[2024-08-27 14:49:05] root: ERROR: samtools is not installed [2024-08-27 14:49:05] root: ERROR: Pipeline aborted [2024-08-27 14:52:44] root: ERROR: samtools is not installed [2024-08-27 14:52:44] root: ERROR: Pipeline aborted [2024-08-27 14:56:40] root: ERROR: samtools is not installed [2024-08-27 14:56:40] root: ERROR: Pipeline aborted [2024-08-27 15:00:14] root: ERROR: samtools is not installed [2024-08-27 15:00:14] root: ERROR: Pipeline aborted [2024-08-27 15:01:28] root: ERROR: polishing binary was not found. Did you run 'make'? [2024-08-27 15:01:28] root: ERROR: Pipeline aborted [2024-08-27 15:05:23] root: INFO: Starting Flye 2.9.3-b1797 [2024-08-27 15:05:23] root: DEBUG: Cmd: /data/tools/Flye/bin/flye --threads 100 --meta --keep-haplotypes --nano-hq /data/longreads_basic_pipe/LEVASSEUR/diag/scan/reads/chr10/12677262-102018167_9f48.fasta -o tmp_meta/ [2024-08-27 15:05:23] root: DEBUG: Python version: 3.8.10 (default, Nov 22 2023, 10:22:35) [GCC 9.4.0] [2024-08-27 15:05:23] root: INFO: >>>STAGE: configure [2024-08-27 15:05:23] root: INFO: Configuring run [2024-08-27 15:05:23] root: INFO: Total read length: 133206 [2024-08-27 15:05:23] root: INFO: Reads N50/N90: 9776 / 4807 [2024-08-27 15:05:23] root: INFO: Minimum overlap set to 5000 [2024-08-27 15:05:23] root: INFO: >>>STAGE: assembly [2024-08-27 15:05:23] root: INFO: Assembling disjointigs [2024-08-27 15:05:23] root: DEBUG: -----Begin assembly log------ [2024-08-27 15:05:23] root: DEBUG: Running: flye-modules assemble --reads /data/longreads_basic_pipe/LEVASSEUR/diag/scan/reads/chr10/12677262-102018167_9f48.fasta --out-asm /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_meta/00-assembly/draft_assembly.fasta --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_meta/flye.log --threads 100 --meta --min-ovlp 5000 --extra-params aggressive_dup_filter=0 [2024-08-27 15:05:23] DEBUG: Build date: May 16 2023 00:48:26 [2024-08-27 15:05:23] DEBUG: Total RAM: 503 Gb [2024-08-27 15:05:23] DEBUG: Available RAM: 420 Gb [2024-08-27 15:05:23] DEBUG: Total CPUs: 160 [2024-08-27 15:05:23] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 15:05:23] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 15:05:23] DEBUG: big_genome_threshold=29000000 [2024-08-27 15:05:23] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 15:05:23] DEBUG: chain_large_gap_penalty=2 [2024-08-27 15:05:23] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 15:05:23] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 15:05:23] DEBUG: max_jump_gap=500 [2024-08-27 15:05:23] DEBUG: max_coverage_drop_rate=5 [2024-08-27 15:05:23] DEBUG: max_extensions_drop_rate=5 [2024-08-27 15:05:23] DEBUG: chimera_window=100 [2024-08-27 15:05:23] DEBUG: chimera_overhang=1000 [2024-08-27 15:05:23] DEBUG: min_reads_in_disjointig=4 [2024-08-27 15:05:23] DEBUG: max_inner_reads=10 [2024-08-27 15:05:23] DEBUG: max_inner_fraction=0.25 [2024-08-27 15:05:23] DEBUG: aggressive_dup_filter=1 [2024-08-27 15:05:23] DEBUG: max_separation=500 [2024-08-27 15:05:23] DEBUG: unique_edge_length=50000 [2024-08-27 15:05:23] DEBUG: min_repeat_res_support=0.51 [2024-08-27 15:05:23] DEBUG: out_paths_ratio=5 [2024-08-27 15:05:23] DEBUG: graph_cov_drop_rate=5 [2024-08-27 15:05:23] DEBUG: coverage_estimate_window=100 [2024-08-27 15:05:23] DEBUG: max_bubble_length=50000 [2024-08-27 15:05:23] DEBUG: loop_coverage_rate=1.5 [2024-08-27 15:05:23] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 15:05:23] DEBUG: weak_detach_rate=5 [2024-08-27 15:05:23] DEBUG: tip_coverage_rate=2 [2024-08-27 15:05:23] DEBUG: tip_length_rate=2 [2024-08-27 15:05:23] DEBUG: output_gfa_before_rr=1 [2024-08-27 15:05:23] DEBUG: remove_alt_edges=0 [2024-08-27 15:05:23] DEBUG: