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zengxiaofei / HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
https://www.nature.com/articles/s41477-024-01755-3
BSD 3-Clause "New" or "Revised" License
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The command "haphic pipeline asm.fa HiC.filtered.bam 11" encountered an error: "<Signals.SIGSEGV: 11>". #57

Closed S-iff closed 2 months ago

S-iff commented 2 months ago

I ran the command: /share/org/HapHiC/haphic pipeline MM.p_ctg.fa MMHiC.filtered.bam 11 with the species karyotype of 2N=2X=22. The method used for genome assembly is "hifiasm + Hi-C". The N10-N90 values are as follows:

scaffold statistics

Nx Number Length N10 1 70351424 N20 2 38104393 N30 3 36331428 N40 4 36272373 N50 5 35837822 N60 7 29728330 N70 8 22796425 N80 10 17587200 N90 167 70139 longest scaffold: 70351424, shortest scaffold: 19888 total number: 1154, total length: 426116389 However, I encountered the following error log:

Line 6: /share/org/pth/HapHiC/haphic check
Line 9: /share/org/pth/HapHiC/haphic pipeline MM.p_ctg.fa MMHiC.filtered.bam 11
2024-08-29 20:14:51 <HapHiC_pipeline.py> [main] Pipeline started, HapHiC version: 1.0.5 (update: 2024.08.08)
2024-08-29 20:14:51 <HapHiC_pipeline.py> [main] Python version: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
2024-08-29 20:14:51 <HapHiC_pipeline.py> [main] Command: /share/org/pth/HapHiC/scripts/HapHiC_pipeline.py MM.p_ctg.fa MMHiC.filtered.bam 11
2024-08-29 20:14:51 <HapHiC_pipeline.py> [haphic_cluster] Step1: Execute preprocessing and Markov clustering for contigs...
2024-08-29 20:15:01 <HapHiC_cluster.py> [run] Program started, HapHiC version: 1.0.5 (update: 2024.08.08)
2024-08-29 20:15:01 <HapHiC_cluster.py> [run] Python version: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
2024-08-29 20:15:01 <HapHiC_cluster.py> [run] Command: /share/org/pth/HapHiC/scripts/HapHiC_pipeline.py MM.p_ctg.fa MMHiC.filtered.bam 11
2024-08-29 20:15:01 <HapHiC_cluster.py> [detect_format] The file for Hi-C read alignments is detected as being in BAM format
2024-08-29 20:15:01 <HapHiC_cluster.py> [parse_fasta] Parsing input FASTA file...
2024-08-29 20:15:03 <HapHiC_cluster.py> [stat_fragments] Making some statistics of fragments (contigs / bins)
2024-08-29 20:15:03 <HapHiC_cluster.py> [stat_fragments] bin_size is calculated to be 1291261 bp
2024-08-29 20:15:04 <HapHiC_cluster.py> [parse_alignments] Parsing input alignments...
2024-08-29 20:17:47 <HapHiC_cluster.py> [output_pickle] Writing HT_link_dict to HT_links.pkl...
2024-08-29 20:17:47 <HapHiC_cluster.py> [output_clm] Writing clm_dict to paired_links.clm...
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] Filtering fragments...
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] [Nx filtering] 265 fragments kept
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] [RE sites filtering] 0 fragments removed, 265 fragments kept
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] [link density filtering] Parameter --density_lower 0.2X is set to "multiple" mode and equivalent to 0.0 in "fraction" mode
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] [link density filtering] Parameter --density_upper 1.9X is set to "multiple" mode and equivalent to 1.0 in "fraction" mode
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] [link density filtering] 0 fragments removed, 265 fragments kept
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] [rank sum filtering] Q1=246.0, median=280.0, Q3=346.0, IQR=Q3-Q1=100.0
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] [rank sum filtering] Parameter --rank_sum_upper 1.5X is set to "multiple" mode and equivalent to 0.9056603773584906 in "fraction" mode
2024-08-29 20:18:16 <HapHiC_cluster.py> [filter_fragments] [rank sum filtering] 25 fragments removed, 240 fragments kept
2024-08-29 20:18:16 <HapHiC_cluster.py> [output_pickle] Writing full_link_dict to full_links.pkl...
2024-08-29 20:18:16 <HapHiC_cluster.py> [run] Hi-C linking matrix was constructed in 194.95615482330322s
2024-08-29 20:18:16 <HapHiC_cluster.py> [run_mcl_clustering] Performing Markov clustering...
