QUAST failed! Make sure you are using the latest version of QUAST

[ZhangDengwei]

Hi,

I installed AGB using bioconda according to your tutorial, but I consistently got the following error:

Parsing ../H13_4/assembly_graph_with_scaffolds.gfa... Finish parsing. Extracting edge sequences from ../H13_4/assembly_graph_with_scaffolds.gfa... Running QUAST... No information about contig mappings to the reference genome QUAST failed! Make sure you are using the latest version of QUAST No information about edge mappings to the reference genome Building JSON files... Traceback (most recent call last): File "/home/dengwei/toolkit/anaconda/envs/AGB/bin/agb.py", line 154, in main() File "/home/dengwei/toolkit/anaconda/envs/AGB/bin/agb.py", line 147, in main html = embed_css_and_scripts(html) File "/home/dengwei/toolkit/anaconda/envs/AGB/lib/python3.6/site-packages/agb_src/scripts/utils.py", line 221, in embed_css_and_scripts with os.io.open(fpath, 'r', encoding="utf-8") as f: contents = f.read() AttributeError: module 'os' has no attribute 'io'

I confirmed that the version of the dependent "QUAST" was 5.0.0, then I manually updated it to 5.0.2. However, it still didn't work. May you offer any suggestion? Many thanks.

[ZhangDengwei]

I forgot attaching my command, which was nohup agb.py -a SPAdes -o ./H13_4 -r GCF_000010245.2_ASM1024v1_genomic.fna -t 6 -i ../H13_4/ &

[pbravakos]

Hi, I am having the exact same error when trying to run agb on the fastg output of Spades with the following command

agb.py --graph assembly_graph_with_scaffolds.gfa -a SPAdes