Open zhangyuxin1012 opened 6 months ago
I have been using 3D-DNA to mount Hi-C data, and it has been running for more than 50 days without any output results. I would like to confirm if there is an issue or how to accelerate this process. The genome data is a haplotype HAP1 file generated by the hifiasm software, with a genome size of about 6.7 gigabytes. This is the current log file." 3d.log /public/home/yudunyang/Tools/3d-dna-201008/run-asm-pipeline.sh -r 2 /public/home/zhangyuxin/Agropyron_cristatum/WHXWZB-2023080085A/raw_data/PB/CCS/MB-89/bam/hifi_fq/01_Assembly/genome/3ddna/juicer/reference/genome.fasta /public/home/zhangyuxin/Agropyron_cristatum/WHXWZB-2023080085A/raw_data/PB/CCS/MB-89/bam/hifi_fq/01_Assembly/genome/3ddna/juicer/aligned/merged_nodups.txt version: 190716 -r|--rounds flag was triggered, will run 2 round(s) of misjoin correction. ############### Starting iterating scaffolding with editing: ...starting round 0 of scaffolding: :) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true. :) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size :) -q flag was triggered, starting calculations with 1 threshold mapping quality ...Using cprops file: genome.0.cprops ...Using merged_nodups file: genome.mnd.0.txt ...Scaffolding all scaffolds and contigs greater or equal to 15000 bp. ...Starting iteration # 1 ...Starting iteration # 2 ...Starting iteration # 3 ...Starting iteration # 4 ...Starting iteration # 5 ...Starting iteration # 6 ...Starting iteration # 7 ...Starting iteration # 8 ...Starting iteration # 9 ...Starting iteration # 10 ...Starting iteration # 11 ...Starting iteration # 12 ...Starting iteration # 13 ...Starting iteration # 14 ...Starting iteration # 15 ...Starting iteration # 16 ...Starting iteration # 17 ...Starting iteration # 18 ...Starting iteration # 19 ...Starting iteration # 20 ...Starting iteration # 21 ...Starting iteration # 22 ...Starting iteration # 23 ...Starting iteration # 24 ...Starting iteration # 25 ...Starting iteration # 26 ...Starting iteration # 27 ...Starting iteration # 28 ...Starting iteration # 29 ...Starting iteration # 30 ...Starting iteration # 31 ...Starting iteration # 32 ...Starting iteration # 33 ...Starting iteration # 34 ...Starting iteration # 35 ...Starting iteration # 36 ...Starting iteration # 37 ...Starting iteration # 38 ...Starting iteration # 39 ...Starting iteration # 40 ...Starting iteration # 41 ...Starting iteration # 42 ...Starting iteration # 43 ...Starting iteration # 44 ...Starting iteration # 45 ...Starting iteration # 46 ...Starting iteration # 47 ...Starting iteration # 48
I have been using 3D-DNA to mount Hi-C data, and it has been running for more than 50 days without any output results. I would like to confirm if there is an issue or how to accelerate this process. The genome data is a haplotype HAP1 file generated by the hifiasm software, with a genome size of about 6.7 gigabytes. This is the current log file." 3d.log /public/home/yudunyang/Tools/3d-dna-201008/run-asm-pipeline.sh -r 2 /public/home/zhangyuxin/Agropyron_cristatum/WHXWZB-2023080085A/raw_data/PB/CCS/MB-89/bam/hifi_fq/01_Assembly/genome/3ddna/juicer/reference/genome.fasta /public/home/zhangyuxin/Agropyron_cristatum/WHXWZB-2023080085A/raw_data/PB/CCS/MB-89/bam/hifi_fq/01_Assembly/genome/3ddna/juicer/aligned/merged_nodups.txt version: 190716 -r|--rounds flag was triggered, will run 2 round(s) of misjoin correction. ############### Starting iterating scaffolding with editing: ...starting round 0 of scaffolding: :) -p flag was triggered. Running LIGer with GNU Parallel support parameter set to true. :) -s flag was triggered, starting calculations with 15000 threshold starting contig/scaffold size :) -q flag was triggered, starting calculations with 1 threshold mapping quality ...Using cprops file: genome.0.cprops ...Using merged_nodups file: genome.mnd.0.txt ...Scaffolding all scaffolds and contigs greater or equal to 15000 bp. ...Starting iteration # 1 ...Starting iteration # 2 ...Starting iteration # 3 ...Starting iteration # 4 ...Starting iteration # 5 ...Starting iteration # 6 ...Starting iteration # 7 ...Starting iteration # 8 ...Starting iteration # 9 ...Starting iteration # 10 ...Starting iteration # 11 ...Starting iteration # 12 ...Starting iteration # 13 ...Starting iteration # 14 ...Starting iteration # 15 ...Starting iteration # 16 ...Starting iteration # 17 ...Starting iteration # 18 ...Starting iteration # 19 ...Starting iteration # 20 ...Starting iteration # 21 ...Starting iteration # 22 ...Starting iteration # 23 ...Starting iteration # 24 ...Starting iteration # 25 ...Starting iteration # 26 ...Starting iteration # 27 ...Starting iteration # 28 ...Starting iteration # 29 ...Starting iteration # 30 ...Starting iteration # 31 ...Starting iteration # 32 ...Starting iteration # 33 ...Starting iteration # 34 ...Starting iteration # 35 ...Starting iteration # 36 ...Starting iteration # 37 ...Starting iteration # 38 ...Starting iteration # 39 ...Starting iteration # 40 ...Starting iteration # 41 ...Starting iteration # 42 ...Starting iteration # 43 ...Starting iteration # 44 ...Starting iteration # 45 ...Starting iteration # 46 ...Starting iteration # 47 ...Starting iteration # 48