======== SOAPdenovo2 ========== ['SOAPdenovo-63mer', 'all', '-s', 'SOAPdenovo2-1.config', '-o', 'SOAPdenovo2-1', '-K', '55', '-N', '184000000', '-R', '-M', '1', '-L', '200', '-p', '32'] Start time: 2021-06-12 09:42:19.147763 Version 2.04: released on July 13th, 2012 Compile Apr 5 2019 17:00:46 ******************** Pregraph ******************** Parameters: pregraph -s SOAPdenovo2-1.config -K 55 -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.all3/2008-09allU.fq Import reads from file: /local/genbank/workspace/reads.all3/3-6.2-7.2GBallU.fq Import reads from file: /local/genbank/workspace/reads.all3/AGRFUall.fq Import reads from file: /local/genbank/workspace/reads.all3/454U.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_7_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_8_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_6_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_6_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_7_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_8_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_6_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_6_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_7_R2.fq --- 100000000th reads. Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_8_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/AB2kb_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/AB2kb_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/AB4kb_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/AB4kb_R2.fq --- 200000000th reads. Time spent on hashing reads: 827s, 209710528 read(s) processed. LIB(s) information: [LIB] 0, avg_ins 0, reverse 0. [LIB] 1, avg_ins 239, reverse 0. [LIB] 2, avg_ins 239, reverse 0. [LIB] 3, avg_ins 1600, reverse 0. [LIB] 4, avg_ins 2200, reverse 0. 885476656 node(s) allocated, 5080058533 kmer(s) in reads, 5080058533 kmer(s) processed. done hashing nodes 824841220 linear node(s) marked. Time spent on marking linear nodes: 15s. Time spent on pre-graph construction: 843s. Start to remove frequency-one-kmer tips shorter than 110. Total 29569320 tip(s) removed. 32 thread(s) initialized. 13020258 linear node(s) marked. Start to remove tips with minority links. 6749472 tip(s) removed in cycle 1. 119403 tip(s) removed in cycle 2. 1489 tip(s) removed in cycle 3. 11 tip(s) removed in cycle 4. 0 tip(s) removed in cycle 5. Total 6870375 tip(s) removed. 32 thread(s) initialized. 0 linear node(s) marked. Time spent on removing tips: 1702s. 4587772 (2294354) edge(s) and 248108 extra node(s) constructed. Time spent on constructing edges: 843s. 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.all3/2008-09allU.fq Import reads from file: /local/genbank/workspace/reads.all3/3-6.2-7.2GBallU.fq Import reads from file: /local/genbank/workspace/reads.all3/AGRFUall.fq Import reads from file: /local/genbank/workspace/reads.all3/454U.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_7_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_8_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_6_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_6_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_7_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_8_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_6_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_6_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_7_R2.fq --- 100000000th reads. Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_8_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/AB2kb_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/AB2kb_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/AB4kb_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/AB4kb_R2.fq --- 200000000th reads. 