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pandora_lib_ass...
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tmp_meta
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flye.log

flye.log 11 KB
История Исходник

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  1. [2024-08-27 14:49:05] root: ERROR: samtools is not installed
    2. 

  2. [2024-08-27 14:49:05] root: ERROR: Pipeline aborted
    3. 

  3. [2024-08-27 14:52:44] root: ERROR: samtools is not installed
    4. 

  4. [2024-08-27 14:52:44] root: ERROR: Pipeline aborted
    5. 

  5. [2024-08-27 14:56:40] root: ERROR: samtools is not installed
    6. 

  6. [2024-08-27 14:56:40] root: ERROR: Pipeline aborted
    7. 

  7. [2024-08-27 15:00:14] root: ERROR: samtools is not installed
    8. 

  8. [2024-08-27 15:00:14] root: ERROR: Pipeline aborted
    9. 

  9. [2024-08-27 15:01:28] root: ERROR: polishing binary was not found. Did you run 'make'?
    10. 

  10. [2024-08-27 15:01:28] root: ERROR: Pipeline aborted
    11. 

  11. [2024-08-27 15:05:23] root: INFO: Starting Flye 2.9.3-b1797
    12. 

  12. [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/
    13. 

  13. [2024-08-27 15:05:23] root: DEBUG: Python version: 3.8.10 (default, Nov 22 2023, 10:22:35) 
    14. 

  14. [GCC 9.4.0]
    15. 

  15. [2024-08-27 15:05:23] root: INFO: >>>STAGE: configure
    16. 

  16. [2024-08-27 15:05:23] root: INFO: Configuring run
    17. 

  17. [2024-08-27 15:05:23] root: INFO: Total read length: 133206
    18. 

  18. [2024-08-27 15:05:23] root: INFO: Reads N50/N90: 9776 / 4807
    19. 

  19. [2024-08-27 15:05:23] root: INFO: Minimum overlap set to 5000
    20. 

  20. [2024-08-27 15:05:23] root: INFO: >>>STAGE: assembly
    21. 

  21. [2024-08-27 15:05:23] root: INFO: Assembling disjointigs
    22. 

  22. [2024-08-27 15:05:23] root: DEBUG: -----Begin assembly log------
    23. 

  23. [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
    24. 

  24. [2024-08-27 15:05:23] DEBUG: Build date: May 16 2023 00:48:26
    25. 

  25. [2024-08-27 15:05:23] DEBUG: Total RAM: 503 Gb
    26. 

  26. [2024-08-27 15:05:23] DEBUG: Available RAM: 420 Gb
    27. 

  27. [2024-08-27 15:05:23] DEBUG: Total CPUs: 160
    28. 

  28. [2024-08-27 15:05:23] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg
    29. 

  29. [2024-08-27 15:05:23] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg
    30. 

  30. [2024-08-27 15:05:23] DEBUG: 	big_genome_threshold=29000000
    31. 

  31. [2024-08-27 15:05:23] DEBUG: 	meta_read_filter_kmer_freq=100
    32. 

  32. [2024-08-27 15:05:23] DEBUG: 	chain_large_gap_penalty=2
    33. 

  33. [2024-08-27 15:05:23] DEBUG: 	chain_small_gap_penalty=0.5
    34. 

  34. [2024-08-27 15:05:23] DEBUG: 	chain_gap_jump_threshold=100
    35. 

  35. [2024-08-27 15:05:23] DEBUG: 	max_jump_gap=500
    36. 

  36. [2024-08-27 15:05:23] DEBUG: 	max_coverage_drop_rate=5
    37. 

  37. [2024-08-27 15:05:23] DEBUG: 	max_extensions_drop_rate=5
    38. 

  38. [2024-08-27 15:05:23] DEBUG: 	chimera_window=100
    39. 

  39. [2024-08-27 15:05:23] DEBUG: 	chimera_overhang=1000
    40. 

  40. [2024-08-27 15:05:23] DEBUG: 	min_reads_in_disjointig=4
    41. 

  41. [2024-08-27 15:05:23] DEBUG: 	max_inner_reads=10
    42. 

  42. [2024-08-27 15:05:23] DEBUG: 	max_inner_fraction=0.25
    43. 

  43. [2024-08-27 15:05:23] DEBUG: 	aggressive_dup_filter=1
    44. 

  44. [2024-08-27 15:05:23] DEBUG: 	max_separation=500
    45. 

  45. [2024-08-27 15:05:23] DEBUG: 	unique_edge_length=50000
    46. 

  46. [2024-08-27 15:05:23] DEBUG: 	min_repeat_res_support=0.51
    47. 

  47. [2024-08-27 15:05:23] DEBUG: 	out_paths_ratio=5
    48. 

