Closed wynhhh closed 2 years ago
I'm not sure what you're asking. A separate gkpStore from what? The store is built using the gatekeeperCreate
command, run it w/o options to see usage. You can't just replace a gkpStore in the middle of a run of Canu though, that wouldn't work. I'd also advice against using 1.6 as it's very old.
Hello @skoren : I am an absolute beginner.I am planning to try canu(v.2.2) using the B.taurus dataset to do trio binning assembly.
There are Illumina short-read sequencing pair-end files for parents (Angus_1.fasta, Angus_2.fasta and Brahman_1.fasta, Brahman_2.fasta). I merger these two fasta file into a single Angus (Brahman) fasta file, i use Angus.fasta(~52X Illumina coverage) and Brahman.fasta(~56X Illumina coverage), and F1_Sequel.fasta(~68× PacBio coverage for their male F1 offspring) as input files of TrioCanu.
For this command: canu \ -p BOS -d bosTrio \ genomeSize=3g \ -haplotypeBrahman Brahman.fasta \ -haplotypeAngus Angus.fasta \ -pacbio F1_Sequel.fasta
My output directory looks like this:
At present, the program is stuck in the place 'meryl' (meryl-count) and has not output any files for a long time. I would like to ask you whether my input parameters are missing or what other problems may exist.
Any input would be appreciated. Thanks!
If there's no error reported, then the jobs are running and there's nothing to do. You can look at their individual output files and/or the load on your system to see how much CPU they are using.
Duplicate of #2067
Hi, many thanks for developing Canu.
My question is how do I get a separate gkpStore database by performing the following step: load read into read database to get gkpStore.
We are using canu v1.6 and working in a Linux environment.
Any input would be appreciated. Thanks!