Question: error invoking makeblastdb
0
gravatar for SeaStar
15 months ago by
SeaStar30
Ocean
SeaStar30 wrote:

I was using the software repeatmasker setting a -species for my analysis. when I run the command line: $ /home/pc/RepeatMasker -species danio -gff -s genome.fa it reports me this message:

RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
Search Engine: NCBI/RMBLAST [ 2.6.0+ ]
Master RepeatMasker Database: /home/pc/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: dc20181026-rb20181026 )


Building species libraries in: /home/pc/RepeatMasker/Libraries/dc20181026-rb20181026/danio
   - 260 ancestral and ubiquitous sequence(s) for danio
   - 2325 lineage specific sequence(s) for danio
,

    RepeatMasker::createLib(): Error invoking /home/pc/anaconda/pkgs/rmblast-2.6.0-h4422958_0//bin/makeblastdb on file /home/pc/RepeatMasker/Libraries/dc20181026-rb20181026/danio/specieslib.

anyone does know what's the problem?

repeatmasker genome • 508 views
ADD COMMENTlink modified 14 months ago by Biostar ♦♦ 20 • written 15 months ago by SeaStar30

do you have the rmblast installed , and accessible? aka, can you do ls /home/pc/anaconda/pkgs/rmblast-2.6.0-h4422958_0//bin/makeblastdb

ADD REPLYlink written 15 months ago by lieven.sterck8.5k

I suppose yes, the output of the command is:

$ ls /home/pc/anaconda/pkgs/rmblast-2.6.0-h4422958_0//bin/makeblastdb
/home/pc/anaconda/pkgs/rmblast-2.6.0-h4422958_0//bin/makeblastdb
ADD REPLYlink written 15 months ago by SeaStar30
$ makeblastdb
USAGE
  makeblastdb [-h] [-help] [-in input_file] [-input_type type]
    -dbtype molecule_type [-title database_title] [-parse_seqids]
    [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
    [-mask_desc mask_algo_descriptions] [-gi_mask]
    [-gi_mask_name gi_based_mask_names] [-out database_name]
    [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID]
    [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
   Application to create BLAST databases, version 2.5.0+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Argument "dbtype". Mandatory value is missing:  `String, `nucl', `prot''
Error:  (CArgException::eNoArg) Argument "dbtype". Mandatory value is missing:  `String, `nucl', `prot''

I don't know what mean these kind of errors

ADD REPLYlink written 15 months ago by SeaStar30

OK, yes don't mind the error for now , it looks like blast is installed.

can you access (or does it exist) this file /home/pc/RepeatMasker/Libraries/dc20181026-rb20181026/danio/specieslib ?

ADD REPLYlink written 15 months ago by lieven.sterck8.5k

Yes I can access to it

ADD REPLYlink written 15 months ago by SeaStar30

is it a file or a directory? in case of the latter: does it contain any files? in case of the former: does the file contain data?

ADD REPLYlink written 15 months ago by lieven.sterck8.5k

It is a file, and it contains sequences (of transposable elements found in danio, I suppose)

ADD REPLYlink written 15 months ago by SeaStar30

Have you tried the solution for the libpcre.so.0 issue at Error Invoking Makeblastdb?

ADD REPLYlink written 15 months ago by SMK1.9k

Yes I solved this problem in the past. It works fine with human database ( without -species option)

ADD REPLYlink written 15 months ago by SeaStar30
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