Hello,
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.
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.
Hello, 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!