======== SOAPdenovo2 ========== ['SOAPdenovo-63mer', 'all', '-s', 'SOAPdenovo2.config', '-o', 'SOAPdenovo2', '-K', '55', '-N', '184000000', '-R', '-M', '1', '-L', '200', '-p', '32'] Start time: 2021-06-05 12:43:16.813546 Version 2.04: released on July 13th, 2012 Compile Apr 5 2019 17:00:46 ******************** Pregraph ******************** Parameters: pregraph -s SOAPdenovo2.config -K 55 -p 32 -R -o SOAPdenovo2 In SOAPdenovo2.config, 4 lib(s), maximum read length 100, maximum name length 256. 32 thread(s) initialized. Import reads from file: /local/genbank/workspace/reads.all/20090202_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/20090202_7_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/20090202_8_1_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/20090202_8_2_valid_2P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_6_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_6_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_7_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_8_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_8_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_6_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_6_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_7_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_8_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_8_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB2kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB2kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB4kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB4kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq Time spent on hashing reads: 213s, 70134528 read(s) processed. LIB(s) information: [LIB] 0, avg_ins 339, reverse 0. [LIB] 1, avg_ins 339, reverse 0. [LIB] 2, avg_ins 2000, reverse 0. [LIB] 3, avg_ins 4000, reverse 0. 531804388 node(s) allocated, 2168832259 kmer(s) in reads, 2168832259 kmer(s) processed. done hashing nodes 502899135 linear node(s) marked. Time spent on marking linear nodes: 9s. Time spent on pre-graph construction: 224s. Start to remove frequency-one-kmer tips shorter than 110. Total 14898989 tip(s) removed. 32 thread(s) initialized. 5538253 linear node(s) marked. Start to remove tips with minority links. 3863859 tip(s) removed in cycle 1. 83111 tip(s) removed in cycle 2. 1021 tip(s) removed in cycle 3. 5 tip(s) removed in cycle 4. 0 tip(s) removed in cycle 5. Total 3947996 tip(s) removed. 32 thread(s) initialized. 0 linear node(s) marked. Time spent on removing tips: 693s. 3071558 (1536051) edge(s) and 125554 extra node(s) constructed. Time spent on constructing edges: 233s. In file: SOAPdenovo2.config, max seq len 100, max name len 256. 32 thread(s) initialized. Import reads from file: /local/genbank/workspace/reads.all/20090202_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/20090202_7_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/20090202_8_1_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/20090202_8_2_valid_2P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_6_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_6_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_7_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_8_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_8_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_6_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_6_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_7_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_8_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_8_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB2kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB2kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB4kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB4kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq 70134528 read(s) processed. Time spent on: importing reads: 74s, chopping reads to kmers: 21s, searching kmers: 128s, aligning reads to edges: 28s, searching (K+1)mers: 18s, adding pre-arcs: 22s, recording read paths: 12s. 103765122 marker(s) output. Reads alignment done, 19640268 read(s) deleted, 1723059 pre-arc(s) added. LIB(s) information: [LIB] 0, avg_ins 339, reverse 0. [LIB] 1, avg_ins 339, reverse 0. [LIB] 2, avg_ins 2000, reverse 0. [LIB] 3, avg_ins 4000, reverse 0. Time spent on aligning reads: 311s. 1898417 vertex(es) output. Overall time spent on constructing pre-graph: 24m. ******************** Contig ******************** Parameters: contig -g SOAPdenovo2 -M 1 -R -s SOAPdenovo2.config -p 32 There are 1898417 kmer(s) in vertex file. There are 3071558 edge(s) in edge file. Kmers sorted. 