2024-08-29 20:18:17 <HapHiC_cluster.py> [mcl] The matrix has converged after 66 rounds of iterations (expansion: 2, inflation: 1.1, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:20 <HapHiC_cluster.py> [mcl] The matrix has converged after 33 rounds of iterations (expansion: 2, inflation: 1.2, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:34 <HapHiC_cluster.py> [mcl] The matrix has converged after 22 rounds of iterations (expansion: 2, inflation: 1.3, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:38 <HapHiC_cluster.py> [mcl] The matrix has converged after 17 rounds of iterations (expansion: 2, inflation: 1.4, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:40 <HapHiC_cluster.py> [mcl] The matrix has converged after 23 rounds of iterations (expansion: 2, inflation: 1.5, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:40 <HapHiC_cluster.py> [mcl] The matrix has converged after 18 rounds of iterations (expansion: 2, inflation: 1.6, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:41 <HapHiC_cluster.py> [mcl] The matrix has converged after 16 rounds of iterations (expansion: 2, inflation: 1.7, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:41 <HapHiC_cluster.py> [mcl] The matrix has converged after 15 rounds of iterations (expansion: 2, inflation: 1.8, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:41 <HapHiC_cluster.py> [mcl] The matrix has converged after 15 rounds of iterations (expansion: 2, inflation: 1.9, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 18 rounds of iterations (expansion: 2, inflation: 2.0, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 19 rounds of iterations (expansion: 2, inflation: 2.1, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 22 rounds of iterations (expansion: 2, inflation: 2.2, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 15 rounds of iterations (expansion: 2, inflation: 2.3, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 12 rounds of iterations (expansion: 2, inflation: 2.4, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 13 rounds of iterations (expansion: 2, inflation: 2.5, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 11 rounds of iterations (expansion: 2, inflation: 2.6, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 10 rounds of iterations (expansion: 2, inflation: 2.7, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 11 rounds of iterations (expansion: 2, inflation: 2.8, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 13 rounds of iterations (expansion: 2, inflation: 2.9, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [mcl] The matrix has converged after 10 rounds of iterations (expansion: 2, inflation: 3.0, maximum iterations: 200, pruning threshold: 0.0001)
2024-08-29 20:18:42 <HapHiC_cluster.py> [recommend_inflation] The length ratio (0.75) might be too strict, trying a lower one...
2024-08-29 20:18:42 <HapHiC_cluster.py> [recommend_inflation] The length ratio (0.7) might be too strict, trying a lower one...
2024-08-29 20:18:42 <HapHiC_cluster.py> [recommend_inflation] The length ratio (0.65) might be too strict, trying a lower one...
2024-08-29 20:18:42 <HapHiC_cluster.py> [recommend_inflation] The length ratio (0.6) might be too strict, trying a lower one...
2024-08-29 20:18:42 <HapHiC_cluster.py> [recommend_inflation] The length ratio (0.55) might be too strict, trying a lower one...
2024-08-29 20:18:42 <HapHiC_cluster.py> [recommend_inflation] You could try inflation from 2.0 (length ratio = 0.5)
2024-08-29 20:18:42 <HapHiC_cluster.py> [run] 20 round(s) of Markov clustering finished in 25.706380128860474s, average 1.2853190064430238s per round
2024-08-29 20:18:42 <HapHiC_cluster.py> [output_statistics] Making some statistics for the next HapHiC reassignment step...
2024-08-29 20:18:55 <HapHiC_cluster.py> [run] Program finished in 233.30833339691162s
2024-08-29 20:18:55 <HapHiC_pipeline.py> [haphic_reassign] Step2: Reassign and rescue contigs...
2024-08-29 20:19:07 <HapHiC_reassign.py> [run] Program started, HapHiC version: 1.0.5 (update: 2024.08.08)
2024-08-29 20:19:07 <HapHiC_reassign.py> [run] Python version: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
2024-08-29 20:19:07 <HapHiC_reassign.py> [run] Command: /share/org/pth/HapHiC/scripts/HapHiC_pipeline.py MM.p_ctg.fa MMHiC.filtered.bam 11
2024-08-29 20:19:07 <HapHiC_cluster.py> [parse_fasta] Parsing input FASTA file...
2024-08-29 20:19:08 <HapHiC_reassign.py> [parse_pickle] Parsing input pickle file...
2024-08-29 20:19:08 <HapHiC_reassign.py> [parse_clusters] Parsing .clusters.txt file...
