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Asking about ragtag patch runtime #195

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Abieskawa opened this issue Mar 21, 2025 · 0 comments
Open

Asking about ragtag patch runtime #195

Abieskawa opened this issue Mar 21, 2025 · 0 comments

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@Abieskawa
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Abieskawa commented Mar 21, 2025

Hi,
I am running ragtag patch with following command:
ragtag.py patch 00_fcs_gx/Tilapia_MTW01_clean.fasta GCF_001858045.2_O_niloticus_UMD_NMBU_genomic.fna -o 00_gap_filling/ -t 128 -i 0.05 -u
I got a genome with 698 scaffolds.
and its printout:

Wed Mar 19 15:39:33 2025 --- VERSION: RagTag v2.1.0
Wed Mar 19 15:39:33 2025 --- WARNING: This is a beta version of `ragtag patch`
Wed Mar 19 15:39:33 2025 --- CMD: ragtag.py patch 00_fcs_gx/Tilapia_MTW01_clean.fasta GCF_001858045.2_O_niloticus_UMD_NMBU_genomic.fna -o 00_gap_filling/ -t 128 -i 0.05 -u
Wed Mar 19 15:39:33 2025 --- INFO: Running: ragtag_splitasm.py -o /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.ctg.agp /home/abieskawa/output/tilapia_MTW01/00_fcs_gx/Tilapia_MTW01_clean.fasta > /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.ctg.fasta 2> /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.err
Wed Mar 19 15:40:22 2025 --- INFO: Finished running : ragtag_splitasm.py -o /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.ctg.agp /home/abieskawa/output/tilapia_MTW01/00_fcs_gx/Tilapia_MTW01_clean.fasta > /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.ctg.fasta 2> /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.err
Wed Mar 19 15:40:22 2025 --- INFO: Running: ragtag_rename.py /home/abieskawa/output/tilapia_MTW01/GCF_001858045.2_O_niloticus_UMD_NMBU_genomic.fna -p qseq -o /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.rename.agp > /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.rename.fasta 2> /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.err
Wed Mar 19 15:40:35 2025 --- INFO: Finished running : ragtag_rename.py /home/abieskawa/output/tilapia_MTW01/GCF_001858045.2_O_niloticus_UMD_NMBU_genomic.fna -p qseq -o /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.rename.agp > /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.rename.fasta 2> /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.err
Wed Mar 19 15:40:35 2025 --- INFO: Writing: /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.comps.fasta
Wed Mar 19 15:40:55 2025 --- INFO: Mapping the query genome to the target genome
Wed Mar 19 15:40:55 2025 --- INFO: Running: nucmer --maxmatch -l 100 -c 500 -p /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.asm /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.ctg.fasta /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.rename.fasta 2> /home/abieskawa/output/tilapia_MTW01/00_gap_filling/ragtag.patch.asm.delta.log

It is still running until now, I am worry that if there is any abnormal reaction during the process and lead to indefinite loop.
Thanks~

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