3071558 edge(s) input. 2297876 pre-arcs loaded. 20199556 markers overall. 20199556 markers loaded. 767239 none-palindrome edge(s) swapped, 0 palindrome edge(s) processed. 3071558 edge(s) sorted. Arcs sorted. 4736 repeat(s) are solvable, 9474 more edge(s). 18948 dead arc(s) removed. Time spent on solving repeat: 0s. Start to pinch bubbles, cutoff 0.100000, MAX NODE NUM 3, MAX DIFF NUM 2. 793280 start points, 940552 dheap nodes. 129748 pair(s) found, 12312 pair of path(s) compared, 9213 pair(s) merged. Sequence comparison failed: Path crossing deleted edge 0 Length difference of two paths greater than two 1354 Mismatch score greater than cutoff (2) 965 Mismatch score ratio greater than cutoff (0.1) 0 Path length shorter than (Kmer-1) 780 DFibHeap: 40071 node(s) allocated. 59421 edge(s) concatenated in cycle 1. 610 edge(s) concatenated in cycle 2. 1 edge(s) concatenated in cycle 3. 0 edge(s) concatenated in cycle 4. Time spent on pinching bubbles: 4s. Start to destroy weak inner edges. 33535 weak inner edge(s) destroyed in cycle 1. 336 weak inner edge(s) destroyed in cycle 2. 0 weak inner edge(s) destroyed in cycle 3. 66931 dead arc(s) removed. 18751 inner edge(s) with coverage lower than or equal to 1 destroyed. 39072 dead arc(s) removed. 81772 edge(s) concatenated in cycle 1. 213 edge(s) concatenated in cycle 2. 0 edge(s) concatenated in cycle 3. Before compacting, 3081032 edge(s) existed. After compacting, 2671948 edge(s) left. Strict: 0, cutoff length: 110. 514054 tips cut in cycle 1. 48974 tips cut in cycle 2. 9038 tips cut in cycle 3. 2808 tips cut in cycle 4. 1277 tips cut in cycle 5. 720 tips cut in cycle 6. 516 tips cut in cycle 7. 314 tips cut in cycle 8. 216 tips cut in cycle 9. 163 tips cut in cycle 10. 104 tips cut in cycle 11. 90 tips cut in cycle 12. 67 tips cut in cycle 13. 65 tips cut in cycle 14. 55 tips cut in cycle 15. 33 tips cut in cycle 16. 27 tips cut in cycle 17. 23 tips cut in cycle 18. 14 tips cut in cycle 19. 8 tips cut in cycle 20. 3 tips cut in cycle 21. 3 tips cut in cycle 22. 4 tips cut in cycle 23. 7 tips cut in cycle 24. 1 tips cut in cycle 25. 3 tips cut in cycle 26. 4 tips cut in cycle 27. 3 tips cut in cycle 28. 5 tips cut in cycle 29. 5 tips cut in cycle 30. 4 tips cut in cycle 31. 0 tips cut in cycle 32. 211285 dead arc(s) removed. 163522 edge(s) concatenated in cycle 1. 3138 edge(s) concatenated in cycle 2. 6 edge(s) concatenated in cycle 3. 1 edge(s) concatenated in cycle 4. 0 edge(s) concatenated in cycle 5. Before compacting, 2671948 edge(s) existed. After compacting, 1181398 edge(s) left. There are 493180 contig(s) longer than 100, sum up 157064411 bp, with average length 318. The longest length is 39531 bp, contig N50 is 329 bp,contig N90 is 180 bp. 590967 contig(s) longer than 56 output. Time spent on constructing contig: 1m. ******************** Map ******************** Parameters: map -s SOAPdenovo2.config -g SOAPdenovo2 -p 32 -K 55 Kmer size: 55. Contig length cutoff: 57. 590967 contig(s), maximum sequence length 39531, minimum sequence length 56, maximum name length 10. Time spent on parsing contigs file: 0s. 32 thread(s) initialized. Time spent on hashing contigs: 12s. 131580211 node(s) allocated, 131795875 kmer(s) in contigs, 131795875 kmer(s) processed. Time spent on graph construction: 13s. Time spent on aligning long reads: 0s. In file: SOAPdenovo2.config, max seq len 100, max name len 256 32 thread(s) initialized. 