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Old 08-17-2014, 11:59 PM   #1
rangel
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Location: Germany

Join Date: Mar 2012
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Default tblastx in blast+ gives an error regareding a DB alias but blastall works fine

I'm trying to run `tblastx` locally. For this I created my own database using the command:
`makeblastdb -in all_seqs.fasta -dbtype nucl -title "my_db" -out my_db -hash_index -parse_seqids`

Then running my query against it using `blastall` works:
`blastall -p tblastx -d my_db -i reads.fasta -o my_blast.out -v 1 -b 1 -m 8 -S 1 -a 5`

Still I'd like to use blast+ because it's recommended by NCBI to phase out blastall and because I'd like to use the option `max_target_seqs` which to my knowledge does not exist in blastall.

Running the equivalent command to the previous one:
`tblastx -db my_db -query reads.fasta -num_threads 5 -num_alignments 1 -out my_blast.out -outfmt 6`

Gives an error:
`BLAST Database error: No alias or index file found for nucleotide database [...my_db] in search path [...reads::]`

Googling it a bit showed that I was missing an alias file `.nal`.

Why didn't `makeblastdb` create it and why is it needed for blast+ but not for blastall?
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Old 08-18-2014, 12:26 AM   #2
maubp
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The *.nal or for protein databases *.pal files are used for very large databases made of several parts. That is not the case here.

Are you doing all this in the same directory?

Can you try giving the -db argument as an absolute path?
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Old 08-19-2014, 12:42 AM   #3
rangel
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The DB and the query are not in the same directory (I used a relative path for the DB, but didn't supply it in my example).
Following your comment I tried running the command from the DB directory so that I could just supply its name and have the path pointing to the query and output and that indeed worked.
Thanks for the help!
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