Empty faa file for 1008392 produces error with diamond about phylostratr HOT 2 CLOSED

I am following the online supplementary document and find this problem too.

When I try
strata <- strata_blast(strata, blast_args=list(nthreads=16L)) %>%
+ strata_besthits

I get

Error in (function (fastafile, blastdb = "blastdb", verbose = FALSE) :

Failed to make blast database blastdb/1008392.faa
In addition: Warning message:
In system2("makeblastdb", stderr = TRUE, stdout = TRUE, args = c("-dbtype", :
running command ''makeblastdb' -dbtype prot -in uniprot-seqs/1008392.faa -out blastdb/1008392.faa 2>&1' had status 1`

Then I remove this TaxID by strata <- prune(strata, '1008392', type='name')
It works. Meanwhile, the "TaxID.tab" need a header. Otherwise, you will get this error message.

The following named parsers don't match the column names: qseqid, sseqid, qstart, qend, sstart, send, evalue, score, staxid

from phylostratr.

@urmi-21 @haojingshao you are exactly right. See issue #11 where we just now fixed this issue by removing the species 1008392, as suggested by @urmi-21, from the default set of representatives for bacteria. Apparently the proteome was removed this year from UniProt. Everything should work fine in the latest commit.

@haojingshao the BLAST headers in phylostratr are definitely a pain. You may submit a separate issue report for cleaning up header handling and error messages if you want.

I'll close this issue for now since the immediate problem of the missing 1008392 strain is solved in #11 and the general problem of missing sequences can be avoided by removing them as @haojingshao shows.

from phylostratr.