1181398 edge(s) in the graph. Import reads from file: /local/genbank/workspace/reads.all/20090202_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/20090202_7_2_2P.fastq.corrected.fq Current insert size is 339, map_len is 32. Import reads from file: /local/genbank/workspace/reads.all/20090202_8_1_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/20090202_8_2_valid_2P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_6_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_6_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_7_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_8_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae6.2GB_8_2_2P.fastq.corrected.fq Current insert size is 339, map_len is 32. Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_6_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_6_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_7_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_7_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_8_1_1P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/Algae7.2GB_8_2_2P.fastq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB2kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB2kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq Current insert size is 2000, map_len is 35. Import reads from file: /local/genbank/workspace/reads.all/AB4kb_R1.illumina-1.8+_valid_1P.fq.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB4kb_R2.illumina-1.8+_valid_2P.fq.corrected.fq Current insert size is 4000, map_len is 35. Total reads 70134528 Reads in gaps 20091542 Ratio 28.6% Reads on contigs 51916779 Ratio 74.0% 4 pe insert size, the largest boundary is 70134528. LIB(s) information: [LIB] 0, avg_ins 339, reverse 0. [LIB] 1, avg_ins 339, reverse 0. [LIB] 2, avg_ins 2000, reverse 0. [LIB] 3, avg_ins 4000, reverse 0. Time spent on aligning reads: 639s. Overall time spent on alignment: 10m. ******************** Scaff ******************** Parameters: scaff -g SOAPdenovo2 -p 32 -L 200 -N 184000000 gzip: stdout: Broken pipe Files for scaffold construction are OK. There are 4 grad(s), 70134528 read(s), max read len 100. Kmer size: 55 There are 1181398 edge(s) in edge file. Mask contigs with coverage lower than 0.7 or higher than 14.0, and strict length 0. Average contig coverage is 7, 154325 contig(s) masked. Mask contigs shorter than 200, 641834 contig(s) masked. 405762 arc(s) loaded, average weight is 7. 590967 contig(s) loaded. Done loading updated edges. Time spent on loading updated edges: 14s. ***************************************************** Start to load paired-end reads information. For insert size: 339 Total PE links 2601528 Normal PE links on same contig 769586 Incorrect oriented PE links 89 PE links of too small insert size 32320 PE links of too large insert size 0 Correct PE links 1799307 Accumulated connections 1129330 Use contigs longer than 339 to estimate insert size: PE links 645376 Average insert size 240 SD 68 564665 new connections. For insert size: 339 Total PE links 7103915 Normal PE links on same contig 2605372 Incorrect oriented PE links 171 PE links of too small insert size 24223 PE links of too large insert size 0 Correct PE links 4473278 Accumulated connections 1709726 Use contigs longer than 339 to estimate insert size: PE links 2112007 Average insert size 241 SD 68 854863 new connections. For insert size: 2000 Total PE links 7628300 Normal PE links on same contig 445590 Incorrect oriented PE links 973 PE links of too small insert size 2139035 PE links of too large insert size 0 Correct PE links 4816114 Accumulated connections 8618578 Use contigs longer than 2000 to estimate insert size: PE links 217475 Average insert size 308 SD 134 4309289 new connections. For insert size: 4000 Total PE links 3569781 Normal PE links on same contig 706845 Incorrect oriented PE links 486 PE links of too small insert size 37789 PE links of too large insert size 0 Correct PE links 2784463 Accumulated connections 2017018 Use contigs longer than 4000 to estimate insert size: PE links 35994 Average insert size 254 SD 66 1008509 new connections. All paired-end reads information