Robert Vaser
Robert Vaser
What do you mean by truncated contig? The log tells me that racon finished polishing the first file but it is odd that it did not start on the second....
Look at the last few lines of your log file and paste them here please. Contigs are passed to stdout while the log and error messages are printed to stderr....
Well I am not familiar with SLURM but a fast google search suggests to run `#SBATCH --error=racon.log` and `#SBATCH --output=contigs.fasta`. Try running that with a small data set to verify...
Well it should parse both files. :D You can try greping "loaded target sequences" in your log file, there should be two occurrences.
Yes, the log file should look something like that.
Hi Jeff, if your data won't fit in your memory then you should use the wrapper. Although it runs the splitted files sequentially, each run is parallelized by feeding the...
Which version of racon are you running? I doubt that there might be a problem because it took quite long to process one file. If you have multiple nodes, you...
Which commit? If you don't have the latest one then you might have the error causing an infinite loop.
Hi Elena, it is probably due to RAM shortage. How much memory does your machine have? Best regards, Robert
Unfortunately, 64GB of memory will not be sufficient to run Racon with your input. You can try and split your assembled genome by contigs, run graphmap and Racon on each...