Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Stop without error message on "Reading whole genome alignments" #165

Open
Wzuoqi opened this issue Jun 6, 2023 · 0 comments
Open

Stop without error message on "Reading whole genome alignments" #165

Wzuoqi opened this issue Jun 6, 2023 · 0 comments

Comments

@Wzuoqi
Copy link

Wzuoqi commented Jun 6, 2023

Hi,
When I tried to scaffold or correct my fasta file, this tool always stop on "Reading whole genome alignments". And there were only paf, err and log files in ragtag_output, while the ragtag.scaffole.err file is empty. This problem has been confusing me during a period of time. If you can offer me some advice, I will be of great grateful.
The report is as follow:
Wed Jun 7 11:54:40 2023 --- VERSION: RagTag v2.1.0 Wed Jun 7 11:54:40 2023 --- CMD: ragtag.py scaffold GCF_914767665.1_icHarAxyr1.1_genomic.fna xyq_raw_reads.fa -t 24 Wed Jun 7 11:54:40 2023 --- WARNING: Without '-u' invoked, some component/object AGP pairs might share the same ID. Some external programs/databases don't like this. To ensure valid AGP format, use '-u'. Wed Jun 7 11:54:40 2023 --- INFO: Mapping the query genome to the reference genome Wed Jun 7 11:54:40 2023 --- INFO: Retaining pre-existing file: /home/wangzuoqi/02_dataset/xiaoyiqi/ragtag_output/ragtag.scaffold.asm.paf Wed Jun 7 11:54:40 2023 --- INFO: Reading whole genome alignments

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant