search

zhangrengang / Centromics

Centromics: visualing centromeres with multiple omics data
GNU General Public License v3.0
22 stars 10 forks source link

Searching for centromere（hifi and hic） #1

Open hushaoqiang opened 1 year ago

hushaoqiang commented 1 year ago

Hello, I would like to use hifi and hic data to find the centromere sequence of the genome. However, when using HIC data, a Juice Box interface may appear. Then I imported merged_nodups.hic file, and what should be done afterwards. Looking forward to your reply, thank you.

The command is as follows: centromics -l /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifi.fq.gz -g /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/ref.fa -pre hifihic -hic /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic -outdir hifihic -tmpdir hifihic.tmp -ncpu 10

Running process: (RepCent) hsqhsq /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data $ centromics -l /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifi.fq.gz -g /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_dhic /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic -outdir hifihic -tmpdir hifihic.tmp -ncpu 10 23-04-11 18:56:58 [INFO] Command: /home/hsqhsq/miniconda3/envs/RepCent/bin/centromics -l /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/ex/home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/ref.fa -pre hifihic -hic /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/mhifihic -tmpdir hifihic.tmp -ncpu 10 23-04-11 18:56:58 [INFO] Version: 0.3 23-04-11 18:56:58 [INFO] Arguments: {'genome': '/home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/ref.fa', 'long': ['/home/hsq/hli/example_data/hifi.fq.gz'], 'hic': '/home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic', 'chip': None, 'prefi'hifihic', 'tmpdir': 'hifihic.tmp', 'subsample_x': 5, 'subsample_n': 100000, 'trf_opts': '1 1 2 80 5 200 2000 -d -h', 'min_cov': 0monomer_len': 1, 'clust_opts': '-m jaccard -k 15 -c 0.2 -x 2 -I 2', 'min_ratio': 0.1, 'window_size': 200000, 'chr_prefix': 'chr[\eanup': False, 'overwrite': False} 23-04-11 18:56:58 [INFO] ##Step: Processing long reads data 23-04-11 18:56:59 [INFO] Genome size: 132,081,078 bp 23-04-11 18:56:59 [INFO] Subsample 5x reads from ['/home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifi.fq.gz'] 23-04-11 18:57:02 [INFO] Subsampled 42,150 reads(660,394,773 bases) 23-04-11 18:57:02 [INFO] Run TRF to identify tandem repeats in reads 23-04-11 18:57:16 [INFO] 20 commands in /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf/cmds.list, 0 chsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf/cmds.list.completed 23-04-11 18:57:16 [INFO] continue to run 20 commands 23-04-11 18:57:16 [INFO] VARS: {'tc_tasks': 10, 'mode': 'local', 'grid_opts': '-tc {tc}', 'cpu': 1, 'mem': '1g', 'cont': True, 're'out_path': '/home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf/cmds.list.out', 'completed': '/home/hsq/hli/example_data/hifihic.tmp/hifihic.trf/cmds.list.completed', 'cmd_sep': '\n\n\n', 'kargs': {}} 23-04-11 18:57:16 [INFO] running 20 commands: try 1 23-04-11 18:57:16 [INFO] reset tc_tasks to 10 by [10, 32, 129, 20] 23-04-11 18:57:16 [INFO] Start Pool with 10 process(es) 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.2.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.2.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.1.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.1.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.3.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.3.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.4.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.4.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.5.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.5.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.6.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.6.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.7.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.7.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.8.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.8.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.9.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_zhic.tmp/hifihic.trf/chunks.9.fasta.*.dat 23-04-11 18:57:16 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.10.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.10.fasta.*.dat 23-04-11 19:02:19 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.11.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.11.fasta.*.dat 23-04-11 19:02:28 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.12.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.12.fasta.*.dat 23-04-11 19:02:29 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.13.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.13.fasta.*.dat 23-04-11 19:02:31 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.14.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.14.fasta.*.dat 23-04-11 19:02:35 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.15.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.15.fasta.*.dat 23-04-11 19:02:39 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.16.