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marbl
Hi, I used parsnp for closed genomes with defined numbers of plasmids and recognized that the calculated genome size in the log file deviated from the given size of the...
**I have 1654 strains ,each is about 7M. the command is: _./parsnp -g merge.chr12.gbk -d test -c -o test.out2 -p 15._** **and the error message is as follow:** |--Parsnp v1.2--|...
The following command failed: >>fasttree -nt -quote -gamma -slow -boot 100 /home/hitesh/Downloads/P_2019_05_03_114053207553/parsnp.snps.mblocks > /home/hitesh/Downloads/P_2019_05_03_114053207553/parsnp.tree Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development...
I am trying to build Parsnp on my Linux machine, I have built libMUSCLE succesfully but while bulding Parsnp it is giving me these errors. ``` $ sudo make install...
I'm trying to use parsnp to infer core genes (and importantly, get rid of signal introduced by recombination in core genes) on around 1000 bins retrieved from metagenomes. The problem...
Hi, I was trying to align 16 genomes from different pathotypes of the same protist species, but the program only recruited 12. Is there a reason for this? In the...
I've downloaded the .ggr file on my linux machine but could not open the downloaded file. The message reads: Could not open "run_mers.gingr1.ggr" Archive type not supported. I tried running...
Dear team parsnp I have a directory with **1320 assemblies genomes**. I run the command parsnp -g ../../DB_all/genome_reference_VP/CP007004.gbk,../../DB_all/genome_reference_VP/CP007005.gbk -d ../../Data/all_v_p_for_parsnp/ -p 6 **It works well but only aligment 73 genomes.**...
Hi, I used parsnp on 26 bacterial genomes from the same subspecies, each about 2.8 Mb in length. The reference genome is a single chromosome, but all of the other...
Hi, What are the gray zones in the alignment bar, please? Unaligned regions in the reference? That would be strange in my genomes set.  Thanks.
