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Thanks for developing ragtag! It`s a really nice tool!
I have approxiamte 4,500,000 HiFi ccs reads with average length arround 15 kb and I want to assemble a genome using a related species as reference. I wonder if ragtag pipeline can begin directly with those ccs reads as contigs? like correcting the reads with reference sequences at first. Is there any suggestions for parameter settings?
Also, I`ve actually tried, but it seemed to stuck, which has already been more than 2 days, after building index and the minimap alignment seemed not using all reads input, as shown below:
Sun Nov 3 16:55:33 2024 --- VERSION: RagTag v2.1.0
Sun Nov 3 16:55:33 2024 --- CMD: ragtag.py correct -t 28 -u /home/wsq_pkuhpc/lustre2/user/lhy/results/genome_asm/homo_asm/ragtag_from_hifiasm/../ref/GCF_016881025.1_HiC_Itri_2_genomic.fna /home/wsq_pkuhpc/lustre2/user/lhy/gsgenome/01.CCS/merged_hifi_css.fasta -o /home/wsq_pkuhpc/lustre2/user/lhy/results/genome_asm/homo_asm/ragtag_from_hifiasm/pipe_from_ccs
Sun Nov 3 16:55:33 2024 --- INFO: Mapping the query genome to the reference genome
Sun Nov 3 16:55:33 2024 --- INFO: Running: minimap2 -x asm5 -t 28 /home/wsq_pkuhpc/lustre2/user/lhy/results/genome_asm/homo_asm/ref/GCF_016881025.1_HiC_Itri_2_genomic.fna /home/wsq_pkuhpc/lustre2/user/lhy/gsgenome/01.CCS/merged_hifi_css.fasta > /home/wsq_pkuhpc/lustre2/user/lhy/results/genome_asm/homo_asm/ragtag_from_hifiasm/pipe_from_ccs/ragtag.correct.asm.paf 2> /home/wsq_pkuhpc/lustre2/user/lhy/results/genome_asm/homo_asm/ragtag_from_hifiasm/pipe_from_ccs/ragtag.correct.asm.paf.log
Sun Nov 3 17:09:14 2024 --- INFO: Finished running : minimap2 -x asm5 -t 28 /home/wsq_pkuhpc/lustre2/user/lhy/results/genome_asm/homo_asm/ref/GCF_016881025.1_HiC_Itri_2_genomic.fna /home/wsq_pkuhpc/lustre2/user/lhy/gsgenome/01.CCS/merged_hifi_css.fasta > /home/wsq_pkuhpc/lustre2/user/lhy/results/genome_asm/homo_asm/ragtag_from_hifiasm/pipe_from_ccs/ragtag.correct.asm.paf 2> /home/wsq_pkuhpc/lustre2/user/lhy/results/genome_asm/homo_asm/ragtag_from_hifiasm/pipe_from_ccs/ragtag.correct.asm.paf.log
Sun Nov 3 17:09:14 2024 --- INFO: Reading whole genome alignments
Sun Nov 3 17:16:14 2024 --- INFO: Filtering and merging alignments
[fai_load] build FASTA index.
Thanks for developing ragtag! It`s a really nice tool!
I have approxiamte 4,500,000 HiFi ccs reads with average length arround 15 kb and I want to assemble a genome using a related species as reference. I wonder if ragtag pipeline can begin directly with those ccs reads as contigs? like correcting the reads with reference sequences at first. Is there any suggestions for parameter settings?
Also, I`ve actually tried, but it seemed to stuck, which has already been more than 2 days, after building index and the minimap alignment seemed not using all reads input, as shown below:
Thanks in advance for your help!
Lyu
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