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sanger-pathogens / circlator

A tool to circularize genome assemblies
http://sanger-pathogens.github.io/circlator/
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Assembler canu run gets terminated #177

Open Rmmendoza opened 2 years ago

Rmmendoza commented 2 years ago

Hello, I am trying to run circlator using canu (v 1.9)as the assembler

circlator all --assembler canu ~/Desktop/CANU/KU15176/assembly/KU15176.contigs.fasta ~/Desktop/CANU/KU15176/corrected_KU15176/KU15176.correctedReads.fasta.gz ~/Desktop/Circulator_KU15176CANU

however the run gets terminated and I am getting the following error: Traceback (most recent call last): File "/usr/bin/circlator", line 58, in exec('circlator.tasks.' + task + '.run()') File "", line 1, in File "/home/rem/.local/lib/python3.8/site-packages/circlator/tasks/all.py", line 169, in run a.run() File "/home/rem/.local/lib/python3.8/site-packages/circlator/assemble.py", line 179, in run self.run_canu() File "/home/rem/.local/lib/python3.8/site-packages/circlator/assemble.py", line 172, in run_canu os.rename(original_gfa, renamed_gfa) FileNotFoundError: [Errno 2] No such file or directory: '/home/rem/Desktop/Circulator_KU15176CANU/03.assemble/canu.contigs.gfa' -> '/home/rem/Desktop/Circulator_KU15176CANU/03.assemble/contigs.gfa'

Can anybody help me on this? your assistance will be greatly appreciated. Thank you very much!

youngDouble commented 1 year ago

Now that contigs.gfa got removed. The contigs.gfa file has not been generated sinceCanu v1.9, downgrading canu should fix this error. see circular contigs and contigs.gfa #1551