======== SOAPdenovo2 ========== ['SOAPdenovo-63mer', 'all', '-s', 'SOAPdenovo2-1.config', '-o', 'SOAPdenovo2-1', '-K', '41', '-N', '184000000', '-R', '-M', '1', '-L', '200', '-p', '32'] Start time: 2021-06-03 19:54:22.255806 Version 2.04: released on July 13th, 2012 Compile Apr 5 2019 17:00:46 ******************** Pregraph ******************** Parameters: pregraph -s SOAPdenovo2-1.config -K 41 -p 32 -R -o SOAPdenovo2-1 In SOAPdenovo2-1.config, 5 lib(s), maximum read length 100, maximum name length 256. 32 thread(s) initialized. Import reads from file: /local/genbank/workspace/reads.all/2008SE.fq Import reads from file: /local/genbank/workspace/reads.all/20090202.pollux.unpaired.fq Import reads from file: /local/genbank/workspace/reads.all/367GB.fq Import reads from file: /local/genbank/workspace/reads.all/454.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB4kbUnpaired.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/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/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: 403s, 92789812 read(s) processed. LIB(s) information: [LIB] 0, avg_ins 0, reverse 0. [LIB] 1, avg_ins 239, reverse 0. [LIB] 2, avg_ins 300, reverse 0. [LIB] 3, avg_ins 2000, reverse 0. [LIB] 4, avg_ins 4000, reverse 0. 620804727 node(s) allocated, 3909413254 kmer(s) in reads, 3909413254 kmer(s) processed. done hashing nodes 591143994 linear node(s) marked. Time spent on marking linear nodes: 8s. Time spent on pre-graph construction: 411s. Start to remove frequency-one-kmer tips shorter than 82. Total 13341149 tip(s) removed. 32 thread(s) initialized. 7234516 linear node(s) marked. Start to remove tips with minority links. 2816345 tip(s) removed in cycle 1. 35071 tip(s) removed in cycle 2. 227 tip(s) removed in cycle 3. 0 tip(s) removed in cycle 4. Total 2851643 tip(s) removed. 32 thread(s) initialized. 0 linear node(s) marked. Time spent on removing tips: 355s. 13933990 (6968176) edge(s) and 744291 extra node(s) constructed. Time spent on constructing edges: 453s. In file: SOAPdenovo2-1.config, max seq len 100, max name len 256. 32 thread(s) initialized. Import reads from file: /local/genbank/workspace/reads.all/2008SE.fq Import reads from file: /local/genbank/workspace/reads.all/20090202.pollux.unpaired.fq Import reads from file: /local/genbank/workspace/reads.all/367GB.fq Import reads from file: /local/genbank/workspace/reads.all/454.corrected.fq Import reads from file: /local/genbank/workspace/reads.all/AB4kbUnpaired.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/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/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 92789812 read(s) processed. Time spent on: importing reads: 76s, chopping reads to kmers: 12s, searching kmers: 173s, aligning reads to edges: 27s, searching (K+1)mers: 77s, adding pre-arcs: 81s, recording read paths: 40s. 704963810 marker(s) output. Reads alignment done, 8425372 read(s) deleted, 12067582 pre-arc(s) added. LIB(s) information: [LIB] 0, avg_ins 0, reverse 0. [LIB] 1, avg_ins 239, reverse 0. [LIB] 2, avg_ins 300, reverse 0. [LIB] 3, avg_ins 2000, reverse 0. [LIB] 4, avg_ins 4000, reverse 0. Time spent on aligning reads: 506s. 5665643 vertex(es) output. Overall time spent on constructing pre-graph: 29m. ******************** Contig ******************** Parameters: contig -g SOAPdenovo2-1 -M 1 -R -s SOAPdenovo2-1.config -p 32 There are 5665643 kmer(s) in vertex file. There are 13933990 edge(s) in edge file. Kmers sorted. 13933990 edge(s) input. 16131926 pre-arcs loaded. 204009682 markers overall. 204009682 markers loaded. 3483106 none-palindrome edge(s) swapped, 0 palindrome edge(s) processed. 13933990 edge(s) sorted. Arcs sorted. 20193 repeat(s) are solvable, 40394 more edge(s). 80788 dead arc(s) removed. Time spent on solving repeat: 4s. Start to pinch bubbles, cutoff 0.100000, MAX NODE NUM 3, MAX DIFF NUM 2. 1073438 start points, 9457141 dheap nodes. 2339196 pair(s) found, 85558 pair of path(s) compared, 59845 pair(s) merged. Sequence comparison failed: Path crossing deleted edge 0 Length difference of two paths greater than two 12408 Mismatch score greater than cutoff (2) 5965 Mismatch score ratio greater than cutoff (0.1) 0 Path length shorter than (Kmer-1) 7340 DFibHeap: 472373 node(s) allocated. 393089 edge(s) concatenated in cycle 1. 3461 edge(s) concatenated in cycle 2. 0 edge(s) concatenated in cycle 3. Time spent on pinching bubbles: 27s. Start to destroy weak inner edges. 866950 weak inner edge(s) destroyed in cycle 1. 