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.16.fasta.*.dat 23-04-11 19:02:42 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.17.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.17.fasta.*.dat 23-04-11 19:02:44 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.18.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.18.fasta.*.dat 23-04-11 19:02:54 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.19.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.19.fasta.*.dat 23-04-11 19:03:10 [INFO] run CMD: cd /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.trf && trf /home/hsqsili/example_data/hifihic.tmp/hifihic.trf/chunks.20.fasta 1 1 2 80 5 200 2000 -d -h > /dev/null; ls /home/hsq/hhh/hsqhsqhsq/ceshi_ihic.tmp/hifihic.trf/chunks.20.fasta.*.dat 23-04-11 19:09:06 [INFO] finished with 0 commands uncompleted 23-04-11 19:09:07 [INFO] Cluster tandem repeats to identify TR families 23-04-11 19:09:07 [INFO] run CMD: REPclust /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/ hifihic.tmp/hifihic.trf.fa -m jaccard -k 15 -c 0.2 -x 2 -I 2 -pre hifihic. -outdir /home/hsq/hhh /hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.clust -tmpdir /home/hsq/hhh/hsqhsqhsq /ceshi_zhuosili/example_data/hifihic.tmp/hifihic.clust -p 10 23-04-11 19:09:25 [INFO] Filter tandem repeats as putive centromeric 23-04-11 19:09:37 [INFO] Align with genome and count 23-04-11 19:09:37 [INFO] run CMD: makeblastdb -in /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/exampl e_data/hifihic.tmp/hifihic.blast/hifihic..blastqry -dbtype nucl -out /home/hsq/hhh/hsqhsqhsq/ces hi_zhuosili/example_data/hifihic.tmp/hifihic.blast/hifihic..blastqry 23-04-11 19:09:38 [INFO] run CMD: blastn -query /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_ data/ref.fa -db /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.blast/hi fihic..blastqry -out /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.bla st/hifihic..blastqry.blastout -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qen d sstart send evalue bitscore qlen slen sstrand' -num_threads 10 -task blastn-short -word_size 9 -dust no -soft_masking false 23-04-11 19:09:53 [INFO] Parse blast out 23-04-11 19:09:54 [INFO] New check point file: /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_d ata/hifihic.tmp/hifihic.hifihic.trf.count.ok 23-04-11 19:09:54 [INFO] ##Step: Processing Hi-C data 23-04-11 19:09:54 [INFO] 28 commands in /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifi hic.tmp/hifihic.hic.matrix100000.sh, 0 commands in /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/exampl e_data/hifihic.tmp/hifihic.hic.matrix100000.sh.completed 23-04-11 19:09:54 [INFO] VARS: {'tc_tasks': 10, 'mode': 'local', 'grid_opts': '-tc {tc}', 'cpu': 1, 'mem': '1g', 'cont': False, 'retry': 2, 'script': None, 'out_path': '/home/hsq/hhh/hsqhsqhsq /ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix100000.sh.out', 'completed': '/home/h sq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix100000.sh.completed', 'cmd_sep': '\n\n\n', 'kargs': {}} 23-04-11 19:09:54 [INFO] running 28 commands: try 1 23-04-11 19:09:54 [INFO] reset tc_tasks to 10 by [10, 32, 128, 28] 23-04-11 19:09:54 [INFO] Start Pool with 10 process(es) 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr1 Chr1 BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr1-Chr1.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr1 Chr2 BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr1-Chr2.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr1 Chr3 BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr1-Chr3.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr1 Chr4 BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr1-Chr4.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr1 Chr5 BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr1-Chr5.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr1 ChrM BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr1-ChrM.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr1 ChrC BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr1-ChrC.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr2 Chr2 BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr2-Chr2.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr2 Chr3 BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr2-Chr3.100000.mat 23-04-11 19:09:54 [INFO] run CMD: java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/ site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /hom e/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr2 Chr4 BP 100000 /home/hsq/ hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr2-Chr4.100000.mat

zhangrengang commented 1 year ago

Hi. It is strange for a Juice Box interface (I never see a Juice Box interface from juicebox_tools.jar). I think you may fix this issue firstly. Is it related to environment variables such as DISPLAY. You can test with these commands, such as:

java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/merged_nodups.hic Chr2 Chr4 BP 100000 /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/example_data/hifihic.tmp/hifihic.hic.matrix/Chr2-Chr4.100000.mat
hushaoqiang commented 1 year ago

