LisaBlazek
commented
4 years ago hello! i let minimap2 ran on its default settings and now it worked :)
Closed LisaBlazek closed 4 years ago
LisaBlazek
commented
4 years ago hello! i let minimap2 ran on its default settings and now it worked :)
hello! i have the problem, that after some minutes LRScaf stops due to the error: "PathBuilder ： The Edges could not be empty"
this is the command i use: $ java -jar /home/programs/LRScaf/LRScaf-1.1.9.jar -c ../KDH -a ../longreads_against_kdh.paf -t mm -i 0.1 -o .
this is the output i get: 2020-04-30 18:18:55 [ INFO ] Launching... 2020-04-30 18:18:55 [ INFO ] The output folder existed! 2020-04-30 18:18:55 [ INFO ] Building output folder, erase time: 0 ms 2020-04-30 18:19:15 [ INFO ] Reading contigs, erase times: 19442 ms 2020-04-30 18:19:15 [ INFO ] The output file /binfl/LRScaff_output/draft_summary.info existed. It will overwrite. 2020-04-30 18:20:11 [ INFO ] Valid Aligned Records: 0 2020-04-30 18:20:11 [ INFO ] Reading Aligned Records, erase time: 55991 ms 2020-04-30 18:20:11 [ INFO ] Repeat count: 0 2020-04-30 18:20:11 [ INFO ] Finding repeat, erase time: 0 ms 2020-04-30 18:20:11 [ INFO ] Valid Links Acount: 0 2020-04-30 18:20:11 [ INFO ] Building Link, erase time : 7 ms 2020-04-30 18:20:11 [ INFO ] The output file /binfl/LRScaff_output/links.info existed. It will overwrite. 2020-04-30 18:20:11 [ INFO ] The output file /binfl/LRScaff_output/triadlinks.info existed. It will overwrite. 2020-04-30 18:20:11 [ ERROR ] PathBuilder ： The Edges could not be empty! 2020-04-30 18:20:11 [ INFO ] Ending... 2020-04-30 18:20:11 [ INFO ] Scaffolding erase time: 75 s.
the alignment was done with minimap2 minimap2 -ax map-ont -t 16 ../KDH /project/ALL_reads.fasta > longreads_against_kdh.sam paftools sam2paf longreads_against_kdh.sam > longreads_against_kdh.paf
even tough i looked into the other tickets, i'm not sure what the problem is in this case. i'm not very experienced so it would be really great if you could help me.