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Dear Sir,
When I used dRep v3.4 to compare 56910 genomes with parameters " --multiround_primary_clustering --greedy_secondary_clustering --debug", the clustering stopped due to PANDAS error like bel…
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**Describe the issue**
When running RepeatModeler, I am consistently getting the same issue at the clustering step of the LTR Pipeline. I am getting essentially the same error message as in #241, h…
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Hi!
I'm running the new OrthoFinder3 on two species sets - Species51 and Species67. Species in both represent animal phyla or their major unicellular outgroups. Phylogenetically, it is structured a…
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"Originally, we estimated it would take about 14 months to download the 600,000 Salmonella genomes in the SRA. Fortunately, another research group had assembled all the bacterial genomes (18), and we …
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Hi Dr.Camargo:
I find this nice project when I read your IMG/VR v4 manuscripts published on Nucleic Acids Research. I have some doubts about this and hope you can help me about them.
1.I tried this…
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Hi,
I use vclust script to classify viruses into species and genera following ICTV standards.
The script of assigning viruses into putative species (tANI ≥ 95%) is:
`vclust cluster -i ani.tsv -o …
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Hello,
I am running ppanggolin on about 40K species, on a slurm managed cluster, and after some time the multi-threaded processes hang indefinitely.
My initial thinking was that the total memory …
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Hi, I'm trying to do a n ANI Matrix usign this command line. but i have some problems.
I used this command line https://github.com/asadprodhan/Average-Nucleotide-Identity-ANI-analysis.git and I fol…
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When dereplicating sequences, it is crucial to cluster genomes that significantly overlap each other (i.e., high bidirectional coverage) to avoid clustering sequences where one is entirely contained w…
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Present meeting: Thomas, Karin, Håkon, Magdalena and Eve (me)
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- [ ] Prepare next meeting with the rest of the results also available, incl also snps and continue the report
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- [ ] co…