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Hi,
I was trying to extract the cps loci for which seroba has identified as untypable.
I am getting this error in the PANAROO_REF_COMPARISON step.
`RuntimeError: Nearly all clusters have been tri…
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Since cluster module needs too much memory. (I have 2 million nucleotide seqs, about 30G, and 1T memory, and segment fault occurred).
I try to use LINCLUST instead. But I also want a better perf…
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Vsearch seems to never detect chimera with default parameters.
I think it lies on the fact that sequences are not dereplicated and therefore do not have a "count" section in fasta header.
However…
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If EMIRGE cannot reconstruct any sequences due to low read coverage, it currently gets to the clustering stage where usearch throws a segfault and emirge exits without an informative error message.
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Hi, I am trying to run isONclust2 first for isONcorrect, but I got this error for all the batches, one example:
Loaded input batch from batches/isONbatch_9.cer:
Batch number: 9
Bat…
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Hi,
I'm trying to run on the example dataset using the command
`python ~/Broccoli/broccoli.py -dir ~/Broccoli/example_dataset/ -ext '.fasta'`
with diamond version 4.0.515 and fasttree versio…
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If you have own unpublished sequence data or data from other repositories not included in PrimerMiner, the should be an option to add your own sequences manually before clustering (in fasta format)
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Hi,
I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
```
# extract consensus sequences from profiles
…
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## Expected Behavior
Hi! I'm clustering ~60000 nucleotide sequences, each 250bp to 500bp.
Here is the command I use
mmseqs cluster shrimpDB shrimp.clu97 tmp97 --cluster-mode 0 -s 7.5 --min-seq-id…
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Dear foldseek developers,
my questions are about UniProt50 DB. I read your preprint and it says UniProt50 is
> Uniprot/AlphaFold database clustered to 50% sequence identity
First question i…