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Hello,
I ran the tool on a FASTA file representing a genome which contains many different contigs. I used `python Promotech-master/promotech.py -g -i results/ -o results/` to generate the final res…
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I noticed we are missing some CCHF sequences , e.g. https://www.ncbi.nlm.nih.gov/nuccore/OQ633003.1. From the ingest logs after alignment we drop from 4760 segment sequences on NCBI virus (https://www…
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The new documentation #552 contains also a revamped tutorial. However, some important sets of functionalities miss a tutorial:
- [ ] `tantan` application interface: `tutorial/application/tantan`
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## Expected Behavior
Hello, when I run mmseq_gpu on my own data set, this error is reported. Is there any command restriction to prevent it from reporting such an error?
## Context
stdout:
sear…
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I am aligning nucleotide sequences, but veryfasttree doesn't recognize it. it ignores all a t g c n characters... What to do?
veryfasttree -nt test.aln > test.nwk
Command: veryfasttree -nt test.al…
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## Expected Behavior
easy-search should finish execution without errors
## Current Behavior
Error during pre-filter step
> Index table k-mer threshold: 0 at k-mer size 15
> Index table: …
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Hi David,
Thank you for your previous reply. I would really appreciate your help if you could clarify my following doubts:
1. Can orthofinder produce single copy orthologue file using the nucleotide…
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## Expected Behavior
mmseqs createindex "colabfold_envdb_202108_db"
## Current Behavior
Not enough memory to keep dbreader/write in memory!
Memory limit: 14845796352 dbreader/writer need: 2275…
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Hi, apologies if this is a rather simple issue, however, I was wondering if it would be possible to modify the overlap() function to calculate overlap based on the Sequence and not the CDR3.nt column?…
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Hi,
I am currently working on phenotype prediction from unique strains of antitubercular agents. Thanks for this great work, SPECTRA would be helpful to test the model that I am working on. I was …