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"*.contig.fa.misasm.break.fa" may be a binary file. #69
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Same problem!
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" |
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 |
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.
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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 |
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!
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