  48. [2024-08-27 15:05:23] DEBUG: 	graph_cov_drop_rate=5
    49. 

  49. [2024-08-27 15:05:23] DEBUG: 	coverage_estimate_window=100
    50. 

  50. [2024-08-27 15:05:23] DEBUG: 	max_bubble_length=50000
    51. 

  51. [2024-08-27 15:05:23] DEBUG: 	loop_coverage_rate=1.5
    52. 

  52. [2024-08-27 15:05:23] DEBUG: 	repeat_edge_cov_mult=1.75
    53. 

  53. [2024-08-27 15:05:23] DEBUG: 	weak_detach_rate=5
    54. 

  54. [2024-08-27 15:05:23] DEBUG: 	tip_coverage_rate=2
    55. 

  55. [2024-08-27 15:05:23] DEBUG: 	tip_length_rate=2
    56. 

  56. [2024-08-27 15:05:23] DEBUG: 	output_gfa_before_rr=1
    57. 

  57. [2024-08-27 15:05:23] DEBUG: 	remove_alt_edges=0
    58. 

  58. [2024-08-27 15:05:23] DEBUG: 	low_cutoff_warning=0
    59. 

  59. [2024-08-27 15:05:23] DEBUG: 	kmer_size=17
    60. 

  60. [2024-08-27 15:05:23] DEBUG: 	use_minimizers=1
    61. 

  61. [2024-08-27 15:05:23] DEBUG: 	minimizer_window=10
    62. 

  62. [2024-08-27 15:05:23] DEBUG: 	reads_base_alignment=1
    63. 

  63. [2024-08-27 15:05:23] DEBUG: 	meta_read_top_kmer_rate=0.75
    64. 

  64. [2024-08-27 15:05:23] DEBUG: 	maximum_jump=1500
    65. 

  65. [2024-08-27 15:05:23] DEBUG: 	maximum_overhang=1500
    66. 

  66. [2024-08-27 15:05:23] DEBUG: 	repeat_kmer_rate=100
    67. 

  67. [2024-08-27 15:05:23] DEBUG: 	assemble_ovlp_divergence=0.05
    68. 

  68. [2024-08-27 15:05:23] DEBUG: 	assemble_divergence_relative=1
    69. 

  69. [2024-08-27 15:05:23] DEBUG: 	repeat_graph_ovlp_divergence=0.05
    70. 

  70. [2024-08-27 15:05:23] DEBUG: 	read_align_ovlp_divergence=0.10
    71. 

  71. [2024-08-27 15:05:23] DEBUG: 	hpc_scoring_on=1
    72. 

  72. [2024-08-27 15:05:23] DEBUG: 	add_unassembled_reads=0
    73. 

  73. [2024-08-27 15:05:23] DEBUG: 	extend_contigs_with_repeats=0
    74. 

  74. [2024-08-27 15:05:23] DEBUG: 	min_read_cov_cutoff=3
    75. 

  75. [2024-08-27 15:05:23] DEBUG: 	short_tip_length=20000
    76. 

  76. [2024-08-27 15:05:23] DEBUG: 	long_tip_length=100000
    77. 

  77. [2024-08-27 15:05:23] DEBUG: Extrta parameters:
    78. 

  78. [2024-08-27 15:05:23] DEBUG: 	aggressive_dup_filter=0
    79. 

  79. [2024-08-27 15:05:23] DEBUG: Running with k-mer size: 17
    80. 

  80. [2024-08-27 15:05:23] DEBUG: Running with minimum overlap 5000
    81. 

  81. [2024-08-27 15:05:23] DEBUG: Metagenome mode: Y
    82. 

  82. [2024-08-27 15:05:23] DEBUG: Short mode: N
    83. 

  83. [2024-08-27 15:05:23] INFO: Reading sequences
    84. 

  84. [2024-08-27 15:05:23] DEBUG: Building positional index
    85. 

  85. [2024-08-27 15:05:23] DEBUG: Total sequence: 116049 bp
    86. 

  86. [2024-08-27 15:05:23] INFO: Building minimizer index
    87. 

  87. [2024-08-27 15:05:23] INFO: Pre-calculating index storage
    88. 

  88. [2024-08-27 15:05:23] DEBUG: Mean k-mer frequency: 2.91841
    89. 

  89. [2024-08-27 15:05:23] DEBUG: Repetitive k-mer frequency: 291
    90. 

  90. [2024-08-27 15:05:23] DEBUG: Filtered 0 repetitive k-mers (0)
    91. 

  91. [2024-08-27 15:05:24] INFO: Filling index
    92. 

  92. [2024-08-27 15:05:24] DEBUG: Sorting k-mer index
    93. 

  93. [2024-08-27 15:05:24] DEBUG: Selected k-mers: 7157
    94. 

