Error: bash: line 1: 66955 Killed python /.../hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/.../hylight_out//1.split_fastx/s1.fa -c sub06600014 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads #1
Description
Hi,
I encountered some errors while using HyLight. I hope to get your help.
Content of work.sh:
#!/usr/bin/bash
export PATH=/public/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/bin/:$PATH
hylight -s /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/short_read_interleaved.fastq -l /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/01.data_stats/LR_01.hifi_reads.fastq -o /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out/ -t 20 --corrected --average_read_len 150 --insert_size 350
Running resources:
The data size of LR_01.hifi_reads.fastq is 21.16 Gbp. The data size of short_read_interleaved.fastq is 7.25 Gbp.
sbatch -N 1 -n 1 -c 20 --mem=150g -p xhacexclu16,xhacexclu03,xhacexclu19 work.sh
The run log reads as follows:
2025-01-26 17:04:02,964 - /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/HyLight.py[line:115] - INFO: generate overlap information among long reads
2025-01-26 17:12:28,776 - /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/HyLight.py[line:123] - INFO: computing all-vs-all long read overlaps and then filter wrong overlap by SNPs and sort overlap by overlap score.
bash: line 1: 66955 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600014 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600014_tmp_overlap4.paf: No such file or directory
bash: line 1: 66979 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600024 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600024_tmp_overlap4.paf: No such file or directory
bash: line 1: 66982 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600035 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600035_tmp_overlap4.paf: No such file or directory
bash: line 1: 66988 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600033 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600033_tmp_overlap4.paf: No such file or directory
bash: line 1: 234101 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600047 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600047_tmp_overlap4.paf: No such file or directory
Traceback (most recent call last):
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py", line 410, in
sys.exit(main())
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py", line 63, in main
(snp, map_po, start_po) = prpare_mutation2(paf_file2)
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py", line 310, in prpare_mutation2
refposi = len_sp[7]
IndexError: list index out of range
bash: line 1: 66973 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600021 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600021_tmp_overlap4.paf: No such file or directory
bash: line 1: 66956 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600022 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600022_tmp_overlap4.paf: No such file or directory
bash: line 1: 66965 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600026 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600026_tmp_overlap4.paf: No such file or directory
bash: line 1: 63013 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600050 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600050_tmp_overlap4.paf: No such file or directory
bash: line 1: 177385 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600043 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600043_tmp_overlap4.paf: No such file or directory
bash: line 1: 45591 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600049 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600049_tmp_overlap4.paf: No such file or directory
bash: line 1: 66990 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600039 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600039_tmp_overlap4.paf: No such file or directory
bash: line 1: 66647 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600052 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600052_tmp_overlap4.paf: No such file or directory
bash: line 1: 66976 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600020 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600020_tmp_overlap4.paf: No such file or directory
bash: line 1: 232809 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600045 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600045_tmp_overlap4.paf: No such file or directory
bash: line 1: 66967 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600016 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600016_tmp_overlap4.paf: No such file or directory
bash: line 1: 86101 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600056 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600056_tmp_overlap4.paf: No such file or directory
Don't execute the command: minimap2 -N 40 -t 3 -L --eqx -cx ava-pb -Hk19 -m100 -g10000 --max-chain-skip 25 sub06600041 /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa 2> /dev/null | python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py -len 30 -oh 3 > sub06600041_tmp_overlap2.paf
Traceback (most recent call last):
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py", line 110, in
sys.exit(main())
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py", line 41, in main
[qseqid, qlen, qstart, qend, qori, sseqid, slen, sstart, send, matchcount, length] = line.split('\t')[:11]
ValueError: not enough values to unpack (expected 11, got 1)
bash: line 1: 17324 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600027 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600027_tmp_overlap4.paf: No such file or directory
bash: line 1: 83027 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600029 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600029_tmp_overlap4.paf: No such file or directory
bash: line 1: 153066 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600015 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600015_tmp_overlap4.paf: No such file or directory
bash: line 1: 66984 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600037 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600037_tmp_overlap4.paf: No such file or directory
bash: line 1: 223962 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600019 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600019_tmp_overlap4.paf: No such file or directory
bash: line 1: 66981 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600031 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600031_tmp_overlap4.paf: No such file or directory
bash: line 1: 87732 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600030 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600030_tmp_overlap4.paf: No such file or directory
bash: line 1: 148798 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600036 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600036_tmp_overlap4.paf: No such file or directory
bash: line 1: 195714 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600044 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600044_tmp_overlap4.paf: No such file or directory
bash: line 1: 138829 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600034 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600034_tmp_overlap4.paf: No such file or directory
bash: line 1: 26418 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600055 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600055_tmp_overlap4.paf: No such file or directory
bash: line 1: 233403 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600023 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600023_tmp_overlap4.paf: No such file or directory
bash: line 1: 240285 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600025 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600025_tmp_overlap4.paf: No such file or directory
bash: line 1: 178416 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600017 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600017_tmp_overlap4.paf: No such file or directory
bash: line 1: 186805 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub06600042 -t 3 -len 6000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub06600042_tmp_overlap4.paf: No such file or directory
2025-01-28 21:06:41,354 - /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/HyLight.py[line:133] - INFO: assemble long reads with clean graph
[M::main] ===> Step 1: reading read mappings <===
[M::ma_hit_read::21.4311.00] read 21795981 hits; stored 43591962 hits and 741704 sequences (11402327219 bp)
[M::main] ===> Step 2: 1-pass (crude) read selection <===
[M::ma_hit_sub::27.2931.00] 741704 query sequences remain after sub
[M::ma_hit_cut::27.8281.00] 43561270 hits remain after cut
[M::ma_hit_flt::28.4431.00] 43561270 hits remain after filtering; crude coverage after filtering: 28.89
[M::main] ===> Step 3: 2-pass (fine) read selection <===
[M::ma_hit_sub::31.0871.00] 741311 query sequences remain after sub
[M::ma_hit_cut::31.6121.00] 43561266 hits remain after cut
[M::ma_hit_contained::32.522*1.00] 161837 sequences and 570070 hits remain after containment removal
[M::main] ===> Step 4: graph cleaning <===
[M::ma_sg_gen] read 570070 arcs
[M::main] ===> Step 4.1: transitive reduction <===
[M::asg_arc_del_trans] transitively reduced 282712 arcs
[M::asg_arc_del_multi] removed 0 multi-arcs
[M::asg_arc_del_asymm] removed 7602 asymmetric arcs
[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===
[M::asg_cut_tip] cut 92315 tips
[M::asg_pop_bubble] popped 1108 bubbles and trimmed 100 tips
[M::main] ===> Step 4.3: cutting short overlaps (1 rounds in total) <===
[M::asg_arc_del_short] removed 0 short overlaps
[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===
[M::asg_cut_internal] cut 4622 internal sequences
[M::asg_cut_biloop] cut 522 small bi-loops
[M::asg_cut_tip] cut 422 tips
[M::asg_pop_bubble] popped 10 bubbles and trimmed 8 tips
[M::main] ===> Step 4.5: aggressively cutting short overlaps <===
[M::asg_arc_del_multi] removed 0 multi-arcs
[M::asg_arc_del_asymm] removed 1261 asymmetric arcs
[M::asg_arc_del_short] removed 1875 short overlaps
[M::asg_cut_tip] cut 280 tips
[M::asg_pop_bubble] popped 18 bubbles and trimmed 6 tips
[M::main] ===> Step 5: generating unitigs <===
[M::main] Version: 0.3-r179
[M::main] CMD: /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/tools/miniasm/miniasm -d 10000 -n 1 -e 1 -c 1 -f /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//2.overlap/s1_s1.paf
[M::main] Real time: 59.261 sec; CPU: 54.879 sec
2025-01-28 21:07:41,448 - /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/HyLight.py[line:145] - INFO: Start assemble short reads
2025-01-28 21:07:41,449 - /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/HyLight.py[line:147] - INFO: generate overlap between reads and temporary reference
Don't execute the command: minimap2 -N 40 -t 3 -L --eqx -cx ava-pb -Hk19 -m100 -g10000 --max-chain-skip 25 sub67400022 /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa 2> /dev/null | python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py -len 30 -oh 3 > sub67400022_tmp_overlap2.paf
Traceback (most recent call last):
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py", line 110, in
sys.exit(main())
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py", line 41, in main
[qseqid, qlen, qstart, qend, qori, sseqid, slen, sstart, send, matchcount, length] = line.split('\t')[:11]
ValueError: not enough values to unpack (expected 11, got 9)
bash: line 1: 104189 Killed python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_overlap_slr2.py -r /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa -c sub67400000 -t 3 -len 3000 -mc 2 -iden 0.95 -long_reads
sort: cannot read: sub67400000_tmp_overlap4.paf: No such file or directory
Don't execute the command: minimap2 -N 40 -t 3 -L --eqx -cx ava-pb -Hk19 -m100 -g10000 --max-chain-skip 25 sub67400016 /work/frasergen/META/project/p2025/20250103.242496.wxy.metagenome.HiFi_reads/02.assembly_Hybrid/07.HyLight/hylight_out//1.split_fastx/s1.fa 2> /dev/null | python /work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py -len 30 -oh 3 > sub67400016_tmp_overlap2.paf
Traceback (most recent call last):
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py", line 110, in
sys.exit(main())
File "/work/frasergen/META/software/miniconda/miniconda3-py312_24.11.1-0/envs/hylight-1.0.0/lib/python3.6/site-packages/HyLight/script/filter_trans_ovlp_inline_v4.py", line 41, in main
[qseqid, qlen, qstart, qend, qori, sseqid, slen, sstart, send, matchcount, length] = line.split('\t')[:11]
ValueError: not enough values to unpack (expected 11, got 8)