How do I get a separate gkpStore database?

[wynhhh]

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!

[skoren]

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.

[wynhhh]

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!

[skoren]

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.

[skoren]

Duplicate of #2067