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Downloading the nr_euk database using the kaiju-makedb is failing with the following error:
Extracting taxdump.tar.gz/...
gzip: stdin: invalid compressed data--format violated
tar: Unexpected EOF …
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# Script
db="ncbi_nt/ncbi_nt"
kma -ipe A16_S5_3_F22_S139_R1_001.atria.fastq.gz A16_S5_3_F22_S139_R2_001.atria.fastq.gz -o A16_S5_3_F22_S139_out_kma -t_db $db -t 20 -1t1 -mem_mode -and -apm f
# …
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The list of arguments differs in documentation and program
sidr default -d [taxdump path] -b [bamfile] -f [assembly FASTA] -r [BLAST results] -m model.dot -k tokeep.contigids -x toremove.contigids …
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Hi,
I'm trying to use this tool but it's unclear where the names and nodes files comes from in the documentation.
```
$ metaDMG config raw_data/alignment.sorted.bam \
--names raw_data/names-mdm…
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Hello, it's me again.
I wondered if the Microeukaryotic DB can be used with the MMSEQS2 taxonomy module. I am interested in using this database to assign taxonomy at the contig level rather than t…
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Hi there,
I am trying to update the GTDB -r207 database I have downloaded using Struo2 with my own MAGs. It is not clear how I get some of the information including "ncbi_organism_name", "gtdb_taxi…
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- [ ] Create a function that takes a vector of genera and returns another vector of the same length and order, providing NCBI taxid wherever possible and wherever unknown.
- [ ] save taxids in the …
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Hi,
I am having similar problem to ( Error: Invalid taxonomic rank. #366 and Error: Invalid taxonomic rank #352 ) creating a diamondb.
$ diamond makedb -p 16 --in reference_proteomes.fasta.gz --…
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Would it be possible to add an option to `resolve()` to preserve the original filename? Sometimes (for better or worse) there is useful metadata in the filename that one may want. My specific use-case…
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Hello every one,
I'm, trying to run the tool. However, after creating the DB via the mmseqs2 by my download NR.fasta that I had before, I run the homology search and I failed, and the feedback like …