zhangrengang
OSError: [Errno 12] Cannot allocate memory
(SubPhaser) eck@DESKTOP-ED16O0T:~/SubPhaser$ subphaser -i genome.fasta.gz -c sg.config
24-08-11 22:55:26 [WARNING] Grid computing is not available because DRMAA not installed: No module named 'drmaa'
24-08-11 22:55:26 [INFO] No DRMAA (see https://github.com/pygridtools/drmaa-python), Switching to local mode.
24-08-11 22:55:28 [WARNING] Grid computing is not available because DRMAA not installed: No module named 'drmaa'
24-08-11 22:55:28 [INFO] No DRMAA (see https://github.com/pygridtools/drmaa-python), Switching to local mode.
24-08-11 22:55:28 [INFO] Command: /home/eck/miniconda3/envs/SubPhaser/bin/subphaser -i genome.fasta.gz -c sg.config
24-08-11 22:55:28 [INFO] Version: 1.2.6
24-08-11 22:55:28 [INFO] Arguments: {'genomes': ['genome.fasta.gz'], 'sg_cfgs': ['sg.config'], 'labels': None, 'no_label': False, 'target': None, 'sg_assigned': None, 'sep': '|', 'custom_features': None, 'prefix': None, 'outdir': 'phase-results', 'tmpdir': 'tmp', 'colors': ['#f9c00c', '#00b9f1', '#7200da', '#f9320c', '#00b8a9', '#F4A460', '#009999', '#00C02E', '#980000', '#00ffff', '#0000ff', '#ff0000', '#4a86e8', '#ff9900', '#ffff00', '#00ff00', '#9900ff', '#ff00ff', '#20124d', '#274e13', '#000000', '#cccccc', '#7f6000', '#a64d79', '#6aa84f', '#fff2cc', '#47a952', '#3ea6b6', '#a5b805', '#8f9276', '#ca8d7c'], 'k': 15, 'min_fold': 2, 'min_freq': 200, 'baseline': 1, 'ratio': 1, 'lower_count': 3, 'min_prop': None, 'max_freq': 1000000000.0, 'max_prop': None, 'low_mem': None, 'by_count': False, 're_filter': False, 'nsg': None, 'replicates': 1000, 'jackknife': 50, 'max_pval': 0.05, 'test_method': 'ttest_ind', 'figfmt': 'pdf', 'heatmap_colors': ('green', 'black', 'red'), 'heatmap_options': "Rowv=T,Colv=T,scale='col',dendrogram='row',labCol=F,trace='none',key=T,key.title=NA,density.info='density',main=NA,xlab='Differential kmers',margins=c(2.5,12)", 'just_core': False, 'disable_ltr': False, 'ltr_detectors': ['ltr_harvest'], 'ltr_finder_options': '-w 2 -D 15000 -d 1000 -L 7000 -l 100 -p 20 -C -M 0.8', 'ltr_harvest_options': '-seqids yes -similar 80 -vic 10 -seed 20 -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6', 'tesorter_options': '-db rexdb -dp2', 'all_ltr': False, 'intact_ltr': False, 'exclude_exchanges': False, 'non_specific': False, 'mu': 1.3e-08, 'disable_ltrtree': False, 'subsample': 1000, 'ltr_domains': ['INT', 'RT', 'RH'], 'trimal_options': '-automated1', 'tree_method': 'FastTree', 'tree_options': '', 'ggtree_options': "branch.length='none', layout='circular'", 'disable_circos': False, 'window_size': 1000000, 'disable_blocks': False, 'aligner': 'minimap2', 'aligner_options': '-x asm20 -n 10', 'min_block': 100000, 'alt_cfgs': None, 'chr_ordered': None, 'ncpu': 4, 'max_memory': '11.5G', 'cleanup': False, 'overwrite': False}
24-08-11 22:55:28 [INFO] Target chromosomes: ['chr01a', 'chr01b', 'chr01c', 'chr01d', 'chr02a', 'chr02b', 'chr02c', 'chr02d', 'chr03a', 'chr03b', 'chr03c', 'chr03d', 'chr04a', 'chr04b', 'chr04c', 'chr04d', 'chr05a', 'chr05b', 'chr05c', 'chr05d', 'chr06a', 'chr06b', 'chr06c', 'chr06d', 'chr07a', 'chr07b', 'chr07c', 'chr07d']
24-08-11 22:55:28 [INFO] Splitting genomes by chromosome into /home/eck/SubPhaser/tmp/
24-08-11 22:55:28 [INFO] Check point file: /home/eck/SubPhaser/tmp/split.ok exists; skip this step
24-08-11 22:55:29 [INFO] Chromosomes: ['chr01a', 'chr01b', 'chr01c', 'chr01d', 'chr02a', 'chr02b', 'chr02c', 'chr02d', 'chr03a', 'chr03b', 'chr03c', 'chr03d', 'chr04a', 'chr04b', 'chr04c', 'chr04d', 'chr05a', 'chr05b', 'chr05c', 'chr05d', 'chr06a', 'chr06b', 'chr06c', 'chr06d', 'chr07a', 'chr07b', 'chr07c', 'chr07d']
24-08-11 22:55:29 [INFO] Chromosome Number: 28
24-08-11 22:55:29 [INFO] CONFIG: [[['chr01a'], ['chr01b'], ['chr01c'], ['chr01d']], [['chr02a'], ['chr02b'], ['chr02c'], ['chr02d']], [['chr03a'], ['chr03b'], ['chr03c'], ['chr03d']], [['chr04a'], ['chr04b'], ['chr04c'], ['chr04d']], [['chr05a'], ['chr05b'], ['chr05c'], ['chr05d']], [['chr06a'], ['chr06b'], ['chr06c'], ['chr06d']], [['chr07a'], ['chr07b'], ['chr07c'], ['chr07d']]]
24-08-11 22:55:29 [INFO] Genome size: 1,892,584,152 bp
24-08-11 22:55:29 [INFO] ###Step: Kmer Count
24-08-11 22:55:29 [INFO] Counting kmer by jellyfish
24-08-11 22:55:29 [INFO] Start Pool with 4 process(es)
