Hi, I am using Spades for bitter melon WGS fastq data. now it's been one week but it is still running and there is no contig.fasta file has been created yet. now only these folder has created yet.
ls assembly_graph_after_simplification.gfa contigs.paths K21 mismatch_corrector run_spades.yaml tmp assembly_graph.fastg corrected K33 params.txt scaffolds.fasta assembly_graph_with_scaffolds.gfa dataset.info K55 pipeline_state scaffolds.paths before_rr.fasta input_dataset.yaml misc run_spades.sh spades.log
command i used -
spades.py -t 30 --careful -1 S1_1.fastq -2 S1_2.fastq -o S681
and it is still running.
There are a lot of caveats and recommendations at SPAdes - St. Petersburg genome assembler github site. Have you tried any variations? Or getting subcomponents of the pipeline to run successfully? Does the process have sufficient memory and disk (i.e. your computer is not swapping, etc.). Have you every run it successfully on maybe a smaller genome in the past? (to see how it performs in your environment?).