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
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