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Hello,
I have run FastOMA on about 2200 genomes. It all went fine until the hog_big step but it throws a **"Mafft did not compute any alignments error"** at the hog_rest step. I have attached the er…
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https://mp.weixin.qq.com/s/7oka7hdd5vMn3Bzw4zq4BA
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## Expected Behavior
I created a database of 100% identical amino acid sequences with 100% coverage. I expect after going through the prefiltering step and alignment step I would see 100% identical h…
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## Expected Behavior
Throw an exception or end the program if the number of reads is small that it will fail to be assembled.
## Current Behavior
Entered an infinite loop running on 24 threads (D…
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Hello,
I would like to ask how you use MMSeqs2 to cluster RNA, such as what values are set to parameters such as identity and coverage.
Thanks！
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We are seeing Nhmmer running incredibly slowly (8+ hours with an in-RAM database on a powerful machine) on certain sequences against [RNA Central](https://rnacentral.org/), ant NT RNA.
Both example…
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Hi,
I am using PLASS (v4.687d7) on a set of metagenomes from ~100 cheese samples and it works very well, but still, I have some questions.
In each dataset a high level of protein sequences (on avera…
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Hello, I have been using foldseek to cluster pdbs folded with alphafold and it had been working perfectly. Now I am getting an error trying to cluster.
Here is the code. I have left out all of the [=…
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## Expected Behavior
I want to remove a sequence that is a substring of a longer sequence.
Looking at https://github.com/soedinglab/MMseqs2/issues/104. I can use `--min-seq-id 1.0 -c 0.9 --cov-m…
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Many thanks for your job! I have almost 12T data that needs to be clustered by the Markov Cluster algorithm, do you have any suggestion?
[mclIO full] reading
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