2024-08-29 20:19:08 <HapHiC_reassign.py> [run] File parsing and data preparation finished in 1.5187973976135254s
2024-08-29 20:19:08 <HapHiC_reassign.py> [run_reassignment] Performing reassignment...
2024-08-29 20:19:08 <HapHiC_reassign.py> [run_reassignment] [result::round1] Total: 1154, consistent: 5, rescued: 8, reassigned: 0, not rescued: 1141
2024-08-29 20:19:08 <HapHiC_reassign.py> [run_reassignment] Performing reassignment...
2024-08-29 20:19:08 <HapHiC_reassign.py> [run_reassignment] [result::round2] Total: 1154, consistent: 13, rescued: 0, reassigned: 0, not rescued: 1141
2024-08-29 20:19:08 <HapHiC_reassign.py> [run] [result::round2] Result has converged after 1 rounds of reassignment, break
2024-08-29 20:19:08 <HapHiC_reassign.py> [run_reassignment] Performing additional round of rescue...
2024-08-29 20:19:08 <HapHiC_reassign.py> [run_reassignment] [result::additional_rescue] Total: 1154, consistent: 21, rescued: 4, reassigned: 0, not rescued: 1129
2024-08-29 20:19:08 <HapHiC_reassign.py> [run] 2 round(s) of reassignment finished in 0.07977032661437988s, average 0.03988516330718994s per round
2024-08-29 20:19:08 <HapHiC_reassign.py> [run] Parameter --nclusters (11) is equal to the number of clusters (11) after reassignment, skip Agglomerative Hierarchical Clustering
2024-08-29 20:19:08 <HapHiC_reassign.py> [split_clm_file] Splitting clm file into subfiles by group...
2024-08-29 20:19:16 <HapHiC_reassign.py> [run] Program finished in 9.750131845474243s
2024-08-29 20:19:16 <HapHiC_pipeline.py> [haphic_sort] Step3: Order and orient contigs within each group...
2024-08-29 20:19:17 <HapHiC_sort.py> [run] Program started, HapHiC version: 1.0.5 (update: 2024.08.08)
2024-08-29 20:19:17 <HapHiC_sort.py> [run] Python version: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
2024-08-29 20:19:17 <HapHiC_sort.py> [run] Command: /share/org/pth/HapHiC/scripts/HapHiC_sort.py /share/org/pth/HiFi/MM.p_ctg.fa /share/org/pth/HiFi/01.cluster/HT_links.pkl /share/org/pth/HiFi/02.reassign/split_clms /share/org/pth/HiFi/02.reassign/final_groups/group5_35837822bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group1_70654378bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group6_32394756bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group8_27911542bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group4_36272373bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group2_38133982bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group9_27568272bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group11_14714105bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group3_37032754bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group7_29728330bp.txt /share/org/pth/HiFi/02.reassign/final_groups/group10_17846258bp.txt --flanking_region 0 --density_cal_method multiplication --confidence_cutoff 1 --mutprob 0.2 --ngen 5000 --npop 100 --seed 42 --processes 8
2024-08-29 20:19:17 <HapHiC_sort.py> [run] Checking the path of ALLHiC...
2024-08-29 20:19:17 <HapHiC_sort.py> [run] ALLHiC has been found in /share/org/pth/HapHiC/scripts
2024-08-29 20:19:17 <HapHiC_sort.py> [parse_fasta] Parsing fasta file...
2024-08-29 20:19:17 <HapHiC_sort.py> [run] Loading input pickle file...
2024-08-29 20:19:17 <HapHiC_sort.py> [run] Parsing group files and clm files...
2024-08-29 20:19:17 <HapHiC_sort.py> [run] Program will be executed in multiprocessing mode (processes=8)
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group5_35837822bp] Performing fast sorting...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group5_35837822bp] Checking the content of input group file...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group5_35837822bp] Only 1 contig in the group file, neither ordering nor orientation is required
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group1_70654378bp] Performing fast sorting...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group1_70654378bp] Checking the content of input group file...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group1_70654378bp] Starting fast sorting iterations...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group6_32394756bp] Performing fast sorting...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group6_32394756bp] Checking the content of input group file...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group6_32394756bp] Only 1 contig in the group file, neither ordering nor orientation is required