  94. [2024-08-27 15:05:24] DEBUG: K-mer index size: 20890
    95. 

  95. [2024-08-27 15:05:24] DEBUG: Mean k-mer frequency: 2.91882
    96. 

  96. [2024-08-27 15:05:24] DEBUG: Minimizer rate: 5.55524
    97. 

  97. [2024-08-27 15:05:24] DEBUG: Peak RAM usage: 0 Gb
    98. 

  98. [2024-08-27 15:05:24] DEBUG: Estimating k-mer identity bias
    99. 

  99. [2024-08-27 15:09:03] root: INFO: Starting Flye 2.9.3-b1797
    100. 

  100. [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/
    101. 

  101. [2024-08-27 15:09:03] root: DEBUG: Python version: 3.8.10 (default, Nov 22 2023, 10:22:35) 
    102. 

  102. [GCC 9.4.0]
    103. 

  103. [2024-08-27 15:09:03] root: INFO: >>>STAGE: configure
    104. 

  104. [2024-08-27 15:09:03] root: INFO: Configuring run
    105. 

  105. [2024-08-27 15:09:03] root: INFO: Total read length: 133206
    106. 

  106. [2024-08-27 15:09:03] root: INFO: Reads N50/N90: 9776 / 4807
    107. 

  107. [2024-08-27 15:09:03] root: INFO: Minimum overlap set to 5000
    108. 

  108. [2024-08-27 15:09:03] root: INFO: >>>STAGE: assembly
    109. 

  109. [2024-08-27 15:09:03] root: INFO: Assembling disjointigs
    110. 

  110. [2024-08-27 15:09:03] root: DEBUG: -----Begin assembly log------
    111. 

  111. [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
    112. 

  112. [2024-08-27 15:09:03] DEBUG: Build date: May 16 2023 00:48:26
    113. 

  113. [2024-08-27 15:09:03] DEBUG: Total RAM: 503 Gb
    114. 

  114. [2024-08-27 15:09:03] DEBUG: Available RAM: 420 Gb
    115. 

  115. [2024-08-27 15:09:03] DEBUG: Total CPUs: 160
    116. 

  116. [2024-08-27 15:09:03] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg
    117. 

  117. [2024-08-27 15:09:03] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg
    118. 

  118. [2024-08-27 15:09:03] DEBUG: 	big_genome_threshold=29000000
    119. 

  119. [2024-08-27 15:09:03] DEBUG: 	meta_read_filter_kmer_freq=100
    120. 

  120. [2024-08-27 15:09:03] DEBUG: 	chain_large_gap_penalty=2
    121. 

  121. [2024-08-27 15:09:03] DEBUG: 	chain_small_gap_penalty=0.5
    122. 

  122. [2024-08-27 15:09:03] DEBUG: 	chain_gap_jump_threshold=100
    123. 

  123. [2024-08-27 15:09:03] DEBUG: 	max_jump_gap=500
    124. 

  124. [2024-08-27 15:09:03] DEBUG: 	max_coverage_drop_rate=5
    125. 

  125. [2024-08-27 15:09:03] DEBUG: 	max_extensions_drop_rate=5
    126. 

  126. [2024-08-27 15:09:03] DEBUG: 	chimera_window=100
    127. 

  127. [2024-08-27 15:09:03] DEBUG: 	chimera_overhang=1000
    128. 

  128. [2024-08-27 15:09:03] DEBUG: 	min_reads_in_disjointig=4
    129. 

  129. [2024-08-27 15:09:03] DEBUG: 	max_inner_reads=10
    130. 

  130. [2024-08-27 15:09:03] DEBUG: 	max_inner_fraction=0.25
    131. 

  131. [2024-08-27 15:09:03] DEBUG: 	aggressive_dup_filter=1
    132. 

  132. [2024-08-27 15:09:03] DEBUG: 	max_separation=500
    133. 

  133. [2024-08-27 15:09:03] DEBUG: 	unique_edge_length=50000
    134. 

  134. [2024-08-27 15:09:03] DEBUG: 	min_repeat_res_support=0.51
    135. 

  135. [2024-08-27 15:09:03] DEBUG: 	out_paths_ratio=5
    136. 

  136. [2024-08-27 15:09:03] DEBUG: 	graph_cov_drop_rate=5
    137. 

  137. [2024-08-27 15:09:03] DEBUG: 	coverage_estimate_window=100
    138. 

  138. [2024-08-27 15:09:03] DEBUG: 	max_bubble_length=50000
    139. 

  139. [2024-08-27 15:09:03] DEBUG: 	loop_coverage_rate=1.5
    140. 

  140. [2024-08-27 15:09:03] DEBUG: 	repeat_edge_cov_mult=1.75
    141. 

