Hi, I am assembling hifi CCS reads generated by the PacBio Revio instrument. When I run hifiasm (hifi only) I get no output files besides the .log file but there are no errors. I have run versions 0.16.1 and 0.19.8, both give the same results. I have run the example file, chr11-2M.fa.gz, and it worked perfectly, generated all of the expected output files and the assembly looked perfect.
Here is the command I used:
/home/ubuntu/code/hifiasm/hifiasm -o Hyhy_hifi -t4 m84066_230921_202639_s1.hifi_reads.fastq.gz 2> hifi_test.log
The genome is approx. 850 Mbp and the fastq.gz sequence file is 22.5 Gb. One issue for assembly might be that the genome is extremely AT-rich, approx. 75% AT.
I am using ubuntu 22.04 running on oracle cloud VM with 8 CPUs and 64 Gb RAM.
You can look at the GenomeScope2 output and kmer frequency histogram here.
Here is the log file from running v. 0.19.8.
hifi_test.log
Hi, I am assembling hifi CCS reads generated by the PacBio Revio instrument. When I run hifiasm (hifi only) I get no output files besides the .log file but there are no errors. I have run versions 0.16.1 and 0.19.8, both give the same results. I have run the example file, chr11-2M.fa.gz, and it worked perfectly, generated all of the expected output files and the assembly looked perfect.
Here is the command I used: /home/ubuntu/code/hifiasm/hifiasm -o Hyhy_hifi -t4 m84066_230921_202639_s1.hifi_reads.fastq.gz 2> hifi_test.log
The genome is approx. 850 Mbp and the fastq.gz sequence file is 22.5 Gb. One issue for assembly might be that the genome is extremely AT-rich, approx. 75% AT.
I am using ubuntu 22.04 running on oracle cloud VM with 8 CPUs and 64 Gb RAM.
You can look at the GenomeScope2 output and kmer frequency histogram here.
Here is the log file from running v. 0.19.8. hifi_test.log
Thank you, I appreciate any help!