A question about "correct" step in RagTag, I need help!

[link-xhx]

I'm just a student new to genome-related research and analysis, I think RagTag software is great！Thank a lot！

Recently, I use RagTag software to help me optimise the contigs I assembled using SOAPdenove2 software. I run programs on linux servers (1.5T running memory), in "correct" step, I input the contigs I assembled using SOAPdenove2 software and reference genome, contigs size 36.41 GB, reference genome size 2.83 GB, and the input code is “nohup ragtag.py correct GCA_025200525.1_XYYC_v1.0_genomic.fna graph_prefix.contig -t 8 &”. But ten days have passed and the "correct" step is not over yet, I don‘t know why！Is this normal? Did I do something wrong?

Now, this is what the server displays when the TOP command is used: PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
366086 xiehaox+ 20 0 155.5g 135.9g 2900 R 99.7 9.0 18992:49 ragtag_correct.
28576 xiehaox+ 20 0 163352 3532 1600 R 1.0 0.0 0:02.03 top

Now, nohup.out file show: Mon Mar 20 02:23:52 2023 --- VERSION: RagTag v2.1.0 Mon Mar 20 02:23:52 2023 --- CMD: ragtag.py correct GCA_025200525.1_XYYC_v1.0_genomic.fna graph_prefix.contig -t 8 Mon Mar 20 02:23:52 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'. Mon Mar 20 02:23:52 2023 --- INFO: Mapping the query genome to the reference genome Mon Mar 20 02:23:52 2023 --- INFO: Running: minimap2 -x asm5 -t 8 /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/GCA_025200525.1_XYYC_v1.0_genomic.fna /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/graph_prefix.contig > /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/ragtag_output/ragtag.correct.asm.paf 2> /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/ragtag_output/ragtag.correct.asm.paf.log Mon Mar 20 02:57:53 2023 --- INFO: Finished running : minimap2 -x asm5 -t 8 /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/GCA_025200525.1_XYYC_v1.0_genomic.fna /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/graph_prefix.contig > /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/ragtag_output/ragtag.correct.asm.paf 2> /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/ragtag_output/ragtag.correct.asm.paf.log Mon Mar 20 02:57:53 2023 --- INFO: Reading whole genome alignments Mon Mar 20 03:03:40 2023 --- INFO: Filtering and merging alignments

Now, ragtag.correct.asm.paf.log file show: [M::mm_idx_gen::42.9701.63] collected minimizers [M::mm_idx_gen::47.4802.12] sorted minimizers [M::main::47.4802.12] loaded/built the index for 790 target sequence(s) [M::mm_mapopt_update::50.8582.05] mid_occ = 456 [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 790 [M::mm_idx_stat::53.1752.00] distinct minimizers: 116480354 (72.38% are singletons); average occurrences: 2.582; average spacing: 9.974; total length: 2999357698 [M::worker_pipeline::197.8046.16] mapped 15625000 sequences [M::worker_pipeline::334.1036.92] mapped 15625000 sequences [M::worker_pipeline::463.5967.23] mapped 15625000 sequences [M::worker_pipeline::571.9067.38] mapped 15625000 sequences [M::worker_pipeline::686.2847.49] mapped 15625000 sequences [M::worker_pipeline::784.1047.56] mapped 15625000 sequences [M::worker_pipeline::880.3837.62] mapped 15625000 sequences [M::worker_pipeline::1007.5967.67] mapped 15625000 sequences [M::worker_pipeline::1110.4507.70] mapped 15625000 sequences [M::worker_pipeline::1192.2087.73] mapped 15454323 sequences [M::worker_pipeline::1269.1747.75] mapped 15151516 sequences [M::worker_pipeline::1326.7337.76] mapped 15151516 sequences [M::worker_pipeline::1380.8377.77] mapped 15151516 sequences [M::worker_pipeline::1435.0377.79] mapped 14992998 sequences [M::worker_pipeline::1486.9327.80] mapped 14705883 sequences [M::worker_pipeline::1530.1147.81] mapped 14705883 sequences [M::worker_pipeline::1580.7017.82] mapped 14403057 sequences [M::worker_pipeline::1621.5867.82] mapped 14285715 sequences [M::worker_pipeline::1661.7787.83] mapped 13977149 sequences [M::worker_pipeline::1697.0567.84] mapped 13810620 sequences [M::worker_pipeline::1729.0137.84] mapped 13513514 sequences [M::worker_pipeline::1757.5447.85] mapped 13186944 sequences [M::worker_pipeline::1784.2777.85] mapped 12873206 sequences [M::worker_pipeline::1809.2067.86] mapped 12506954 sequences [M::worker_pipeline::1831.1287.86] mapped 12090442 sequences [M::worker_pipeline::1851.3747.87] mapped 11686167 sequences [M::worker_pipeline::1869.6267.87] mapped 11215552 sequences [M::worker_pipeline::1886.8717.87] mapped 10713980 sequences [M::worker_pipeline::1901.7067.88] mapped 10210357 sequences [M::worker_pipeline::1917.1027.88] mapped 9686066 sequences [M::worker_pipeline::1934.4397.89] mapped 9168489 sequences [M::worker_pipeline::1953.4197.89] mapped 8662996 sequences [M::worker_pipeline::1970.9887.89] mapped 8194019 sequences [M::worker_pipeline::1980.8767.90] mapped 7936508 sequences [M::worker_pipeline::1990.0967.90] mapped 7936508 sequences [M::worker_pipeline::2001.1727.91] mapped 7852853 sequences [M::worker_pipeline::2011.1307.91] mapped 7066059 sequences [M::worker_pipeline::2021.0357.91] mapped 6136695 sequences [M::worker_pipeline::2027.8297.91] mapped 5248202 sequences [M::worker_pipeline::2034.0977.92] mapped 4269483 sequences [M::worker_pipeline::2038.0547.92] mapped 3085097 sequences [M::worker_pipeline::2039.895*7.91] mapped 1251117 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -x asm5 -t 8 /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/GCA_025200525.1_XYYC_v1.0_genomic.fna /home/xiehaoxing/surveyworkxhx/youcha_survey/zuzhuang/ref_zuzhuang/graph_prefix.contig [M::main] Real time: 2040.596 sec; CPU: 16145.971 sec; Peak RSS: 11.273 GB

and ragtag.correct.err file has no content.

Please help me! Thank you very much!

[yangxinzhi]

I have also encountered the same problem and I would like to ask how long it will take to run with -t 40 in patch. nohup ragtag.py correct ~/gerbil/genome/GCF_000001635.27_GRCm39_genomic.fna ~/gerbil/genome_BIBU/GCA_004026785.1_MerUng_v1_BIUU_genomic.fna -t 50 -o ~/gerbil/genome_BIBU/ -u >~/gerbil/genome_BIBU/BILL_gerbil.log & This is the command I used to run correct when I ran one last time it was over so quickly, why is it taking him so long this time

[stachyris]

Hi both,

Did you folks figure out this issue? I am also facing this. Let me know,

Thanks, Vinay

[link-xhx]

Hi, Vinay! At present, I have not solved this problem, I will continue to work hard, if I have a solution in the future, I will write here.