Pipeline usage with scaffolds.fasta as input file

[Khabibullin543]

Hello! Can I use TORMES with scaffolds.fasta as an input file? I had to run SPAdes manually because of following error:

This is tormes version 1.3.0

Script used:
/home/MZRF/khabibullinnr/miniconda3/envs/tormes-1.3.0/bin/tormes --metadata 233.09_NextGen.txt --genera Klebsiella --output 233.09_NextGen_results_3

Parameters set:
- Metadata file: 233.09_NextGen.txt
- Output directory: /home/MZRF/khabibullinnr/233.09_NextGen_results_3
- Number of threads to use: 1
- Special analysis enabled for: Klebsiella

The analysis will be performed for:
- Number of samples from raw reads: 1
- Number of samples from genomes: 0

TORMES pipeline started at: 2023-12-06 15:58

Quality filtering process started at: 2023-12-06 15:58
- Software for filtering chosen: prinseq
- Minimum quality of reads to survive: 25
- Minimum length of reads to survive: 125
- Number of reads surviving for sample Sample1: 15537810

Assembly started at: 2023-12-06 16:43
- Software for genome assembly chosen: spades
- WARNING: Sample1 did not generate an assembly file and will be excluded for further analysis

Taxonomic identification started at: 2023-12-06 16:43

MLST started at: 2023-12-06 16:43

Antimicrobial resistance and virulence genes search started at: 2023-12-06 16:43

Gene prediction and nnotation started at: 2023-12-06 16:43

WARNING: Pangenome analysis was skipped automatically due to low number of genomes to compare at: 2023-12-06 16:43
Surface polysaccharide locus typing started at: 2023-12-06 16:43
WARNING: K-locus typing was not performed
WARNING: O-locus typing was not performed

Plasmid search started at: 2023-12-06 16:43

Point mutation search started at: 2023-12-06 16:43

Tormes report started at: 2023-12-06 16:43
WARNING: html report file could not be created

TORMES pipeline finished at: 2023-12-06 16:43

Thank you for using TORMES!