3113 weak inner edge(s) destroyed in cycle 2. 11 weak inner edge(s) destroyed in cycle 3. 0 weak inner edge(s) destroyed in cycle 4. 1732563 dead arc(s) removed. 229424 inner edge(s) with coverage lower than or equal to 1 destroyed. 466000 dead arc(s) removed. 1771314 edge(s) concatenated in cycle 1. 83098 edge(s) concatenated in cycle 2. 356 edge(s) concatenated in cycle 3. 0 edge(s) concatenated in cycle 4. Before compacting, 13974384 edge(s) existed. After compacting, 7147274 edge(s) left. Strict: 0, cutoff length: 82. 994090 tips cut in cycle 1. 100405 tips cut in cycle 2. 14831 tips cut in cycle 3. 3857 tips cut in cycle 4. 1522 tips cut in cycle 5. 717 tips cut in cycle 6. 483 tips cut in cycle 7. 427 tips cut in cycle 8. 281 tips cut in cycle 9. 167 tips cut in cycle 10. 102 tips cut in cycle 11. 47 tips cut in cycle 12. 36 tips cut in cycle 13. 14 tips cut in cycle 14. 9 tips cut in cycle 15. 7 tips cut in cycle 16. 18 tips cut in cycle 17. 18 tips cut in cycle 18. 10 tips cut in cycle 19. 6 tips cut in cycle 20. 2 tips cut in cycle 21. 1 tips cut in cycle 22. 6 tips cut in cycle 23. 3 tips cut in cycle 24. 4 tips cut in cycle 25. 0 tips cut in cycle 26. 708064 dead arc(s) removed. 540881 edge(s) concatenated in cycle 1. 7655 edge(s) concatenated in cycle 2. 0 edge(s) concatenated in cycle 3. Before compacting, 7147274 edge(s) existed. After compacting, 3816076 edge(s) left. There are 889347 contig(s) longer than 100, sum up 258154394 bp, with average length 290. The longest length is 12716 bp, contig N50 is 347 bp,contig N90 is 146 bp. 1909066 contig(s) longer than 42 output. Time spent on constructing contig: 3m. ******************** Map ******************** Parameters: map -s SOAPdenovo2-1.config -g SOAPdenovo2-1 -p 32 -K 41 Kmer size: 41. Contig length cutoff: 43. 1909066 contig(s), maximum sequence length 12716, minimum sequence length 42, maximum name length 10. Time spent on parsing contigs file: 1s. 32 thread(s) initialized. Time spent on hashing contigs: 20s. 241722077 node(s) allocated, 243443470 kmer(s) in contigs, 243443470 kmer(s) processed. Time spent on graph construction: 21s. Time spent on aligning long reads: 0s. In file: SOAPdenovo2-1.config, max seq len 100, max name len 256 32 thread(s) initialized. 3816076 edge(s) in the graph. 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 Current insert size is 239, map_len is 32. 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/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 Current insert size is 300, 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 27748679 Ratio 39.6% Reads on contigs 59126022 Ratio 84.3% 4 pe insert size, the largest boundary is 70134528. LIB(s) information: [LIB] 0, avg_ins 0, reverse 0. [LIB] 1, avg_ins 239, reverse 0. [LIB] 2, avg_ins 300, reverse 0. [LIB] 3, avg_ins 2000, reverse 0. [LIB] 4, avg_ins 4000, reverse 0. Time spent on aligning reads: 656s. Overall time spent on alignment: 11m. ******************** Scaff ******************** Parameters: scaff -g SOAPdenovo2-1 -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: 41 There are 3816076 edge(s) in edge file. Mask contigs with coverage lower than 0.8 or higher than 16.0, and strict length 100. Average contig coverage is 8, 1342629 contig(s) masked. Mask contigs shorter than 200, 1813253 contig(s) masked. 3697302 arc(s) loaded, average weight is 8. 1909066 contig(s) loaded. Done loading updated edges. Time spent on loading updated edges: 28s. ***************************************************** Start to load paired-end reads information. For insert size: 239 Total PE links 4463096 Normal PE links on same contig 1211579 Incorrect oriented PE links 1554 PE links of too small insert size 306402 PE links of too large insert size 0 Correct PE links 2943338 Accumulated connections 2380964 Use contigs longer than 239 to estimate insert size: PE links 1122357 Average insert size 240 SD 67 1190482 new connections. For insert size: 300 Total PE links 8183249 Normal PE links on same contig 2779175 Incorrect oriented PE links 4574 PE links of too small insert size 137365 PE links of too large insert size 0 Correct PE links 5261644 Accumulated connections 3426880 Use contigs longer than 300 to estimate insert size: PE links 2472324 Average insert size 246 SD 66 1713440 new connections. For insert size: 2000 Total PE links 9236470 Normal PE links on same contig 251040 Incorrect oriented PE links 170 PE links of too small insert size 10134 PE links of too large insert size 0 Correct PE