loaded. Time spent on loading paired-end reads information: 72s. ***************************************************** Start to construct scaffolds. *************************** For insert size: 339 Total PE links 1419530 PE links to masked contigs 1344159 On same scaffold PE links 0 Report from smallScaf: 0 scaffolds by smallPE. *************************** For insert size: 2000 Total PE links 4309290 PE links to masked contigs 3479645 On same scaffold PE links 0 *************************** For insert size: 4000 Total PE links 1008509 PE links to masked contigs 846961 On same scaffold PE links 0 Cutoff of PE links to make a reliable connection: 5 Report from checkScaf: 0 scaffold segments broken. Active connections 2008154 Weak connections 1839456 Weak ratio 91.6% 428 circles removed. Start to remove transitive connection. Total contigs 1181398 Masked contigs 797871 Remained contigs 383527 None-outgoing-connection contigs 255879 (66.717339%) Single-outgoing-connection contigs 99928 Multi-outgoing-connection contigs 6139 Cycle 1 Two-outgoing-connection contigs 21581 Potential transitive connections 7704 Transitive connections 4265 Transitive ratio 19.8% Cycle 2 Two-outgoing-connection contigs 17046 Potential transitive connections 3434 Transitive connections 30 Transitive ratio 0.2% Cycle 3 Two-outgoing-connection contigs 17016 Potential transitive connections 3404 Transitive connections 0 Transitive ratio 0.0% Start to linearize sub-graph. Picked sub-graphs 15802 Connection-conflict 351 Significant overlapping 12039 Eligible 10 Bubble structures 0 Mask repeats: Puzzles 7722 Masked contigs 4209 Start to remove transitive connection. Total contigs 1181398 Masked contigs 806289 Remained contigs 375109 None-outgoing-connection contigs 252165 (67.224464%) Single-outgoing-connection contigs 120879 Multi-outgoing-connection contigs 195 Cycle 1 Two-outgoing-connection contigs 1870 Potential transitive connections 1215 Transitive connections 484 Transitive ratio 25.9% Cycle 2 Two-outgoing-connection contigs 1372 Potential transitive connections 735 Transitive connections 5 Transitive ratio 0.4% Cycle 3 Two-outgoing-connection contigs 1367 Potential transitive connections 730 Transitive connections 0 Transitive ratio 0.0% Start to linearize sub-graph. Picked sub-graphs 1209 Connection-conflict 64 Significant overlapping 799 Eligible 0 Bubble structures 0 Non-strict linearization. Start to linearize sub-graph. Picked sub-graphs 708 Connection-conflict 64 Significant overlapping 534 Eligible 0 Bubble structures 0 Start to mask puzzles. Masked contigs 341 Remained puzzles 0 Freezing done. Recover contigs. Total recovered contigs 61 Single-route cases 60 Multi-route cases 1 All links loaded. Time spent on constructing scaffolds: 28s. The final rank ******************************* Scaffold number 27237 In-scaffold contig number 493068 Total scaffold length 126142673 Average scaffold length 4631 Filled gap number 86 Longest scaffold 187307 Scaffold and singleton number 433211 Scaffold and singleton length 213759359 Average length 493 N50 4172 N90 149 Weak points 0 ******************************* 1000 scaffolds processed. 2000 scaffolds processed. 3000 scaffolds processed. 4000 scaffolds processed. 5000 scaffolds processed. 6000 scaffolds processed. 7000 scaffolds processed. 8000 scaffolds processed. 9000 scaffolds processed. 10000 scaffolds processed. 11000 scaffolds processed. 12000 scaffolds processed. 13000 scaffolds processed. 14000 scaffolds processed. 15000 scaffolds processed. 16000 scaffolds processed. 17000 scaffolds processed. 18000 scaffolds processed. 19000 scaffolds processed. 20000 scaffolds processed. 21000 scaffolds processed. 22000 scaffolds processed. 23000 scaffolds processed. 24000 scaffolds processed. 25000 scaffolds processed. 26000 scaffolds processed. 27000 scaffolds processed. Done with 27237 scaffolds, 0 gaps finished, 60157 gaps overall. Overall time spent on constructing scaffolds: 74m. Time for the whole pipeline: 110m. Finish time: 2021-06-05 14:33:58.747574 Elapsed time: 1:50:41.934028