Tried using BWA MEM2 on a concatenated FASTQ file from Oxford Nanopore sequencing, using a fasta file (with fai) that was generated using Raven as the reference sequence. For analysis mode I chose 3. Nanopore 2D-reads mode. See attached screen shots of input (first two shots) and output (last shot). The run failed with the error message “An error occurred with this dataset: format bam. database?”. I am not sure what the response should be. In case I chose the wrong analysis mode I repeated with option 1 with the same result. Any advice would be gratefully received.
By the way I had problems persuaded Galaxy to accept my fastq file as a fastq sanger file but followed the advice in one of your previous answers and chose the file type when I re-uploaded the fastq file.
Regards,
Derek
Found an icon in the error red box and clicked on it and within the text was a notice that BWA MEM2 doesn’t cope with long reads or with contigs (I am using both) and to use minimap2 instead. I did and it worked.
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