Running map_genes.sh

[wershofe]

Hi, what is the exact command to enter into the command line to run blast? I tried the following:

./map_genes.sh ./example_data/transcriptomes/planarian_transcriptome.fasta nucl pl2
./example_data/transcriptomes/hydra_transcriptome.fasta nucl hy2
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]
[-blastdb_version version] [-max_file_sz number_of_bytes]
[-logfile File_Name] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
Application to create BLAST databases, version 2.9.0+

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

Error: (CArgException::eNoArg) Argument "dbtype". Mandatory value is missing: String,nucl', `prot''
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]
[-blastdb_version version] [-max_file_sz number_of_bytes]
[-logfile File_Name] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
Application to create BLAST databases, version 2.9.0+

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

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

Thanks in advance Esther

[atarashansky]

Please make sure the command looks something like this:

./map_genes.sh --tr1 {file1} --t1 {type1} --n1 {id1} --tr2 {file2} --t2 {type2} --n2 {id2}

Replace {file1} with the path to your transcriptome (e.g. example_data/transcriptomes/planarian_transcriptome.fasta). Replace {id1} with the id (e.g. pl2). Replace {type1} with nucl. Do similar for file2,type2,id2.

Let me know if this still doesn't work.

[wershofe]

Thanks that works!