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr01a.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr01c.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr02a.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr02c.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr01b.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr01d.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr02b.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr02d.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr03a.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr03c.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr04a.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr04c.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr03b.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr03d.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr04b.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr04d.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr05a.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr05c.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr06a.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr06c.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr05b.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr05d.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr06b.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr06d.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr07a.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr07c.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr07b.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr07d.fasta_15.fa.ok exists; skip this step
24-08-11 22:55:29 [INFO] Loading kmer matrix from jellyfish
24-08-11 22:55:29 [INFO] Start Pool with 4 process(es)
24-08-12 00:29:31 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr01a.fasta_15.fa
24-08-12 00:30:23 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr01b.fasta_15.fa
24-08-12 00:31:03 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr01c.fasta_15.fa
24-08-12 00:31:15 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr01d.fasta_15.fa
24-08-12 00:32:18 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr02a.fasta_15.fa
24-08-12 00:34:03 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr02b.fasta_15.fa
24-08-12 00:34:12 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr02c.fasta_15.fa
24-08-12 00:35:55 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr02d.fasta_15.fa
24-08-12 00:36:03 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr03a.fasta_15.fa
24-08-12 00:36:07 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr03b.fasta_15.fa
24-08-12 00:36:11 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr03c.fasta_15.fa
24-08-12 00:38:07 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr03d.fasta_15.fa
24-08-12 00:38:10 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr04a.fasta_15.fa
24-08-12 00:38:14 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr04b.fasta_15.fa
24-08-12 00:38:17 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr04c.fasta_15.fa
24-08-12 00:38:20 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr04d.fasta_15.fa
24-08-12 00:38:23 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr05a.fasta_15.fa
24-08-12 00:38:27 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr05b.fasta_15.fa
24-08-12 00:38:43 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr05c.fasta_15.fa
24-08-12 00:38:46 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr05d.fasta_15.fa
24-08-12 00:42:05 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr06a.fasta_15.fa
24-08-12 00:42:17 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr06b.fasta_15.fa
24-08-12 00:42:34 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr06c.fasta_15.fa
24-08-12 00:42:48 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr06d.fasta_15.fa
24-08-12 00:43:12 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr07a.fasta_15.fa
24-08-12 00:43:41 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr07b.fasta_15.fa
24-08-12 00:44:07 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr07c.fasta_15.fa
24-08-12 00:44:49 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr07d.fasta_15.fa
24-08-12 00:46:21 [INFO] 28129798 kmers in total
24-08-12 00:46:21 [INFO] Filtering differential kmers
Traceback (most recent call last):
File "/home/eck/miniconda3/envs/SubPhaser/bin/subphaser", line 33, in
You can try -q 200 -lower_count 10 to reduce the kmer number.