low_cutoff_warning=0 [2024-08-27 15:05:23] DEBUG: kmer_size=17 [2024-08-27 15:05:23] DEBUG: use_minimizers=1 [2024-08-27 15:05:23] DEBUG: minimizer_window=10 [2024-08-27 15:05:23] DEBUG: reads_base_alignment=1 [2024-08-27 15:05:23] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 15:05:23] DEBUG: maximum_jump=1500 [2024-08-27 15:05:23] DEBUG: maximum_overhang=1500 [2024-08-27 15:05:23] DEBUG: repeat_kmer_rate=100 [2024-08-27 15:05:23] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 15:05:23] DEBUG: assemble_divergence_relative=1 [2024-08-27 15:05:23] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 15:05:23] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 15:05:23] DEBUG: hpc_scoring_on=1 [2024-08-27 15:05:23] DEBUG: add_unassembled_reads=0 [2024-08-27 15:05:23] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 15:05:23] DEBUG: min_read_cov_cutoff=3 [2024-08-27 15:05:23] DEBUG: short_tip_length=20000 [2024-08-27 15:05:23] DEBUG: long_tip_length=100000 [2024-08-27 15:05:23] DEBUG: Extrta parameters: [2024-08-27 15:05:23] DEBUG: aggressive_dup_filter=0 [2024-08-27 15:05:23] DEBUG: Running with k-mer size: 17 [2024-08-27 15:05:23] DEBUG: Running with minimum overlap 5000 [2024-08-27 15:05:23] DEBUG: Metagenome mode: Y [2024-08-27 15:05:23] DEBUG: Short mode: N [2024-08-27 15:05:23] INFO: Reading sequences [2024-08-27 15:05:23] DEBUG: Building positional index [2024-08-27 15:05:23] DEBUG: Total sequence: 116049 bp [2024-08-27 15:05:23] INFO: Building minimizer index [2024-08-27 15:05:23] INFO: Pre-calculating index storage [2024-08-27 15:05:23] DEBUG: Mean k-mer frequency: 2.91841 [2024-08-27 15:05:23] DEBUG: Repetitive k-mer frequency: 291 [2024-08-27 15:05:23] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 15:05:24] INFO: Filling index [2024-08-27 15:05:24] DEBUG: Sorting k-mer index [2024-08-27 15:05:24] DEBUG: Selected k-mers: 7157 [2024-08-27 15:05:24] DEBUG: K-mer index size: 20890 [2024-08-27 15:05:24] DEBUG: Mean k-mer frequency: 2.91882 [2024-08-27 15:05:24] DEBUG: Minimizer rate: 5.55524 [2024-08-27 15:05:24] DEBUG: Peak RAM usage: 0 Gb [2024-08-27 15:05:24] DEBUG: Estimating k-mer identity bias [2024-08-27 15:09:03] root: INFO: Starting Flye 2.9.3-b1797 [2024-08-27 15:09:03] root: DEBUG: Cmd: /data/tools/Flye/bin/flye --threads 100 --meta --keep-haplotypes --nano-hq /data/longreads_basic_pipe/LEVASSEUR/diag/scan/reads/chr10/12677262-102018167_9f48.fasta -o tmp_meta/ [2024-08-27 15:09:03] root: DEBUG: Python version: 3.8.10 (default, Nov 22 2023, 10:22:35) [GCC 9.4.0] [2024-08-27 15:09:03] root: INFO: >>>STAGE: configure [2024-08-27 15:09:03] root: INFO: Configuring run [2024-08-27 15:09:03] root: INFO: Total read length: 133206 [2024-08-27 15:09:03] root: INFO: Reads N50/N90: 9776 / 4807 [2024-08-27 15:09:03] root: INFO: Minimum overlap set to 5000 [2024-08-27 15:09:03] root: INFO: >>>STAGE: assembly [2024-08-27 15:09:03] root: INFO: Assembling disjointigs [2024-08-27 15:09:03] root: DEBUG: -----Begin assembly log------ [2024-08-27 15:09:03] root: DEBUG: Running: flye-modules assemble --reads /data/longreads_basic_pipe/LEVASSEUR/diag/scan/reads/chr10/12677262-102018167_9f48.fasta --out-asm /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_meta/00-assembly/draft_assembly.fasta --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_meta/flye.log --threads 100 --meta --min-ovlp 5000 --extra-params aggressive_dup_filter=0 [2024-08-27 15:09:03] DEBUG: Build date: May 16 2023 00:48:26 [2024-08-27 15:09:03] DEBUG: Total RAM: 503 Gb [2024-08-27 15:09:03] DEBUG: Available RAM: 420 Gb [2024-08-27 15:09:03] DEBUG: Total CPUs: 160 [2024-08-27 15:09:03] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg [2024-08-27 