Improper

[BirdmanRidesAgain]

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:

[racon::Polisher::initialize] loaded target sequences 7.326854 s


terminate called after throwing an instance of 'std::invalid_argument'
  what():  [bioparser::SamParser] error: invalid file format
Aborted (core dumped)

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.

[rvaser]

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