你好，我想着用中文来您交流。这样效率高些。 我刚才运行了命令，还是会出现juicebox的界面。 一般用juicerbox调整congtig的顺序我用过这个，现在也也出现了是什么情况啊。

zhangrengang commented 1 year ago

很奇怪，有窗口界面的那个是juicerbox.jar, 不是这个juicebox_tools.jar

hushaoqiang commented 1 year ago

是不是我安装软件有问题啊，当时我第一次用hic数据跑的时候，说是在文件夹/home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/缺少juicebox_tools.jar这个软件，于是我下载了Juicebox_1.11.08.jar，然后软连接ln -s Juicebox_1.11.08.jar juicebox_tools.jar。 是不是这个操作出现了问题啊。请问juicebox_tools.jar在哪下载啊

zhangrengang commented 1 year ago

我在命令行下运行是这样的：

$ java -jar Centromics/bin/juicebox_tools.jar
Juicebox and Juicer Command Line Tools Usage:
                dump <observed/oe> <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize> [outfile]
dump <norm/expected> <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr> <BP/FRAG> <binsize> [outfile]
dump <loops/domains> <hicFile URL> [outfile]
                pre [options] <infile> <outfile> <genomeID>
                apa <hicFile(s)> <PeaksFile> <SaveFolder>
                arrowhead <hicFile(s)> <output_file>
                hiccups <hicFile> <outputDirectory>
                hiccupsdiff <firstHicFile> <secondHicFile> <firstLoopList> <secondLoopList> <outputDirectory>
                validate <hicFile>
Type juicebox <commandName> for more detailed usage instructions
hushaoqiang commented 1 year ago

请问您juicebox_tools.jar在哪里下载的啊。或者您的这个可以发我一份吗 十分感谢

zhangrengang commented 1 year ago

稍等，我在往上push，github的网比较差

hushaoqiang commented 1 year ago

好

zhangrengang commented 1 year ago

在https://github.com/zhangrengang/Centromics/tree/master/Centromics/bin. 重新clone一次就可以。

hushaoqiang commented 1 year ago

好滴，我在运行一下，现在太晚了。运行完我就回去了，明天我来反馈一下结果

zhangrengang commented 1 year ago

是不是我安装软件有问题啊，当时我第一次用hic数据跑的时候，说是在文件夹/home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/bin/缺少juicebox_tools.jar这个软件，于是我下载了Juicebox_1.11.08.jar，然后软连接ln -s Juicebox_1.11.08.jar juicebox_tools.jar。 是不是这个操作出现了问题啊。请问juicebox_tools.jar在哪下载啊

你应当是下载错了，下成了Juicebox.jar。他官网上还有个juicebox_tools.jar，是命令行工具。

hushaoqiang commented 1 year ago

好滴

hushaoqiang commented 1 year ago

23-04-11 22:34:39 [WARNING] exit code 1 for CMD java -jar /home/hsqhsq/miniconda3/envs/RepCent/lib/python3.8/si te-packages/Centromics-0.3-py3.8.egg/Centromics/bin/juicebox_tools.jar dump observed NONE /home/hsq/hhh/hsqhsqhs q/ceshi_zhuosili/example_data/merged_nodups.hic Chr1 Chr2 BP 100000 /home/hsq/hhh/hsqhsqhsq/ceshi_zhuosili/examp le_data/hifihic.tmp/hifihic.hic.matrix/Chr1-Chr2.100000.mat: 23-04-11 22:34:39 [WARNING]

STDOUT:<< HiC file version: 8

STDERR:<< Exception in thread "main" java.lang.NullPointerException

at juicebox.tools.clt.old.Dump.extractChromosomeRegionIndices(Dump.java:467) at juicebox.tools.clt.old.Dump.readArguments(Dump.java:364) at juicebox.tools.HiCTools.main(HiCTools.java:85)

