significant snp labels in spite of the fact there are plenty listed in NodeChiSquares.txt. Any suggestions where I am going wrong? For info I am running kSNP3.1_Linux_package....
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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 On Aug 14, 2017, at 3:39 AM, Vincent Greffe greffevincent@users.sf.net wrote: 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...
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Vincent Greffe posted a comment on discussion General Discussion
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...
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