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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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Problem with prokka annotation #459

Open tmurillocorrales opened 2 years ago

tmurillocorrales commented 2 years ago

Hi, Thanks for developing metawrap!

I am attempting to annotate the reassemble bins with prokka, however I am getting the following error message:

Please rename your contigs or use --centre XXX to generate clean contig names. Which apparently means that the name of the contigs are too long or incorrect according to the NCBI format.

I tried to solve the issues by using the command -- centre XXX from prokka but it is not recognize by metawrap.

Thus, I would like to ask if there is another solution available to proceed with the annotation?

Thanks, Tatiana

nelsonruth11 commented 2 years ago

I also had this problem. Looking in the prokka log files, I saw

[13:44:45] Contig ID must <= 20 chars long: NODE_10_length_187849.

I'm running the whole metawrap pipeline in a shell script, so before running annotate_bins I included this little sed command to remove "length" from the contig names. Probably not best practices but it did the trick for me.

sed -i 's/_length//g' BIN_REASSEMBLY/reassembled_bins/bin*