Error: mdb_env_open: Bad file descriptor
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
blastn Error: mdb_env_open: Cannot allocate memory
written by Mehmet
-
blastn error : mdb_env_open: No such file or directory
written by Sowmya Pulapet •
-
Online and remote blastn producing different results
written by e •
-
preformatted bastdb nt volume/alias file missing
written by pe_se •
-
Snakemake error with blast
written by kamanovae •
-
Error running blastn on Linux: Critical [blastn] External MBEDTLS version mismatch: 2.16.2 headers …
written by 2jackcummins •
-
Adding -type arguments of blastn in Bioperl
written by adhirajnath14 •
-
blastn: how to show all query list in my blastn results, even if they have no match.
written by nuria.mauri •
-
Cannot reproduce BLAST results returned by the WEB API on the shell-based BLAST+ 2.7.1
written by xerygi •
-
BLAST-2.6.0+ error: No alias or index file found for nucleotide database
written by z.zangishei •
Can you check you have the correct permission to read and/or write to all files you use in your cmdline?
Yes I just checked and I do have read and write permissions to all the files.
Also, I formed the database manually because
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, .nsqfiles.And one more thing, my database and blast+ tool is located in the hard disk.
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?
yes I do have
nt.nalavailable in the folder. All the paths are defined correctly as you mentioned.my fasta file contains multiple sequences, following format:
is this the format of your fasta file as it is in the file?
it should actually be like this:
(not sure this is the cause of the issue though)
yaah..i meant this format only... just a typo..
and when I use :
bin/update_blastdb.pl --passive --decompress ntI 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.
sounds like you don't have write permissions in that specific folder? or there is no space left ?
I checked, all the files have write permissions and there's memory as well. Do line
496 in update_blastdb.plrefers to anything related to this?Though now I have decompressed the files manually. I am just facing the above mentioned issue.
Can ncbi blast+ and the database be at different paths?
yes , absolutely. Just add the correct paths to either of them then (or add them to your $PATH env variable)
okay. I am defining all the paths correctly.