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group8_27911542bp] Performing fast sorting...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group8_27911542bp] Checking the content of input group file...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group8_27911542bp] Starting fast sorting iterations...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group4_36272373bp] Performing fast sorting...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group4_36272373bp] Checking the content of input group file...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group2_38133982bp] Performing fast sorting...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group4_36272373bp] Only 1 contig in the group file, neither ordering nor orientation is required
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group2_38133982bp] Checking the content of input group file...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group9_27568272bp] Performing fast sorting...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group2_38133982bp] Starting fast sorting iterations...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group11_14714105bp] Performing fast sorting...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group9_27568272bp] Checking the content of input group file...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group11_14714105bp] Checking the content of input group file...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group9_27568272bp] Starting fast sorting iterations...
2024-08-29 20:19:17 <HapHiC_sort.py> [fast_sort] [group11_14714105bp] Starting fast sorting iterations...
2024-08-29 20:19:17 <HapHiC_sort.py> [run_allhic_optimization] [group1_70654378bp] Performing ALLHiC optimization...
2024-08-29 20:19:17 <HapHiC_sort.py> [run_allhic_optimization] [group2_38133982bp] Performing ALLHiC optimization...
2024-08-29 20:19:17 <HapHiC_sort.py> [run_allhic_optimization] [group11_14714105bp] Performing ALLHiC optimization...
2024-08-29 20:19:17 <HapHiC_sort.py> [run_allhic_optimization] [group8_27911542bp] Performing ALLHiC optimization...
2024-08-29 20:19:17 <HapHiC_sort.py> [run_allhic_optimization] [group9_27568272bp] Performing ALLHiC optimization...
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group3_37032754bp] Performing fast sorting...
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group7_29728330bp] Performing fast sorting...
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group3_37032754bp] Checking the content of input group file...
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group10_17846258bp] Performing fast sorting...
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group7_29728330bp] Checking the content of input group file...
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group3_37032754bp] Starting fast sorting iterations...
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group10_17846258bp] Checking the content of input group file...
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group7_29728330bp] Only 1 contig in the group file, neither ordering nor orientation is required
2024-08-29 20:19:18 <HapHiC_sort.py> [fast_sort] [group10_17846258bp] Starting fast sorting iterations...
2024-08-29 20:19:18 <HapHiC_sort.py> [run_allhic_optimization] [group3_37032754bp] Performing ALLHiC optimization...
2024-08-29 20:19:18 <HapHiC_sort.py> [run_allhic_optimization] [group10_17846258bp] Performing ALLHiC optimization...
2024-08-29 20:19:24 <HapHiC_sort.py> [check_exceptions] Command '['/share/org/pth/HapHiC/scripts/allhic', 'optimize', '/share/org/pth/HiFi/02.reassign/final_groups/group1_70654378bp.txt', '/share/org/pth/HiFi/02.reassign/split_clms/group1_70654378bp.clm', '--mutapb', '0.2', '--ngen', '5000', '--npop', '100', '--seed', '42', '--resume']' died with <Signals.SIGSEGV: 11>.
2024-08-29 20:19:24 <HapHiC_sort.py> [check_exceptions] Command '['/share/org/pth/HapHiC/scripts/allhic', 'optimize', '/share/org/pth/HiFi/02.reassign/final_groups/group8_27911542bp.txt', '/share/org/pth/HiFi/02.reassign/split_clms/group8_27911542bp.clm', '--mutapb', '0.2', '--ngen', '5000', '--npop', '100', '--seed', '42', '--resume']' died with <Signals.SIGSEGV: 11>.
