makeblastdb failed to run

[jgomezd]

Hi Dom,

I could not run pipeline due to an error with makeblastdb.

This is my code:

wd <- "C:/Users/jorge/Documents/Mente/BIOVERA humboldt"
ncbi_dr <- "C:/Program Files/NCBI/blast-2.7.1+/bin"
txid <- 241806 

setUp(wd=wd, txid=txid, ncbi_dr=ncbi_dr)
run(wd=wd)

Everythin works until cluster. Then it appears the following message:
Error in error(ps = ps, paste0("makeblastdb failed to run. Check BLAST log files.")) :
Error: makeblastdb failed to run. Check BLAST log files.

This is the logfile:
USAGE
makeblastdb.exe [-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 2.7.1+

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

Error: Too many positional arguments (1), the offending value: humboldt/blast/taxon-1203511-typ-subtree-db.fa
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: humboldt/blast/taxon-1203511-typ-subtree-db.fa

I attach you my log file:
log.txt

[DomBennett]

Hi,

This looks like an error to do with Windows and the BLAST+ which the R code is not calling correctly. @hettling do you have ready access to a Windows machine to test this out? (I need to sort one out for myself to check for these sorts of errors.)

Dom

[DomBennett]

Hi @jgomezd,

Are you still having problems with this? I've managed to get a hold of a windows machine and was able to successfully run the pipeline for the ferns.

[DomBennett]

Closing due to inactivity.