2024-08-12 05:57:24"jenny315" @.***>写道：
(SubPhaser) @.:/SubPhaser$ subphaser -i genome.fasta.gz -c sg.config 24-08-11 22:55:26 [WARNING] Grid computing is not available because DRMAA not installed: No module named 'drmaa' 24-08-11 22:55:26 [INFO] No DRMAA (see https://github.com/pygridtools/drmaa-python), Switching to local mode. 24-08-11 22:55:28 [WARNING] Grid computing is not available because DRMAA not installed: No module named 'drmaa' 24-08-11 22:55:28 [INFO] No DRMAA (see https://github.com/pygridtools/drmaa-python), Switching to local mode. 24-08-11 22:55:28 [INFO] Command: /home/eck/miniconda3/envs/SubPhaser/bin/subphaser -i genome.fasta.gz -c sg.config 24-08-11 22:55:28 [INFO] Version: 1.2.6 24-08-11 22:55:28 [INFO] Arguments: {'genomes': ['genome.fasta.gz'], 'sg_cfgs': ['sg.config'], 'labels': None, 'no_label': False, 'target': None, 'sg_assigned': None, 'sep': '|', 'custom_features': None, 'prefix': None, 'outdir': 'phase-results', 'tmpdir': 'tmp', 'colors': ['#f9c00c', '#00b9f1', '#7200da', '#f9320c', '#00b8a9', '#F4A460', '#009999', '#00C02E', '#980000', '#00ffff', '#0000ff', '#ff0000', '#4a86e8', '#ff9900', '#ffff00', '#00ff00', '#9900ff', '#ff00ff', '#20124d', '#274e13', '#000000', '#cccccc', '#7f6000', '#a64d79', '#6aa84f', '#fff2cc', '#47a952', '#3ea6b6', '#a5b805', '#8f9276', '#ca8d7c'], 'k': 15, 'min_fold': 2, 'min_freq': 200, 'baseline': 1, 'ratio': 1, 'lower_count': 3, 'min_prop': None, 'max_freq': 1000000000.0, 'max_prop': None, 'low_mem': None, 'by_count': False, 're_filter': False, 'nsg': None, 'replicates': 1000, 'jackknife': 50, 'max_pval': 0.05, 'test_method': 'ttest_ind', 'figfmt': 'pdf', 'heatmap_colors': ('green', 'black', 'red'), 'heatmap_options': "Rowv=T,Colv=T,scale='col',dendrogram='row',labCol=F,trace='none',key=T,key.title=NA,density.info='density',main=NA,xlab='Differential kmers',margins=c(2.5,12)", 'just_core': False, 'disable_ltr': False, 'ltr_detectors': ['ltr_harvest'], 'ltr_finder_options': '-w 2 -D 15000 -d 1000 -L 7000 -l 100 -p 20 -C -M 0.8', 'ltr_harvest_options': '-seqids yes -similar 80 -vic 10 -seed 20 -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6', 'tesorter_options': '-db rexdb -dp2', 'all_ltr': False, 'intact_ltr': False, 'exclude_exchanges': False, 'non_specific': False, 'mu': 1.3e-08, 'disable_ltrtree': False, 'subsample': 1000, 'ltr_domains': ['INT', 'RT', 'RH'], 'trimal_options': '-automated1', 'tree_method': 'FastTree', 'tree_options': '', 'ggtree_options': "branch.length='none', layout='circular'", 'disable_circos': False, 'window_size': 1000000, 'disable_blocks': False, 'aligner': 'minimap2', 'aligner_options': '-x asm20 -n 10', 'min_block': 100000, 'alt_cfgs': None, 'chr_ordered': None, 'ncpu': 4, 'max_memory': '11.5G', 'cleanup': False, 'overwrite': False} 24-08-11 22:55:28 [INFO] Target chromosomes: ['chr01a', 'chr01b', 'chr01c', 'chr01d', 'chr02a', 'chr02b', 'chr02c', 'chr02d', 'chr03a', 'chr03b', 'chr03c', 'chr03d', 'chr04a', 'chr04b', 'chr04c', 'chr04d', 'chr05a', 'chr05b', 'chr05c', 'chr05d', 'chr06a', 'chr06b', 'chr06c', 'chr06d', 'chr07a', 'chr07b', 'chr07c', 'chr07d'] 24-08-11 22:55:28 [INFO] Splitting genomes by chromosome into /home/eck/SubPhaser/tmp/ 24-08-11 22:55:28 [INFO] Check point file: /home/eck/SubPhaser/tmp/split.ok exists; skip this step 24-08-11 22:55:29 [INFO] Chromosomes: ['chr01a', 'chr01b', 'chr01c', 'chr01d', 'chr02a', 'chr02b', 'chr02c', 'chr02d', 'chr03a', 'chr03b', 'chr03c', 'chr03d', 'chr04a', 'chr04b', 'chr04c', 'chr04d', 'chr05a', 'chr05b', 'chr05c', 'chr05d', 'chr06a', 'chr06b', 'chr06c', 'chr06d', 'chr07a', 'chr07b', 'chr07c', 'chr07d'] 24-08-11 22:55:29 [INFO] Chromosome Number: 28 24-08-11 22:55:29 [INFO] CONFIG: [[['chr01a'], ['chr01b'], ['chr01c'], ['chr01d']], [['chr02a'], ['chr02b'], ['chr02c'], ['chr02d']], [['chr03a'], ['chr03b'], ['chr03c'], ['chr03d']], [['chr04a'], ['chr04b'], ['chr04c'], ['chr04d']], [['chr05a'], ['chr05b'], ['chr05c'], ['chr05d']], [['chr06a'], ['chr06b'], ['chr06c'], ['chr06d']], [['chr07a'], ['chr07b'], ['chr07c'], ['chr07d']]] 24-08-11 22:55:29 [INFO] Genome size: 1,892,584,152 bp 24-08-11 22:55:29 [INFO] ###Step: Kmer Count 24-08-11 22:55:29 [INFO] Counting kmer by jellyfish 24-08-11 22:55:29 [INFO] Start Pool with 4 process(es) 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr01a.