"*.contig.fa.misasm.break.fa" may be a binary file.

[ShuaishuaiTai]

Hi, when we used the corrected ONT Reads for the misassembly correction, there was some error in the .misasm.break.fa file, when we use the command "less -S" open this file, it is said ".misasm.break.fa" may be a binary file. This error result in the RaGoo pipeline could not be continue work in the next step. My script to run RaGoo is "ragoo.py Sample1A.contig.fa.gz assembly.fa.gz -C -s -R Sample1A.correctedReads.fasta.gz -T corr -m minimap2. How to solve this problem? Many thanks!

[ViriatoII]

Same problem!

Traceback (most recent call last):
  File "/home/guerrer/.local/bin/ragoo.py", line 4, in <module>
    __import__('pkg_resources').run_script('RaGOO==1.1', 'ragoo.py')
  File "/home/guerrer/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 658, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/guerrer/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1445, in run_script
    exec(script_code, namespace, namespace)
  File "/home/guerrer/.local/lib/python3.6/site-packages/RaGOO-1.1-py3.6.egg/EGG-INFO/scripts/ragoo.py", line 729, in <module>
  File "/home/guerrer/.local/lib/python3.6/site-packages/RaGOO-1.1-py3.6.egg/EGG-INFO/scripts/ragoo.py", line 84, in write_misasm_broken_ctgs
FileNotFoundError: [Errno 2] No such file or directory: 'INPUT_DIR/INPUT_NAME.misasm.break.fa'

In my case /home/guerrer/.local/lib/python3.6/site-packages/RaGOO-1.1-py3.6.egg is a binary file and not a directory that contains "EGG-INFO/scripts/ragoo.py"

[malonge]

Hi there,

Sorry for the late reply. First of all, I highly recommend you transition to using RagTag if at all possible. It is much improved over RaGOO in many ways.

@ShuaishuaiTai could you also share the exact stdout when you run RaGOO?

Thanks

[ShuaishuaiTai]

OK，I tested the RaGOO software, I found when I used the -R parameter, the input contig file only support the ungzip file, like this: ragoo.py Sample1A.contig.fa ref.fa.gz -s -R Sample1A.correctedReads.fasta.gz -T corr -m minimap2. Then, the RaGOO software can work well.

[malonge]

Hi there,

Thanks for the update. One should be able to use gzip input so this is a bug, and I will leave the issue open in case I ever decide to fix it. I may not as I am now focusing on RagTag and RaGOO will eventually be deprecated.

Thanks