I did a MinION run of some plant pathogen, followed it by canu correction script. I then ran minimap2 to map against the host to exclude the host reads. Now, I need to do an assembly using Miniasm and polishing using Racon.
minimap2 -t 20 $DIR/asm20.unmapped.fasta $DIR/asm20.unmapped.fasta | gzip -1 > asm20.minimap2.paf.gz
and this faithfully generates PAF file of around ~ 3Gb in size.
But during the assembly with miniasm step, it results in a GFA file with no content. There are no apparent errors in the log file to hint as to what might be the issue.
I did a MinION run of some plant pathogen, followed it by canu correction script. I then ran minimap2 to map against the host to exclude the host reads. Now, I need to do an assembly using Miniasm and polishing using Racon.
I am following this procedure for miniasm.
I did all against all overlap with minimap2:
minimap2 -t 20 $DIR/asm20.unmapped.fasta $DIR/asm20.unmapped.fasta | gzip -1 > asm20.minimap2.paf.gz
and this faithfully generates PAF file of around ~ 3Gb in size.But during the assembly with miniasm step, it results in a GFA file with no content. There are no apparent errors in the log file to hint as to what might be the issue.
Here is the command I am running:
NOTE: I generated asm20.unmapped.fastq file from the asm20.unmapped.fasta file to figure out if the file format was the issue, but apparently not.
Here is the relevent log:
Any ideas?