Flye reported an error

[HHHHerbs]

flye.log [2024-05-16 15:59:27] root: INFO: Starting Flye 2.9.4-b1799 [2024-05-16 15:59:27] root: DEBUG: Cmd: /pub4/huangshoubian1/anaconda3/bin/flye --meta --no-alt-contigs --nano-raw test_ont_chr4_L.fasta trim_UP_low_hifi_chr4_L.fasta --out-dir ./asm_out2 --threads 20 [2024-05-16 15:59:27] root: DEBUG: Python version: 3.11.4 (main, Jul 5 2023, 14:15:25) [GCC 11.2.0] [2024-05-16 15:59:27] root: INFO: >>>STAGE: configure [2024-05-16 15:59:27] root: INFO: Configuring run [2024-05-16 15:59:27] root: INFO: Total read length: 175370 [2024-05-16 15:59:27] root: INFO: Reads N50/N90: 6745 / 6745 [2024-05-16 15:59:27] root: INFO: Minimum overlap set to 7000 [2024-05-16 15:59:28] root: INFO: >>>STAGE: assembly [2024-05-16 15:59:28] root: INFO: Assembling disjointigs [2024-05-16 15:59:28] root: DEBUG: -----Begin assembly log------ [2024-05-16 15:59:28] root: DEBUG: Running: flye-modules assemble --reads /pub5/Hshoub/Morus_notabilis/new_ideas/chr4_L/test_ont_chr4_L.fasta,/pub5/Hshoub/Morus_notabilis/new_ideas/chr4_L/trim_UP_low_hifi_chr4_L.fasta --out-asm /pub5/Hshoub/Morus_notabilis/new_ideas/chr4_L/asm_out2/00-assembly/draft_assembly.fasta --config /pub4/huangshoubian1/anaconda3/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg --log /pub5/Hshoub/Morus_notabilis/new_ideas/chr4_L/asm_out2/flye.log --threads 20 --meta --min-ovlp 7000 --extra-params remove_alt_edges=1 [2024-05-16 15:59:28] DEBUG: Build date: May 16 2024 11:26:21 [2024-05-16 15:59:28] DEBUG: Total RAM: 1006 Gb [2024-05-16 15:59:28] DEBUG: Available RAM: 897 Gb [2024-05-16 15:59:28] DEBUG: Total CPUs: 80 [2024-05-16 15:59:28] DEBUG: Loading /pub4/huangshoubian1/anaconda3/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg [2024-05-16 15:59:28] DEBUG: Loading /pub4/huangshoubian1/anaconda3/lib/python3.11/site-packages/flye/config/bin_cfg/asm_defaults.cfg [2024-05-16 15:59:28] DEBUG: big_genome_threshold=29000000 [2024-05-16 15:59:28] DEBUG: meta_read_filter_kmer_freq=100 [2024-05-16 15:59:28] DEBUG: chain_large_gap_penalty=2 [2024-05-16 15:59:28] DEBUG: chain_small_gap_penalty=0.5 [2024-05-16 15:59:28] DEBUG: chain_gap_jump_threshold=100 [2024-05-16 15:59:28] DEBUG: max_jump_gap=500 [2024-05-16 15:59:28] DEBUG: max_coverage_drop_rate=5 [2024-05-16 15:59:28] DEBUG: max_extensions_drop_rate=5 [2024-05-16 15:59:28] DEBUG: chimera_window=100 [2024-05-16 15:59:28] DEBUG: chimera_overhang=1000 [2024-05-16 15:59:28] DEBUG: min_reads_in_disjointig=4 [2024-05-16 15:59:28] DEBUG: max_inner_reads=10 [2024-05-16 15:59:28] DEBUG: max_inner_fraction=0.25 [2024-05-16 15:59:28] DEBUG: aggressive_dup_filter=1 [2024-05-16 15:59:28] DEBUG: max_separation=500 [2024-05-16 15:59:28] DEBUG: unique_edge_length=50000 [2024-05-16 15:59:28] DEBUG: min_repeat_res_support=0.51 [2024-05-16 15:59:28] DEBUG: out_paths_ratio=5 [2024-05-16 15:59:28] DEBUG: graph_cov_drop_rate=5 [2024-05-16 15:59:28] DEBUG: coverage_estimate_window=100 [2024-05-16 15:59:28] DEBUG: max_bubble_length=50000 [2024-05-16 15:59:28] DEBUG: loop_coverage_rate=1.5 [2024-05-16 15:59:28] DEBUG: repeat_edge_cov_mult=1.75 [2024-05-16 15:59:28] DEBUG: weak_detach_rate=5 [2024-05-16 15:59:28] DEBUG: tip_coverage_rate=2 [2024-05-16 15:59:28] DEBUG: tip_length_rate=2 [2024-05-16 15:59:28] DEBUG: output_gfa_before_rr=1 [2024-05-16 15:59:28] DEBUG: remove_alt_edges=0 [2024-05-16 15:59:28] DEBUG: low_cutoff_warning=1 [2024-05-16 15:59:28] DEBUG: kmer_size=17 [2024-05-16 15:59:28] DEBUG: use_minimizers=0 [2024-05-16 15:59:28] DEBUG: reads_base_alignment=0 [2024-05-16 15:59:28] DEBUG: meta_read_top_kmer_rate=0.40 [2024-05-16 15:59:28] DEBUG: maximum_jump=1500 [2024-05-16 15:59:28] DEBUG: maximum_overhang=1500 [2024-05-16 15:59:28] DEBUG: repeat_kmer_rate=100 [2024-05-16 15:59:28] DEBUG: assemble_ovlp_divergence=0.10 [2024-05-16 15:59:28] DEBUG: assemble_divergence_relative=1 [2024-05-16 15:59:28] DEBUG: repeat_graph_ovlp_divergence=0.08 [2024-05-16 15:59:28] DEBUG: read_align_ovlp_divergence=0.25 [2024-05-16 15:59:28] DEBUG: hpc_scoring_on=0 [2024-05-16 15:59:28] DEBUG: add_unassembled_reads=0 [2024-05-16 15:59:28] DEBUG: extend_contigs_with_repeats=0 [2024-05-16 15:59:28] DEBUG: min_read_cov_cutoff=3 [2024-05-16 15:59:28] DEBUG: short_tip_length=20000 [2024-05-16 15:59:28] DEBUG: long_tip_length=100000 [2024-05-16 15:59:28] DEBUG: Extrta parameters: [2024-05-16 15:59:28] DEBUG: remove_alt_edges=1 [2024-05-16 15:59:28] DEBUG: Running with k-mer size: 17 [2024-05-16 15:59:28] DEBUG: Running with minimum overlap 7000 [2024-05-16 15:59:28] DEBUG: Metagenome mode: Y [2024-05-16 15:59:28] DEBUG: Short mode: N [2024-05-16 15:59:28] INFO: Reading sequences [2024-05-16 15:59:28] DEBUG: Building positional index [2024-05-16 15:59:44] INFO: Counting k-mers: [2024-05-16 15:59:44] DEBUG: Updating k-mer histogram [2024-05-16 16:02:18] DEBUG: Hash size: 0 [2024-05-16 16:02:18] DEBUG: Total k-mers 0 [2024-05-16 16:02:18] INFO: Filling index table (1/2) [2024-05-16 16:02:18] DEBUG: Mean k-mer frequency: 0 [2024-05-16 16:02:18] DEBUG: Repetitive k-mer frequency: 0 [2024-05-16 16:02:18] DEBUG: Filtered 0 repetitive k-mers (-nan) [2024-05-16 16:02:18] INFO: Filling index table (2/2) [2024-05-16 16:02:20] DEBUG: Sorting k-mer index [2024-05-16 16:02:20] DEBUG: Selected k-mers: 0 [2024-05-16 16:02:20] DEBUG: Index size: 0 [2024-05-16 16:02:20] DEBUG: Mean k-mer index frequency: -nan [2024-05-16 16:02:20] DEBUG: Peak RAM usage: 8 Gb [2024-05-16 16:02:20] DEBUG: Estimating k-mer identity bias [2024-05-16 16:02:20] root: ERROR: Command '['flye-modules', 'assemble', '--reads', '/pub5/Hshoub/Morus_notabilis/new_ideas/chr4_L/test_ont_chr4_L.fasta,/pub5/Hshoub/Morus_notabilis/new_ideas/chr4_L/trim_UP_low_hifi_chr4_L.fasta', '--out-asm', '/pub5/Hshoub/Morus_notabilis/new_ideas/chr4_L/asm_out2/00-assembly/draft_assembly.fasta', '--config', '/pub4/huangshoubian1/anaconda3/lib/python3.11/site-packages/flye/config/bin_cfg/asm_raw_reads.cfg', '--log', '/pub5/Hshoub/Morus_notabilis/new_ideas/chr4_L/asm_out2/flye.log', '--threads', '20', '--meta', '--min-ovlp', '7000', '--extra-params', 'remove_alt_edges=1']' died with <Signals.SIGFPE: 8>. [2024-05-16 16:02:20] root: ERROR: Pipeline aborted

[HHHHerbs]

Has anyone encountered such a problem? How to solve it? Can you help me? Thank you everyone.

[mikolmogorov]

Hello,

I think it's likely the read length, looks like you only have 175kb of sequence in total. For assembly, you need at minimum 10-15x sequencing depth for each oragnism.

[isabelluo]

@fenderglass could you please teach me where to look for the " 175kb of sequence in total" ? which line tells you that? Cause I did this "awk '{ if(NR%4==2){print length($0);} }' file.fq" and it shows that I should have 196M bases.

Thank you

[mikolmogorov]

@isabelluo this line in the log file: [2024-05-16 15:59:27] root: INFO: Total read length: 175370