15:09:03] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg [2024-08-27 15:09:03] DEBUG: big_genome_threshold=29000000 [2024-08-27 15:09:03] DEBUG: meta_read_filter_kmer_freq=100 [2024-08-27 15:09:03] DEBUG: chain_large_gap_penalty=2 [2024-08-27 15:09:03] DEBUG: chain_small_gap_penalty=0.5 [2024-08-27 15:09:03] DEBUG: chain_gap_jump_threshold=100 [2024-08-27 15:09:03] DEBUG: max_jump_gap=500 [2024-08-27 15:09:03] DEBUG: max_coverage_drop_rate=5 [2024-08-27 15:09:03] DEBUG: max_extensions_drop_rate=5 [2024-08-27 15:09:03] DEBUG: chimera_window=100 [2024-08-27 15:09:03] DEBUG: chimera_overhang=1000 [2024-08-27 15:09:03] DEBUG: min_reads_in_disjointig=4 [2024-08-27 15:09:03] DEBUG: max_inner_reads=10 [2024-08-27 15:09:03] DEBUG: max_inner_fraction=0.25 [2024-08-27 15:09:03] DEBUG: aggressive_dup_filter=1 [2024-08-27 15:09:03] DEBUG: max_separation=500 [2024-08-27 15:09:03] DEBUG: unique_edge_length=50000 [2024-08-27 15:09:03] DEBUG: min_repeat_res_support=0.51 [2024-08-27 15:09:03] DEBUG: out_paths_ratio=5 [2024-08-27 15:09:03] DEBUG: graph_cov_drop_rate=5 [2024-08-27 15:09:03] DEBUG: coverage_estimate_window=100 [2024-08-27 15:09:03] DEBUG: max_bubble_length=50000 [2024-08-27 15:09:03] DEBUG: loop_coverage_rate=1.5 [2024-08-27 15:09:03] DEBUG: repeat_edge_cov_mult=1.75 [2024-08-27 15:09:03] DEBUG: weak_detach_rate=5 [2024-08-27 15:09:03] DEBUG: tip_coverage_rate=2 [2024-08-27 15:09:03] DEBUG: tip_length_rate=2 [2024-08-27 15:09:03] DEBUG: output_gfa_before_rr=1 [2024-08-27 15:09:03] DEBUG: remove_alt_edges=0 [2024-08-27 15:09:03] DEBUG: low_cutoff_warning=0 [2024-08-27 15:09:03] DEBUG: kmer_size=17 [2024-08-27 15:09:03] DEBUG: use_minimizers=1 [2024-08-27 15:09:03] DEBUG: minimizer_window=10 [2024-08-27 15:09:03] DEBUG: reads_base_alignment=1 [2024-08-27 15:09:03] DEBUG: meta_read_top_kmer_rate=0.75 [2024-08-27 15:09:03] DEBUG: maximum_jump=1500 [2024-08-27 15:09:03] DEBUG: maximum_overhang=1500 [2024-08-27 15:09:03] DEBUG: repeat_kmer_rate=100 [2024-08-27 15:09:03] DEBUG: assemble_ovlp_divergence=0.05 [2024-08-27 15:09:03] DEBUG: assemble_divergence_relative=1 [2024-08-27 15:09:03] DEBUG: repeat_graph_ovlp_divergence=0.05 [2024-08-27 15:09:03] DEBUG: read_align_ovlp_divergence=0.10 [2024-08-27 15:09:03] DEBUG: hpc_scoring_on=1 [2024-08-27 15:09:03] DEBUG: add_unassembled_reads=0 [2024-08-27 15:09:03] DEBUG: extend_contigs_with_repeats=0 [2024-08-27 15:09:03] DEBUG: min_read_cov_cutoff=3 [2024-08-27 15:09:03] DEBUG: short_tip_length=20000 [2024-08-27 15:09:03] DEBUG: long_tip_length=100000 [2024-08-27 15:09:03] DEBUG: Extrta parameters: [2024-08-27 15:09:03] DEBUG: aggressive_dup_filter=0 [2024-08-27 15:09:03] DEBUG: Running with k-mer size: 17 [2024-08-27 15:09:03] DEBUG: Running with minimum overlap 5000 [2024-08-27 15:09:03] DEBUG: Metagenome mode: Y [2024-08-27 15:09:03] DEBUG: Short mode: N [2024-08-27 15:09:03] INFO: Reading sequences [2024-08-27 15:09:03] DEBUG: Building positional index [2024-08-27 15:09:03] DEBUG: Total sequence: 116049 bp [2024-08-27 15:09:03] INFO: Building minimizer index [2024-08-27 15:09:03] INFO: Pre-calculating index storage [2024-08-27 15:09:03] DEBUG: Mean k-mer frequency: 2.91841 [2024-08-27 15:09:03] DEBUG: Repetitive k-mer frequency: 291 [2024-08-27 15:09:03] DEBUG: Filtered 0 repetitive k-mers (0) [2024-08-27 15:09:03] INFO: Filling index [2024-08-27 15:09:03] DEBUG: Sorting k-mer index [2024-08-27 15:09:03] DEBUG: Selected k-mers: 7157 [2024-08-27 15:09:03] DEBUG: K-mer index size: 20890 [2024-08-27 15:09:03] DEBUG: Mean k-mer frequency: 2.91882 [2024-08-27 15:09:03] DEBUG: Minimizer rate: 5.55524 [2024-08-27 15:09:03] DEBUG: Peak RAM usage: 0 Gb [2024-08-27 15:09:03] DEBUG: Estimating k-mer identity bias