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Error faidx could not get contig length for contig {1} #1082
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Without the fast5s you'll be unable to run nanopolish since it requires access to the signal data. I recommend medaka instead. |
Ok, so even though I have the reads in fasta (ignore the ".index" portion that was a mistake) for the portion of nanopolish I put above, I am still missing some sort of information that nanopolish would have given? I didn't realize there could be differences in information in fasta files |
What is the exact error message that you got? |
my exact error message is just |
The |
Hello,
I've looked through each of the previous issues with this same error and haven't been able to find a solution that will work for me. I'm trying to polish my assembly (produce by Flye/metaFlye from ONT metagenomic dataset).
This is my current full command:
I have tried different naming conventions within the assembly/contig file including :
with no luck, all the same error. The first portion of the command, before "nanopolish variants --consensus" is called, works fine it seems.
I have 26 (or 28?) contigs in the assembly file. I was not able to use "nanopolish index" to index the fast5 file because I unfortunately do not have access to the fast5 file. I don't know how much that matters?
I am working on Ubuntu 20.04.6 LTS with WSL2
Please let me know what else information would be helpful, as I am not the most experienced! And thank you for any advice.
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