Closed jgomezd closed 5 years ago
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
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.
Closing due to inactivity.
Hi Dom,
I could not run pipeline due to an error with makeblastdb.
This is my code:
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