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From @MariaALaporte
Seems to be failing when there is >1 authority per taxon?
Examples
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=16&lvl=3&lin=f&keep=1&srchmode=1&unlock ->…
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Issue to track the list of software to benchmark
- [Blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
- [Bonsai](https://github.com/dnbaker/bonsai)
-…
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https://github.com/biocore/sortmerna/blob/4405830700ca14485aa2d4081d69cac87c429dbd/include/options.hpp#L147
In `sortmerna` help message, blast output is indicated as `(Blast - m 8 format)`. This co…
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I encountered an error:
BLAST Database error: No alias or index file found for nucleotide database [/pacbio_vectors_db] in search path [/home/liangc/Downloads/PacBio:/scratch/ncbi_blast+/db:]
To…
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```
Failure: test: crb-blast should get number of reciprocals. (TestCRBBlast)
/build/ruby-crb-blast-0.6.6/test/test_test.rb:82:in `block (2 levels) in '
expected but was
diff:
? 11
? 0
```
ruby-c…
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Dear all (is someone still maintaining this?),
I get this error when running the pipeline on just 1 .fastq file following exactly the instructions provided here, and yes, the test worked fine.
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Hi all,
I'm running into an issue that I can't seem to get working when I try to download the Kraken standard db, as well as the NCBI BLAST and taxonomy db's. Here are the outputs I'm getting alon…
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Can I use this tool with blast database (download from ftp://ftp.ncbi.nih.gov/blast/db/)?
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I am trying to download `nr` using `~/bin/ncbi-blast-dbs nr` database but I get this error somewhere in the output:
```
.
.
.
2020-01-07 12:56:50 (2.62 MB/s) - ‘nr.122.tar.gz.md5’ saved [48/48]…
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#### COG Annotation
First, download the cog database;
``` shell
wget ftp://ftp.ncbi.nih.gov/pub/COG/COG/myva;
filter_cog_database.pl whog myva >cog_clean.fa
formatdb -p T -o T -i cog_clean.fa;
```
…