  141. [2024-08-27 15:09:03] DEBUG: 	weak_detach_rate=5
    142. 

  142. [2024-08-27 15:09:03] DEBUG: 	tip_coverage_rate=2
    143. 

  143. [2024-08-27 15:09:03] DEBUG: 	tip_length_rate=2
    144. 

  144. [2024-08-27 15:09:03] DEBUG: 	output_gfa_before_rr=1
    145. 

  145. [2024-08-27 15:09:03] DEBUG: 	remove_alt_edges=0
    146. 

  146. [2024-08-27 15:09:03] DEBUG: 	low_cutoff_warning=0
    147. 

  147. [2024-08-27 15:09:03] DEBUG: 	kmer_size=17
    148. 

  148. [2024-08-27 15:09:03] DEBUG: 	use_minimizers=1
    149. 

  149. [2024-08-27 15:09:03] DEBUG: 	minimizer_window=10
    150. 

  150. [2024-08-27 15:09:03] DEBUG: 	reads_base_alignment=1
    151. 

  151. [2024-08-27 15:09:03] DEBUG: 	meta_read_top_kmer_rate=0.75
    152. 

  152. [2024-08-27 15:09:03] DEBUG: 	maximum_jump=1500
    153. 

  153. [2024-08-27 15:09:03] DEBUG: 	maximum_overhang=1500
    154. 

  154. [2024-08-27 15:09:03] DEBUG: 	repeat_kmer_rate=100
    155. 

  155. [2024-08-27 15:09:03] DEBUG: 	assemble_ovlp_divergence=0.05
    156. 

  156. [2024-08-27 15:09:03] DEBUG: 	assemble_divergence_relative=1
    157. 

  157. [2024-08-27 15:09:03] DEBUG: 	repeat_graph_ovlp_divergence=0.05
    158. 

  158. [2024-08-27 15:09:03] DEBUG: 	read_align_ovlp_divergence=0.10
    159. 

  159. [2024-08-27 15:09:03] DEBUG: 	hpc_scoring_on=1
    160. 

  160. [2024-08-27 15:09:03] DEBUG: 	add_unassembled_reads=0
    161. 

  161. [2024-08-27 15:09:03] DEBUG: 	extend_contigs_with_repeats=0
    162. 

  162. [2024-08-27 15:09:03] DEBUG: 	min_read_cov_cutoff=3
    163. 

  163. [2024-08-27 15:09:03] DEBUG: 	short_tip_length=20000
    164. 

  164. [2024-08-27 15:09:03] DEBUG: 	long_tip_length=100000
    165. 

  165. [2024-08-27 15:09:03] DEBUG: Extrta parameters:
    166. 

  166. [2024-08-27 15:09:03] DEBUG: 	aggressive_dup_filter=0
    167. 

  167. [2024-08-27 15:09:03] DEBUG: Running with k-mer size: 17
    168. 

  168. [2024-08-27 15:09:03] DEBUG: Running with minimum overlap 5000
    169. 

  169. [2024-08-27 15:09:03] DEBUG: Metagenome mode: Y
    170. 

  170. [2024-08-27 15:09:03] DEBUG: Short mode: N
    171. 

  171. [2024-08-27 15:09:03] INFO: Reading sequences
    172. 

  172. [2024-08-27 15:09:03] DEBUG: Building positional index
    173. 

  173. [2024-08-27 15:09:03] DEBUG: Total sequence: 116049 bp
    174. 

  174. [2024-08-27 15:09:03] INFO: Building minimizer index
    175. 

  175. [2024-08-27 15:09:03] INFO: Pre-calculating index storage
    176. 

  176. [2024-08-27 15:09:03] DEBUG: Mean k-mer frequency: 2.91841
    177. 

  177. [2024-08-27 15:09:03] DEBUG: Repetitive k-mer frequency: 291
    178. 

  178. [2024-08-27 15:09:03] DEBUG: Filtered 0 repetitive k-mers (0)
    179. 

  179. [2024-08-27 15:09:03] INFO: Filling index
    180. 

  180. [2024-08-27 15:09:03] DEBUG: Sorting k-mer index
    181. 

  181. [2024-08-27 15:09:03] DEBUG: Selected k-mers: 7157
    182. 

  182. [2024-08-27 15:09:03] DEBUG: K-mer index size: 20890
    183. 

  183. [2024-08-27 15:09:03] DEBUG: Mean k-mer frequency: 2.91882
    184. 

  184. [2024-08-27 15:09:03] DEBUG: Minimizer rate: 5.55524
    185. 

  185. [2024-08-27 15:09:03] DEBUG: Peak RAM usage: 0 Gb
    186. 

  186. [2024-08-27 15:09:03] DEBUG: Estimating k-mer identity bias
    187.