katerinakazantseva
commented
1 year ago Hello, It seems you used the fasta file from the output of flye, but this file contains different names than gfa ("contig" vs "edge"). I would recommend you to run stRainy without -f parameter, in this case it will be created automatically from your gfa file.
mallen6
Hello, I would like to use stRainy on my nanopore metagenomic assembly, but am getting an error.
I first ran flye v2.9.1 with the recommended parameters: flye --nano-raw barcode16_pool.fastq.gz --meta --threads 12 --out-dir stRainy/ --keep-haplotypes --no-alt-contigs -i 0
and then ran stRainy with the command: ./strainy.py -g assembly_graph.gfa -q barcode16_pool.fastq.gz -m nano -o stRainy_results/ -f assembly.fasta -t 12
The error I get is Traceback (most recent call last): File "/home/z2194795/stRainy/strainy.py", line 87, in
main()
File "/home/z2194795/stRainy/strainy.py", line 56, in main
input_graph = gfapy.Gfa.from_file(args.gfa)
File "/srv/scratch/z2194795/miniconda3/envs/strainy/lib/python3.10/site-packages/gfapy/gfa.py", line 235, in from_file
gfa.read_file(filename)
File "/srv/scratch/z2194795/miniconda3/envs/strainy/lib/python3.10/site-packages/gfapy/gfa.py", line 218, in read_file
self.validate()
File "/srv/scratch/z2194795/miniconda3/envs/strainy/lib/python3.10/site-packages/gfapy/gfa.py", line 121, in validate
self.validate_path_links()
File "/srv/scratch/z2194795/miniconda3/envs/strainy/lib/python3.10/site-packages/gfapy/gfa.py", line 281, in validate_path_links
raise gfapy.NotFoundError("A link equivalent to:\n{}\n".format(\
gfapy.error.NotFoundError: A link equivalent to:
L edge_1464 - edge_502 +
does not exist, but is required by the following paths:
P contig_322 edge_1464-,edge_502+,edge_502+,edge_502+,edge_322+
Do have any suggestions for how I can fix this? I did the conda install of stRainy which installed gfapy v1.2.3 (pyhdfd78af_0 from bioconda)
Best regards, M