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marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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The step of gfa for unitigging is very very long time! #568

Closed RobertoRun closed 7 years ago

RobertoRun commented 7 years ago

Canu is a very nice assembler. I have used it to de novo assemble four genomes. But, when i go to the fifth genome, the step of gfa for unitigging (unitigging/4-unitigger) is very very long time (more than 4 days)! But, it's still not finished, there file is also no any update (St.unitigs.aligned.bed.err). Do you think it's regular or not? What i can do in the next if it's failure? Thanks!

-- Reading BED './St.unitigs.bed'. bed: Loaded 770 records. -- Loading sequences from tigStore '../St.utgStore' version 2. -- Loading sequences from tigStore '../St.ctgStore' version 2. -- Aligning 770 records using 4 threads.

brianwalenz commented 7 years ago

This was fixed in the past week or so.

For this assembly, copy unitigging/4-unitigger/St.unitigs.bed to unitigging/4-unitigger/St.unitigs.aligned.bed and restart. The positions in the bed file won't be quite correct. While you're there, create an empty file St.unitigs.aligned.bed.gfa which I keep forgetting to remove. The restart will go immediately to writing outputs and then you're done.

For later assemblies, update to the 'unstable' version, then v1.6 when it comes out.

RobertoRun commented 7 years ago

Thank you so much! I have fixed it and got the results! After failed many times with v1.5, I have updated to the version of July 20th, 2017.

I will try the latest version (July 28th, 2017) to do assemble in the future!