creating blast db failure

[Marta Potrykus]

Hi,

I encountered such a problem on running ductape:

Error: Too many positional arguments (1), the offending value: data/trial2/tmp/proteins/IFB0099second

I attached the log file for my work.

2017-02-03 10:38:11 - ductape.actions - [INFO] - 2 organisms are present
2017-02-03 10:38:11 - ductape.terminal - [INFO] - 1 - Making room
2017-02-03 10:38:11 - ductape.terminal - [INFO] - 2 - Creating Blast DBs
2017-02-03 10:38:11 - ductape.blast - [DEBUG] - Create Blast DB cmd: makeblastdb -in /home/marta/Desktop/omnilog data/trial2/tmp/proteins/IFB0099second -dbtype prot -out /home/marta/Desktop/omnilog data/trial2/tmp/pangenomeDBs/0 -title "Generic Blast DB" -parse_seqids
2017-02-03 10:38:11 - ductape.blast - [WARNING] - Blast DB creation failed with error 1
2017-02-03 10:38:11 - ductape.blast - [WARNING] - 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 2.2.31+

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

Error: Too many positional arguments (1), the offending value: data/trial2/tmp/proteins/IFB0099second

I have no idea why it stops in this step.
Yesterday I have updated my linux but I do not know if this might have caused such problems.

Thanks for help a lot!

[Marco Galardini]

Hi Marta,

thanks for your interest in DuctApe.
I see where the problem might be: you have a white space in the name of one of your directories ("Desktop/omnilog data") and that confuses blast. I will fix my code so that it will not happen in the future, but you can solve it straight away by renaming your directory, from "omnilog data" to "omnilog_data".

Let me know if that works and if you encounter any other problems.

Best,
Marco

[Marta Potrykus]

I have tried it and yes, it seems going further in the analysis!

Thx a lot!
Marta