你好，现在会出现这个问题，我是哪个地方出错了啊

hushaoqiang commented 1 year ago

我把merged_nodups.hic换成merged_nodups.txt好像可以运行了，我先看看结果再跟您反馈

zhangrengang commented 1 year ago

可能hic文件或软件版本有问题。我的hic文件是这么生成的：

java -jar 3d-dna/visualize/juicebox_tools.jar pre -n aligned/merged_nodups.txt merged_nodups.hic ref.fa.chrom.sizes

其中ref.fa.chrom.sizes格式如下（这样hic文件中包含所有染色体）：

chr01   156926036
chr02   151837026
chr03   127138247
chr04   125341739
chr05   112892489
...

juicebox_tools.jar可替换成你3d-dna自带的的3d-dna/visualize/juicebox_tools.jar，保持和生成hic文件的版本一致。

hushaoqiang commented 1 year ago

好滴，十分感谢您的帮助，现在已经跑通了，找到了着丝粒序列。哈哈

Jiangjiangzhang6 commented 1 year ago

朋友们，我的软件咋一直装不上，显示REPcluster这个module装不上，通过pip也不行

Jiangjiangzhang6 commented 1 year ago

image 各位朋友，我也Google不到这个module，一定是哪里出现了问题

hushaoqiang commented 1 year ago

image 各位朋友，我也Google不到这个module，一定是哪里出现了问题

这是我的安装过程 conda install git git clone --recurse-submodules https://github.com/zhangrengang/Centromics ###看看REPcluster文件夹有没有东西 cd Centromics conda env create -f Centromics.yaml conda activate RepCent ./install.sh Centromics -h

Jiangjiangzhang6 commented 1 year ago

我是下载下来，然后进入文件夹中 conda env create -f Centromics.yaml conda activate RepCent ./install.sh 按照这个安装，也显示安装成了 image ran'ho然后发现就是报错

hushaoqiang commented 1 year ago

我是下载下来，然后进入文件夹中 conda env create -f Centromics.yaml conda activate RepCent ./install.sh 按照这个安装，也显示安装成了 image ran'ho然后发现就是报错

你先把之前安装的文件夹还有conda环境删除，按照我这个试试。我前几次安装也有一些报错，报错的内容不记得了。这个是我最后安装成功的方法.

Jiangjiangzhang6 commented 1 year ago

image 各位朋友，我也Google不到这个module，一定是哪里出现了问题

这是我的安装过程 conda install git git clone --recurse-submodules https://github.com/zhangrengang/Centromics ###看看REPcluster文件夹有没有东西 cd Centromics conda env create -f Centromics.yaml conda activate RepCent ./install.sh Centromics -h

我现在是直接这个报错 image 没有这个REP这个东西

hushaoqiang commented 1 year ago

image 各位朋友，我也Google不到这个module，一定是哪里出现了问题

这是我的安装过程 conda install git git clone --recurse-submodules https://github.com/zhangrengang/Centromics ###看看REPcluster文件夹有没有东西 cd Centromics conda env create -f Centromics.yaml conda activate RepCent ./install.sh Centromics -h

我现在是直接这个报错 image 没有这个REP这个东西

那应该是就是这个有问题。你在github里下载到本地在移动到REPcluster文件夹试试。我一开始下载的时候这个文件夹里也没东西，到了第二天下载的时候，这个文件夹里又有这个文件了。这点我没搞懂。然后就安装成功了

Jiangjiangzhang6 commented 1 year ago

cd Centromics conda env create -f Centromics.yaml conda activate RepCent ./install.sh

OK ,装好了

Jiangjiangzhang6 commented 1 year ago

image 这个hic文件是那个是split文件下的哪个还是aligned下main的那个merge.nohup.txt

hushaoqiang commented 1 year ago

image 这个hic文件是那个是split文件下的哪个还是aligned下main的那个merge.nohup.txt

aligned文件夹

Jiangjiangzhang6 commented 1 year ago

现在是java 内存给的不够，找不到这个选项去设置

hushaoqiang commented 1 year ago

现在是java 内存给的不够，找不到这个选项去设置

这个我就不清楚了，我觉得java有参数可以设置给内存的大小，不过我自己没运行过，不是很了解