Error: mdb_env_open: Bad file descriptor

Question

[vasudha]

Hi,

I am trying to use the following command:

blastn -task blastn -db blastdb/nt/nt -query genome_bin.1.fa -out genome1.out

and I am facing the following error:

Error: mdb_env_open: Bad file descriptor

I am not able to find anything regarding the same. It will be really helpful if anyone can guide me through this error. Thanks in advance.

[lieven.sterck]

Can you check you have the correct permission to read and/or write to all files you use in your cmdline?

[vasudha]

Yes I just checked and I do have read and write permissions to all the files.

Also, I formed the database manually because

update_blastdb.pl --passive --decompress nt
`

was throwing an error. Therefore I downloaded all the files and decompressed them manually. I have all the .nhd, .nhi, .nhr, .nin, .nnd, .nni, .nog, .nsq files.

And one more thing, my database and blast+ tool is located in the hard disk.

[lieven.sterck]

what was the error you got from the update_blastdb script ?

you should also have a file called nt.nal , do you have that one too?

are the paths OK? so your blast DB is located in a subfolder where you run this command? (or should it be /blastdb/nt/nt , as starting from a root path?)

your query file is a correct fasta file?

[vasudha]

yes I do have nt.nal available in the folder. All the paths are defined correctly as you mentioned.

my fasta file contains multiple sequences, following format:

>header1 ACTG...
>header2 ATGGC...

[lieven.sterck]

is this the format of your fasta file as it is in the file?

it should actually be like this:

>header1 
ACTG...
>header2 
ATGGC...

(not sure this is the cause of the issue though)

[vasudha]

yaah..i meant this format only... just a typo..

and when I use : bin/update_blastdb.pl --passive --decompress nt

I get

Connected to NCBI Downloading nt (44 volumes) ...

Decompressing nt.00.tar.gz ...Could not write data to '/blastdb/nt/nt.ndb' at /bin/update_blastdb.pl line 496.

Failed to decompress nt.00.tar.gz (Could not write data to '/blastdb/nt/nt.ndb'), please do so manually.

This is same for all 44 files.

[lieven.sterck]

sounds like you don't have write permissions in that specific folder? or there is no space left ?

[vasudha]

I checked, all the files have write permissions and there's memory as well. Do line 496 in update_blastdb.pl refers to anything related to this?

Though now I have decompressed the files manually. I am just facing the above mentioned issue.

[vasudha]

Can ncbi blast+ and the database be at different paths?

[lieven.sterck]

yes , absolutely. Just add the correct paths to either of them then (or add them to your $PATH env variable)

[vasudha]

okay. I am defining all the paths correctly.