2024-08-29 20:19:24 <HapHiC_sort.py> [check_exceptions] Command '['/share/org/pth/HapHiC/scripts/allhic', 'optimize', '/share/org/pth/HiFi/02.reassign/final_groups/group2_38133982bp.txt', '/share/org/pth/HiFi/02.reassign/split_clms/group2_38133982bp.clm', '--mutapb', '0.2', '--ngen', '5000', '--npop', '100', '--seed', '42', '--resume']' died with <Signals.SIGSEGV: 11>.
2024-08-29 20:19:24 <HapHiC_sort.py> [check_exceptions] Command '['/share/org/pth/HapHiC/scripts/allhic', 'optimize', '/share/org/pth/HiFi/02.reassign/final_groups/group9_27568272bp.txt', '/share/org/pth/HiFi/02.reassign/split_clms/group9_27568272bp.clm', '--mutapb', '0.2', '--ngen', '5000', '--npop', '100', '--seed', '42', '--resume']' died with <Signals.SIGSEGV: 11>.
2024-08-29 20:19:24 <HapHiC_sort.py> [check_exceptions] Command '['/share/org/pth/HapHiC/scripts/allhic', 'optimize', '/share/org/pth/HiFi/02.reassign/final_groups/group11_14714105bp.txt', '/share/org/pth/HiFi/02.reassign/split_clms/group11_14714105bp.clm', '--mutapb', '0.2', '--ngen', '5000', '--npop', '100', '--seed', '42', '--resume']' died with <Signals.SIGSEGV: 11>.
2024-08-29 20:19:24 <HapHiC_sort.py> [check_exceptions] Command '['/share/org/pth/HapHiC/scripts/allhic', 'optimize', '/share/org/pth/HiFi/02.reassign/final_groups/group3_37032754bp.txt', '/share/org/pth/HiFi/02.reassign/split_clms/group3_37032754bp.clm', '--mutapb', '0.2', '--ngen', '5000', '--npop', '100', '--seed', '42', '--resume']' died with <Signals.SIGSEGV: 11>.
2024-08-29 20:19:24 <HapHiC_sort.py> [check_exceptions] Command '['/share/org/pth/HapHiC/scripts/allhic', 'optimize', '/share/org/pth/HiFi/02.reassign/final_groups/group10_17846258bp.txt', '/share/org/pth/HiFi/02.reassign/split_clms/group10_17846258bp.clm', '--mutapb', '0.2', '--ngen', '5000', '--npop', '100', '--seed', '42', '--resume']' died with <Signals.SIGSEGV: 11>.
Traceback (most recent call last):
  File "/share/org/pth/HapHiC/scripts/HapHiC_sort.py", line 971, in <module>
    main()
  File "/share/org/pth/HapHiC/scripts/HapHiC_sort.py", line 967, in main
    run(args, log_file='HapHiC_sort.log')
  File "/share/org/pth/HapHiC/scripts/HapHiC_sort.py", line 949, in run
    check_exceptions(result_list)
  File "/share/org/pth/HapHiC/scripts/HapHiC_sort.py", line 768, in check_exceptions
    raise Exception('{} exception(s) detected, please check the log above.'.format(nerrors))
Exception: 7 exception(s) detected, please check the log above.
Traceback (most recent call last):
  File "/share/org/pth/HapHiC/scripts/HapHiC_pipeline.py", line 529, in <module>
    main()
  File "/share/org/pth/HapHiC/scripts/HapHiC_pipeline.py", line 518, in main
    haphic_sort(args)
  File "/share/org/pth/HapHiC/scripts/HapHiC_pipeline.py", line 452, in haphic_sort
    subprocess.run(commands, check=True)
  File "/share/org/pth/.conda/envs/haphic/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/share/org/pth/HapHiC/scripts/HapHiC_sort.py', '/share/org/pth/HiFi/MM.p_ctg.fa', '/share/org/pth/HiFi/01.cluster/HT_links.pkl', '/share/org/pth/HiFi/02.reassign/split_clms', '/share/org/pth/HiFi/02.reassign/final_groups/group5_35837822bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group1_70654378bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group6_32394756bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group8_27911542bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group4_36272373bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group2_38133982bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group9_27568272bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group11_14714105bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group3_37032754bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group7_29728330bp.txt', '/share/org/pth/HiFi/02.reassign/final_groups/group10_17846258bp.txt', '--flanking_region', '0', '--density_cal_method', 'multiplication', '--confidence_cutoff', '1', '--mutprob', '0.2', '--ngen', '5000', '--npop', '100', '--seed', '42', '--processes', '8']' returned non-zero exit status 1.
Traceback (most recent call last):
  File "/share/org/pth/HapHiC/haphic", line 117, in <module>
    subprocess.run(commands, check=True)
  File "/share/org/pth/.conda/envs/haphic/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/share/org/pth/HapHiC/scripts/HapHiC_pipeline.py', 'MM.p_ctg.fa', 'MMHiC.filtered.bam', '11']' returned non-zero exit status 1.
Job 536114 stderr output:

