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nanoporetech / tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
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Tombo Resquiggle - Failed to lead reference genome FASTA #311

Open sr8510 opened 3 years ago

sr8510 commented 3 years ago

Hi, I am trying to analyze RNA Modifications in Direct RNA-seq nanopore datasets. I performed the sequencing using rat cell line, so my reference is Rnor_6. I am trying to perform resquiggle on my Fast5s, but I get an error stating that Minimap failed to load reference genome Fasta. I used difference assemblies from NCBI and Ensemble with the extensions .fna or .fa but I am getting the same error. I got my files from Illumina's iGenome list and also tried from NCBI and Ensemble directly. I tried using the software Geneious to convert my .fna file to .Fasta but didn't help either. Can anyone point me to a potential issue or error I made? Even preprocessing using tombo preprocess command did not help. My Fast5s are basecalled using Guppy. Thanks a lot

SycamoreLeaf commented 3 years ago

Hi @sr8510 . Welcome to GitHub! Would you mind copy-pasting the exact lines of code you run that lead to the error?