makeblastdb and windowsmaker error

Question

[asmariyaz23]

I want to run an aligner, HS-BLASTN for which, I need to run makeblastdb and windowmasker. I ran makeblastdb using fasta file downloaded with rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz without any apparent errors:

/scratch/SOFTWARE/ncbi-blast-2.10.0+-src/c++/ReleaseMT/bin/makeblastdb -in hg38.fa -dbtype nucl -out hg38.fa.blastdb   
Building a new DB, current time: 11/09/2019 08:49:18    
New DB name:   /scratch/hg38/hg38.fa.blastdb   
New DB title:  hg38.fa   
Sequence type: Nucleotide    
Keep MBits: T   
Maximum file size: 1000000000B      
Adding sequences from FASTA; added 455 sequences in 31.7667 seconds.

Here is a listing of the hg38.fa.blastdb:

-rw-r--r--. 1 root root 3273481150 Jan 16  2014 hg38.fa    
-rw-r--r--. 1 root root      20480 Nov  9 08:49 hg38.fa.blastdb.ndb 
-rw-r--r--. 1 root root      37188 Nov  9 08:49 hg38.fa.blastdb.nhr   
-rw-r--r--. 1 root root       5560 Nov  9 08:49 hg38.fa.blastdb.nin   
-rw-r--r--. 1 root root       5468 Nov  9 08:49 hg38.fa.blastdb.not  
-rw-r--r--. 1 root root  802642712 Nov  9 08:49 hg38.fa.blastdb.nsq  
-rw-r--r--. 1 root root      16384 Nov  9 08:49 hg38.fa.blastdb.ntf
-rw-r--r--. 1 root root       1824 Nov  9 08:49 hg38.fa.blastdb.nto

Next, I ran windowmasker and I encounter an error as below:

/scratch/SOFTWARE/ncbi-blast-2.10.0+-src/c++/ReleaseMT/bin/windowmasker -mk_counts -in /scratch/hg38/hg38.fa.blastdb -out /scratch/hg38/hg38.fa.counts -infmt blastdb
computing the genome length      
Error: (106.7) Application's execution failed: mdb_dbi_open: MDB_NOTFOUND: No matching key/data pair found

I also did a blastdbcheck which gave me the same error:

/scratch/SOFTWARE/ncbi-blast-2.10.0+-src/c++/ReleaseMT/bin/blastdbcheck -db hg38.fa.blastdb -verbosity=3    
Writing messages to <stdout> at verbosity (Detailed)    
ISAM testing is ENABLED.    
Legacy testing is DISABLED.    
TaxID testing is DISABLED.    
By default, testing 200 randomly sampled OIDs.           
Testing 1 volume(s).    
 /scratch/hg38/hg38.fa.blastdb    
 [ERROR] caught exception in /scratch/hg38/hg38.fa.blastdb    
mdb_dbi_open: MDB_NOTFOUND: No matching key/data pair found   
 Result=FAILURE. 1 errors reported in 1 volume(s).  
Testing 0 alias(es).    
 Result=SUCCESS. No errors reported for 0 alias(es).
Total errors: 1

Unsure of what I am doing wrong, could you provide me any pointers?

[Mensur Dlakic]

I have no experience with what you are doing, so I am simply trying to interpret the error.

The key/data pair may be referring to difference in your file names. Your starting file is hg38.fa while your database is hg38.fa.blastdb plus .n??. I suggest you rename hg38.fa to hg38.fa.blastdb (or make a symbolic link as shown below) and try again.

ln -s hg38.fa hg38.fa.blastdb

[asmariyaz23]

I played around with 2 scenoarios:

# Moved the fasta file 
mv hg38.fa hg38.fa.blastdb
/scratch/SOFTWARE/ncbi-blast-2.10.0+-src/c++/ReleaseMT/bin/blastdbcheck -db hg38.fa.blastdb -verbosity=3
Writing messages to <stdout> at verbosity (Detailed)
ISAM testing is ENABLED.
Legacy testing is DISABLED.
TaxID testing is DISABLED.
By default, testing 200 randomly sampled OIDs.

Testing 1 volume(s).
 /scratch/hg38/hg38.fa.blastdb
 [ERROR] caught exception in /scratch/hg38/hg38.fa.blastdb
 mdb_dbi_open: MDB_NOTFOUND: No matching key/data pair found
 Result=FAILURE. 1 errors reported in 1 volume(s).
 Testing 0 alias(es).
 Result=SUCCESS. No errors reported for 0 alias(es).

Total errors: 1

 # Symlinked it
 ln -s hg38.fa hg38.fa.blastdb
 /scratch/SOFTWARE/ncbi-blast-2.10.0+-src/c++/ReleaseMT/bin/blastdbcheck -db hg38.fa.blastdb -verbosity=3
 Writing messages to <stdout> at verbosity (Detailed)
 ISAM testing is ENABLED.
 Legacy testing is DISABLED.
 TaxID testing is DISABLED.
 By default, testing 200 randomly sampled OIDs.

Testing 1 volume(s).
 /scratch/hg38/hg38.fa.blastdb
 [ERROR] caught exception in /scratch/hg38/hg38.fa.blastdb
 mdb_dbi_open: MDB_NOTFOUND: No matching key/data pair found
Result=FAILURE. 1 errors reported in 1 volume(s).
Testing 0 alias(es).
 Result=SUCCESS. No errors reported for 0 alias(es).

[asmariyaz23]

MDB_NOTFOUND error refers to some sort of EOF error according to docs here.