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nanoporetech / ont-assembly-polish

ONT assembly and Illumina polishing pipeline
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racon output #17

Closed fanhuan closed 5 years ago

fanhuan commented 5 years ago

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 5 years ago

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