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr01c.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr02a.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr02c.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr01b.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr01d.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr02b.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr02d.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr03a.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr03c.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr04a.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr04c.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr03b.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr03d.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr04b.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr04d.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr05a.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr05c.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr06a.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr06c.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr05b.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr05d.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr06b.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr06d.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr07a.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr07c.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr07b.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Check point file: /home/eck/SubPhaser/tmp/chromosomes/chr07d.fasta_15.fa.ok exists; skip this step 24-08-11 22:55:29 [INFO] Loading kmer matrix from jellyfish 24-08-11 22:55:29 [INFO] Start Pool with 4 process(es) 24-08-12 00:29:31 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr01a.fasta_15.fa 24-08-12 00:30:23 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr01b.fasta_15.fa 24-08-12 00:31:03 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr01c.fasta_15.fa 24-08-12 00:31:15 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr01d.fasta_15.fa 24-08-12 00:32:18 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr02a.fasta_15.fa 24-08-12 00:34:03 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr02b.fasta_15.fa 24-08-12 00:34:12 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr02c.fasta_15.fa 24-08-12 00:35:55 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr02d.fasta_15.fa 24-08-12 00:36:03 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr03a.fasta_15.fa 24-08-12 00:36:07 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr03b.fasta_15.fa 24-08-12 00:36:11 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr03c.fasta_15.fa 24-08-12 00:38:07 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr03d.fasta_15.fa 24-08-12 00:38:10 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr04a.fasta_15.fa 24-08-12 00:38:14 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr04b.fasta_15.fa 24-08-12 00:38:17 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr04c.fasta_15.fa 24-08-12 00:38:20 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr04d.fasta_15.fa 24-08-12 00:38:23 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr05a.fasta_15.fa 24-08-12 00:38:27 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr05b.fasta_15.fa 24-08-12 00:38:43 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr05c.fasta_15.fa 24-08-12 00:38:46 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr05d.fasta_15.fa 24-08-12 00:42:05 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr06a.fasta_15.fa 24-08-12 00:42:17 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr06b.fasta_15.fa 24-08-12 00:42:34 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr06c.fasta_15.fa 24-08-12 00:42:48 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr06d.fasta_15.fa 24-08-12 00:43:12 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr07a.fasta_15.fa 24-08-12 00:43:41 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr07b.fasta_15.fa 24-08-12 00:44:07 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr07c.fasta_15.fa 24-08-12 00:44:49 [INFO] Loading /home/eck/SubPhaser/tmp/chromosomes/chr07d.fasta_15.fa 24-08-12 00:46:21 [INFO] 28129798 kmers in total 24-08-12 00:46:21 [INFO] Filtering differential kmers Traceback (most recent call last): File "/home/eck/miniconda3/envs/SubPhaser/bin/subphaser", line 33, in sys.exit(load_entry_point('subphaser==1.2.6', 'console_scripts', 'subphaser')()) File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/main.py", line 797, in main pipeline.run() File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/main.py", line 422, in run d_mat = dumps.filter(d_mat, lengths, self.sgs, outfig=histfig, #d_targets=d_targets, File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/Jellyfish.py", line 491, in filter for kmer, freqs, tot_freq in pool_func(_filter_kmer, args, self.ncpu, File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.6-py3.8.egg/subphaser/RunCmdsMP.py", line 336, in pool_func pool = multiprocessing.Pool(processors) File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/context.py", line 119, in Pool return Pool(processes, initializer, initargs, maxtasksperchild, File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/pool.py", line 212, in init self._repopulate_pool() File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/pool.py", line 303, in _repopulate_pool return self._repopulate_pool_static(self._ctx, self.Process, File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/pool.py", line 326, in _repopulate_pool_static w.start() File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/process.py", line 121, in start self._popen = self._Popen(self) File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/popen_fork.py", line 19, in init self._launch(process_obj) File "/home/eck/miniconda3/envs/SubPhaser/lib/python3.8/multiprocessing/popen_fork.py", line 70, in _launch self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory (SubPhaser) @.:/SubPhaser$
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
Unfortunately, the same error was raised. Do you know any alternative way?
If the genome is so huge, you can cut a segment from each chromosome to respresent the chromosome.
2024-08-12 15:39:11"jenny315" @.***>写道：
Unfortunately, the same error was raised. Do you know any alternative way?
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>
@emircankaaya I have the same problem how have you solved the problem ?
You can try -q 200 -lower_count 10 to reduce the kmer number.
I tried this command line which iş suggested by Dr. Zhang if you have still some error let me know and we can try another way.
16 Ağu 2024 Cum 13:33 tarihinde Lucas Munnes @.***> şunu yazdı:
@emircankaaya https://github.com/emircankaaya I have the same problem how have you solved the problem ?
— Reply to this email directly, view it on GitHub https://github.com/zhangrengang/SubPhaser/issues/38#issuecomment-2293261931, or unsubscribe https://github.com/notifications/unsubscribe-auth/BJVTSW6MO5OYJZSZIJQ3O7TZRXIP3AVCNFSM6AAAAABMLC2UHWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJTGI3DCOJTGE . You are receiving this because you were mentioned.Message ID: @.***>
You may check your swap and memory information with "free -h"
Then you would increase the values.
"
sudo fallocate -l ...G /swapfile -----------------you would write your free swap to "..." in the command line. E.g. "sudo fallocate -l 32G /swapfile" sudo chmod 600 /swapfile sudo mkswap /swapfile sudo swapon /swapfile
Emir Can Kaya @.***>, 16 Ağu 2024 Cum, 13:43 tarihinde şunu yazdı:
You can try
-q 200 -lower_count 10to reduce the kmer number.I tried this command line which iş suggested by Dr. Zhang if you have still some error let me know and we can try another way.
16 Ağu 2024 Cum 13:33 tarihinde Lucas Munnes @.***> şunu yazdı:
@emircankaaya https://github.com/emircankaaya I have the same problem how have you solved the problem ?
— Reply to this email directly, view it on GitHub https://github.com/zhangrengang/SubPhaser/issues/38#issuecomment-2293261931, or unsubscribe https://github.com/notifications/unsubscribe-auth/BJVTSW6MO5OYJZSZIJQ3O7TZRXIP3AVCNFSM6AAAAABMLC2UHWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJTGI3DCOJTGE . You are receiving this because you were mentioned.Message ID: @.***>