links 8974457 Accumulated connections 16287522 Use contigs longer than 2000 to estimate insert size: PE links 1886 Average insert size 306 SD 95 8143761 new connections. For insert size: 4000 Total PE links 4320347 Normal PE links on same contig 844341 Incorrect oriented PE links 521 PE links of too small insert size 3038 PE links of too large insert size 0 Correct PE links 3469414 Accumulated connections 2731630 Use contigs longer than 4000 to estimate insert size: PE links 2089 Average insert size 261 SD 67 1365815 new connections. All paired-end reads information loaded. Time spent on loading paired-end reads information: 82s. ***************************************************** Start to construct scaffolds. *************************** For insert size: 239 Total PE links 1190483 PE links to masked contigs 1134068 On same scaffold PE links 0 *************************** For insert size: 300 Total PE links 1713441 PE links to masked contigs 1605996 On same scaffold PE links 0 Report from smallScaf: 0 scaffolds by smallPE. *************************** For insert size: 2000 Total PE links 8143762 PE links to masked contigs 7051730 On same scaffold PE links 0 *************************** For insert size: 4000 Total PE links 1365815 PE links to masked contigs 1051169 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 2899776 Weak connections 2626316 Weak ratio 90.6% 341 circles removed. Start to remove transitive connection. Total contigs 3816076 Masked contigs 3157246 Remained contigs 658830 None-outgoing-connection contigs 435678 (66.129044%) Single-outgoing-connection contigs 182727 Multi-outgoing-connection contigs 6128 Cycle 1 Two-outgoing-connection contigs 34297 Potential transitive connections 16344 Transitive connections 8799 Transitive ratio 25.7% Cycle 2 Two-outgoing-connection contigs 25073 Potential transitive connections 7522 Transitive connections 60 Transitive ratio 0.2% Cycle 3 Two-outgoing-connection contigs 25011 Potential transitive connections 7463 Transitive connections 0 Transitive ratio 0.0% Start to linearize sub-graph. Picked sub-graphs 22529 Connection-conflict 832 Significant overlapping 15102 Eligible 12 Bubble structures 0 Mask repeats: Puzzles 10905 Masked contigs 6331 Start to remove transitive connection. Total contigs 3816076 Masked contigs 3169908 Remained contigs 646168 None-outgoing-connection contigs 426662 (66.029579%) Single-outgoing-connection contigs 216569 Multi-outgoing-connection contigs 237 Cycle 1 Two-outgoing-connection contigs 2700 Potential transitive connections 1749 Transitive connections 727 Transitive ratio 26.9% Cycle 2 Two-outgoing-connection contigs 1956 Potential transitive connections 1027 Transitive connections 5 Transitive ratio 0.3% Cycle 3 Two-outgoing-connection contigs 1951 Potential transitive connections 1022 Transitive connections 0 Transitive ratio 0.0% Start to linearize sub-graph. Picked sub-graphs 1869 Connection-conflict 148 Significant overlapping 1262 Eligible 1 Bubble structures 0 Non-strict linearization. Start to linearize sub-graph. Picked sub-graphs 1015 Connection-conflict 99 Significant overlapping 624 Eligible 1 Bubble structures 0 Start to mask puzzles. Masked contigs 402 Remained puzzles 0 Freezing done. Recover contigs. Total recovered contigs 155 Single-route cases 152 Multi-route cases 2 All links loaded. Time spent on constructing scaffolds: 45s. The final rank ******************************* Scaffold number 47717 In-scaffold contig number 889143 Total scaffold length 224171268 Average scaffold length 4697 Filled gap number 9085 Longest scaffold 146875 Scaffold and singleton number 782318 Scaffold and singleton length 368237878 Average length 470 N50 4108 N90 140 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. 28000 scaffolds processed. 29000 scaffolds processed. 30000 scaffolds processed. 31000 scaffolds processed. 32000 scaffolds processed. 33000 scaffolds processed. 34000 scaffolds processed. 35000 scaffolds processed. 36000 scaffolds processed. 37000 scaffolds processed. 38000 scaffolds processed. 39000 scaffolds processed. 40000 scaffolds processed. 41000 scaffolds processed. 42000 scaffolds processed. 43000 scaffolds processed. 44000 scaffolds processed. 45000 scaffolds processed. 46000 scaffolds processed. 47000 scaffolds processed. Done with 47717 scaffolds, 0 gaps finished, 107540 gaps overall. Overall time spent on constructing scaffolds: 129m. Time for the whole pipeline: 173m. Finish time: 2021-06-03 22:47:43.567598 Elapsed time: 2:53:21.311792