Open BirdmanRidesAgain opened 1 year ago
Which racon/minimap2 version are you using? Did you by any chance forgot option -a
while running minimap2? Invalid file format usually indicates mismatch between the file extension and the file format.
Best regards, Robert
Hi, I've been attempting to run racon on a set of draft assemblies. Racon has worked on other assemblies in the past, but when I attempt to run the following line of code:
racon -t 60 ../../../ONT-data/ArdeotisONT/ardeotisONT_trimreads.fq.gz ardeotisONT_flye-assembly_remapped-SO.sam ../polished-flye/ardeotisONT_flye-assembly.fasta > ardeotisONT_assembly-racon.fasta
...this is the output, along with an empty file:
I'm not certain which file is the problematic one, but I used the following code to generate the overlaps file, as I think that's the most likely to be problematic.
minimap2 -t 60 ../polished-flye/ardeotisONT_flye-assembly.fasta -ax map-ont ../../../ONT-data/ArdeotisONT/ardeotisONT_trimreads.fq.gz | samtools sort > houbaraONT_flye-assembly_remapped-SO.sam
Any insight you have into what might be wrong with these commands would be greatly appreciated.