nanoporetech/ont-assembly-polish

racon output

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fanhuan commented

Hi,

Am I missing something or why in analysis.mk(line 45) it goes like:

@$(WDIR)/racon -t $(CORES) $(NANOPORE_READS) $(MINIMAP_OVERLAPS) $(CANU_CONTIGS) $(RACON_CONTIGS)

instead of

@$(WDIR)/racon -t $(CORES) $(NANOPORE_READS) $(MINIMAP_OVERLAPS) $(CANU_CONTIGS) > $(RACON_CONTIGS)

?
I had to add the greater-than sign in order for the pipeline to work. Otherwise racon prints the output to the screen.

Thanks ahead.

bsipos commented

Thanks for reporting this issue! The latest racon versions changed how they output the contigs so your fix was necessary.

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