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shingocat / lrscaf

TGS scaffolding
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Null alignment file #29

Closed JuliaLopezDelgado closed 2 years ago

JuliaLopezDelgado commented 3 years ago

I am trying to run LRScaf with the following commands:

minimap2 -ax map-ont -t 8 assembly.fasta ONT.fasta > align.mm java -Xms200g -Xmx200g -jar LRScaf-1.1.10.jar -c assembly.fasta -a align.mm -t mm -o out

I am getting the following error:

2021-05-12 15:54:44 [ ERROR ] Error: org.apache.commons.cli.MissingArgumentException: The type of aligned file could not be null! at agis.ps.Main.parsering(Main.java:180) at agis.ps.Main.main(Main.java:53) 2021-05-12 15:54:44 [ ERROR ] agis.ps.Main The type of aligned file could not be null! 2021-05-12 15:57:45 [ ERROR ] agis.ps.file.MMReader On lines: 1 For input string: "SN:contig_1" 2021-05-12 15:57:45 [ ERROR ] PathBuilder ： The Edges could not be empty! 2021-05-12 16:00:23 [ ERROR ] agis.ps.file.M4Reader On lines: 1 3 2021-05-12 16:00:23 [ ERROR ] PathBuilder ： The Edges could not be empty! 2021-05-12 16:02:45 [ ERROR ] PathBuilder ： The Edges could not be empty!

Could you please help me with this error?

Thanks in advance! Julia

shingocat commented 3 years ago

Julia,

On your minimap2 alignment command, using "-a" is to output in sam format nor PAF format which it is the type mm format on LRScaf.