*BLAST Database error: DB contains no accession info

Question

[mbrav005]

When I run my blastp search against the NCBI swissprot it works fine. Here is my output

$ sudo blastp -db swissprot -query RpsB.faa -outfmt "7 std taxid" -seqidlist SACC_960_hits_SI2vs5kRpob.pacc.bsl
# BLASTP 2.10.1+
# Query: sp|P0A7V0|RS2_ECOLI 30S ribosomal protein S2 OS=Escherichia coli (strain K12) OX=83333 GN=rpsB PE=1 SV=2
# Database: swissprot
# Fields: query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 2 hits found
sp|P0A7V0|RS2_ECOLI     Q9KW14.1        25.000  24      18      0       201     224     111     134     5.5     15.8
sp|P0A7V0|RS2_ECOLI     Q9KW14.1        28.571  28      12      1       156     183     1319    1338    5.6     15.8
# BLAST processed 1 queries

However, When I run the same blastp against a database i created from a web based blast search i receive the error.

$ sudo blastp -db RpsB_nr_1k.faa  -query RpsB.faa -outfmt "7 std taxid" -seqidlist SACC_960_hits_SI2vs5kRpob.pacc.bsl
BLAST Database error: DB contains no accession info.

Is there a way for me to receive a similar output as the swissprotdb from my database I created? im trying to get rid of this error. Thanks for help

[GenoMax]

Your fasta file may need to be in a certain format for this to work exactly like that example. You have to use the -parse_seqids option when you create the database.

An aside: There is not need to use sudo to run a user program.

[mbrav005]

when I add -parse_seqids it says

$ makeblastdb -in RpsB_nr_1k.faa -dbtype prot -parse_seqids


Building a new DB, current time: 07/09/2020 14:29:29
New DB name:   /home/marcob/Phylogenetic_research/RpsB/RpsB_nr_1k.faa
New DB title:  RpsB_nr_1k.faa
Sequence type: Protein
Deleted existing Protein BLAST database named /home/marcob/Phylogenetic_research/RpsB/RpsB_nr_1k.faa
Keep MBits: T
Maximum file size: 1000000000B
BLAST options error: RpsB_nr_1k.faa does not match input format type, default input type is FASTA

Without -parse_seqids the database is able to be made still

also when I do sudo this happens

$ sudo makeblastdb -in RpsB_nr_1k.faa -parse_seqids -dbtype prot

Building a new DB, current time: 07/09/2020 14:28:06
New DB name:   /home/marcob/Phylogenetic_research/RpsB/RpsB_nr_1k.faa
New DB title:  RpsB_nr_1k.faa
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 978 sequences in 0.0488379 seconds.


terminate called after throwing an instance of 'lmdb::corrupted_error'
  what():  mdb_dbi_open: MDB_CORRUPTED: Located page was wrong type
Aborted (core dumped)

however the database still gets made i believe but I get the same error as before when trying to blastp the database i made.

[GenoMax]

Can you show what your fasta headers look like?

grep "^>" RpsB_nr_1k.faa  | head -3

The solution posted here may be applicable in your case. Give it a try: BLAST Database error: Error pre-fetching sequence data

[mbrav005]

Here are the headers

$ sudo grep "^>" RpsB_nr_1k.faa | head -3
>EFF0795401.1 30S ribosomal protein S2 [Escherichia albertii]
>AAV39589.1 ribosomal protein S [synthetic construct]
>AHA63052.1 SSU ribosomal protein S2P [Shigella dysenteriae 1617]

also, how would I go about changing this parameter?

"BLASTDB_LMDB_MAP_SIZE=1000000

This environment variable is necessary for the makeblastdb command. BUT, the larger your files the larger that size needs to be. If I set it to 1GB, everything works perfectly fine and runs and its just exactly perfect and what is expected"

thanks

[GenoMax]

export BLASTDB_LMDB_MAP_SIZE=1000000 in the terminal where you are running this from.

[mbrav005]

    marcob@DESKTOP-E3I33R3 ~/Phylogenetic_research/RpsB
$ export BLASTDB_LMDB_MAP_SIZE=1000000

marcob@DESKTOP-E3I33R3 ~/Phylogenetic_research/RpsB
$ makeblastdb -in RpsB_nr_1k.faa -parse_seqids -dbtype prot


Building a new DB, current time: 07/09/2020 15:53:24
New DB name:   /home/marcob/Phylogenetic_research/RpsB/RpsB_nr_1k.faa
New DB title:  RpsB_nr_1k.faa
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
BLAST options error: RpsB_nr_1k.faa does not match input format type, default input type is FASTA

I tried the export command but am getting the same error, I also tried $ export BLASTDB_LMDB_MAP_SIZE=1000000000

did not work same error