methylome
commented
1 year ago I downloaded v0.8a1 which did not work. Solved as suggested in https://github.com/vpc-ccg/haslr/issues/18#issuecomment-841536244
Closed methylome closed 1 year ago
methylome
commented
1 year ago I downloaded v0.8a1 which did not work. Solved as suggested in https://github.com/vpc-ccg/haslr/issues/18#issuecomment-841536244
salvatierra8
commented
1 year ago hope you still remember how to use this... i'm trying to fix this by using ISonets's solution. So by
Installing from source? --- If yes... check
by using: conda install -c bioconda haslr? --- if yes... check
by "all" i understand all the haslr bin folder created by step 1 --- if yes... check
No profit :(
Conda and make version do not generate an assembly for the E. coli dataset.
[NOTE] loading contig sequences... processing file: ecoli/sr_k49_a3.contigs.nooverlap.fa... Done in 0.00 CPU seconds (0.00 real seconds) loaded 0 contigs elapsed time 0.00 CPU seconds (0.00 real seconds)
[NOTE] calculating kmer frequency of unique contigs mean: -nan elapsed time 0.00 CPU seconds (0.00 real seconds)
[NOTE] loading long read sequences... processing file: ecoli/lr25x.fasta... Done in 0.40 CPU seconds (0.40 real seconds) loaded 6453 long reads elapsed time 0.41 CPU seconds (0.41 real seconds)
[NOTE] loading alignment between contigs and long reads... processing file: ecoli/map_contigs_k49_a3_lr25x.paf... Done in 0.00 CPU seconds (0.00 real seconds) loaded 0 alignments elapsed time 0.44 CPU seconds (0.45 real seconds)
[NOTE] fixing overlapping alignments... elapsed time 0.44 CPU seconds (0.45 real seconds)
[NOTE] building compact long reads... elapsed time 0.45 CPU seconds (0.45 real seconds)
[NOTE] building the backbone graph... elapsed time 0.45 CPU seconds (0.45 real seconds)
[NOTE] cleaning weak edges... removed 0 edges elapsed time 0.45 CPU seconds (0.45 real seconds)
[NOTE] cleaning tips... removed 0 tips elapsed time 0.45 CPU seconds (0.46 real seconds)
[NOTE] cleaning simple bubbles... removed 0 simple bubbles elapsed time 0.45 CPU seconds (0.46 real seconds)
[NOTE] cleaning super bubbles... removed 0 super bubbles elapsed time 0.45 CPU seconds (0.46 real seconds)
[NOTE] cleaning small bubbles... removed 0 small bubbles elapsed time 0.45 CPU seconds (0.46 real seconds)
[NOTE] calculating long read coordinates between anchors... elapsed time 0.45 CPU seconds (0.46 real seconds)
[NOTE] calling consensus sequence between anchors... elapsed time 0.45 CPU seconds (0.46 real seconds)
[NOTE] generating the assembly from the cleaned backbone graph... elapsed time 0.45 CPU seconds (0.46 real seconds)
[NOTE] cleaning up the memory! [NOTE] elapsed time 0.45 CPU seconds (0.47 real seconds)
BYE