Could you please help me identify what went wrong? Your assistance would be greatly appreciated.

Best regards,

iff

zengxiaofei commented 2 months ago

I have not seen this error message before. But it could be a problem of ALLHiC optimization. You can skip the optimization process using the parameter --skip_allhic. I noticed that your contigs are very long (chromosome-level or near chromosome-level), and the clustering process may have some problems. You may also consider using the quick view mode instead. This approach can skip both the clustering step and the ALLHiC optimization process.

S-iff commented 2 months ago

感谢您的建议，我在添加--quick_view参数后顺利运行完成了这一步。但我在运行下一步 Juicebox curation， bash juicebox.sh时的命令时，/path/to/HapHiC/utils/juicer/scripts/../utils/juicer pre -a -q 1 -o out_JBAT /share/org/HiFi/MMHiC.filtered.bam scaffolds.raw.agp MM.p_ctg.fa.fai >out_JBAT.log 2>&1报Segmentation fault (core dumped)的错误，询问服务器运维人员得知该代码可能自行引用了内存，但我所用集群是禁止程序自行使用内存的，不知这个情况能否解决。 / Line 9: ln -s /share/org/HiFi/MM.p_ctg.fa . ln: failed to create symbolic link './MM.p_ctg.fa': File exists Line 10: samtools faidx MM.p_ctg.fa Line 11: /share/org/HapHiC/scripts/../utils/juicer pre -a -q 1 -o out_JBAT /share/org/HiFi/MMHiC.filtered.bam scaffolds.raw.agp MM.p_ctg.fa.fai /share/org/HiFi/MM04.build/juicebox.sh: line 11: 2377950 Segmentation fault (core dumped)

zengxiaofei commented 2 months ago

I am unsure of the limitations that your system administrators have set. However, it appears that all binary programs pre-compiled by me, including allhic and juicer, did not execute properly. I am uncertain if compiling these two programs yourself could resolve this issue. You can access the source code for these programs here: allhic (Golang) at https://github.com/zengxiaofei/allhic and yahs (C language) at https://github.com/zengxiaofei/yahs.

zengxiaofei commented 2 months ago

Close this issue as there has been no response for two weeks.