209710528 read(s) processed. Time spent on: importing reads: 265s, chopping reads to kmers: 64s, searching kmers: 477s, aligning reads to edges: 97s, searching (K+1)mers: 102s, adding pre-arcs: 76s, recording read paths: 50s. 287072320 marker(s) output. Reads alignment done, 36044497 read(s) deleted, 3151340 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 239, reverse 0. [LIB] 3, avg_ins 1600, reverse 0. [LIB] 4, avg_ins 2200, reverse 0. Time spent on aligning reads: 1145s. 2521411 vertex(es) output. Overall time spent on constructing pre-graph: 76m. ******************** Contig ******************** Parameters: contig -g SOAPdenovo2-1 -M 1 -R -s SOAPdenovo2-1.config -p 32 There are 2521411 kmer(s) in vertex file. There are 4587772 edge(s) in edge file. Kmers sorted. 4587772 edge(s) input. 4051902 pre-arcs loaded. 42251782 markers overall. 42251782 markers loaded. 1145195 none-palindrome edge(s) swapped, 0 palindrome edge(s) processed. 4587772 edge(s) sorted. Arcs sorted. 7173 repeat(s) are solvable, 14350 more edge(s). 28700 dead arc(s) removed. Time spent on solving repeat: 1s. Start to pinch bubbles, cutoff 0.100000, MAX NODE NUM 3, MAX DIFF NUM 2. 918883 start points, 1762035 dheap nodes. 280210 pair(s) found, 24942 pair of path(s) compared, 18210 pair(s) merged. Sequence comparison failed: Path crossing deleted edge 0 Length difference of two paths greater than two 2324 Mismatch score greater than cutoff (2) 2516 Mismatch score ratio greater than cutoff (0.1) 0 Path length shorter than (Kmer-1) 1892 DFibHeap: 76772 node(s) allocated. 102672 edge(s) concatenated in cycle 1. 1438 edge(s) concatenated in cycle 2. 2 edge(s) concatenated in cycle 3. 0 edge(s) concatenated in cycle 4. Time spent on pinching bubbles: 9s. Start to destroy weak inner edges. 63684 weak inner edge(s) destroyed in cycle 1. 615 weak inner edge(s) destroyed in cycle 2. 9 weak inner edge(s) destroyed in cycle 3. 1 weak inner edge(s) destroyed in cycle 4. 0 weak inner edge(s) destroyed in cycle 5. 127196 dead arc(s) removed. 32532 inner edge(s) with coverage lower than or equal to 1 destroyed. 67575 dead arc(s) removed. 147323 edge(s) concatenated in cycle 1. 625 edge(s) concatenated in cycle 2. 0 edge(s) concatenated in cycle 3. Before compacting, 4602122 edge(s) existed. After compacting, 3864820 edge(s) left. Strict: 0, cutoff length: 110. 718484 tips cut in cycle 1. 86559 tips cut in cycle 2. 15228 tips cut in cycle 3. 4554 tips cut in cycle 4. 1946 tips cut in cycle 5. 1012 tips cut in cycle 6. 649 tips cut in cycle 7. 409 tips cut in cycle 8. 284 tips cut in cycle 9. 237 tips cut in cycle 10. 163 tips cut in cycle 11. 137 tips cut in cycle 12. 99 tips cut in cycle 13. 82 tips cut in cycle 14. 71 tips cut in cycle 15. 76 tips cut in cycle 16. 37 tips cut in cycle 17. 35 tips cut in cycle 18. 19 tips cut in cycle 19. 20 tips cut in cycle 20. 19 tips cut in cycle 21. 10 tips cut in cycle 22. 15 tips cut in cycle 23. 7 tips cut in cycle 24. 7 tips cut in cycle 25. 3 tips cut in cycle 26. 1 tips cut in cycle 27. 2 tips cut in cycle 28. 5 tips cut in cycle 29. 3 tips cut in cycle 30. 5 tips cut in cycle 31. 3 tips cut in cycle 32. 1 tips cut in cycle 33. 0 tips cut in cycle 34. 362958 dead arc(s) removed. 286981 edge(s) concatenated in cycle 1. 6410 edge(s) concatenated in cycle 2. 25 edge(s) concatenated in cycle 3. 0 edge(s) concatenated in cycle 4. Before compacting, 3864820 edge(s) existed. After compacting, 1617624 edge(s) left. There are 589777 contig(s) longer than 100, sum up 271354402 bp, with average length 460. The longest length is 110960 bp, contig N50 is 656 bp,contig N90 is 196 bp. 809271 contig(s) longer than 56 output. Time spent on constructing contig: 2m. ******************** Map ******************** Parameters: map -s SOAPdenovo2-1.config -g SOAPdenovo2-1 -p 32 -K 55 Kmer size: 55. Contig length cutoff: 57. 809271 contig(s), maximum sequence length 110960, minimum sequence length 56, maximum name length 10. Time spent on parsing contigs file: 1s. 32 thread(s) initialized. Time spent on hashing contigs: 25s. 241801881 node(s) allocated, 242287494 kmer(s) in contigs, 242287494 kmer(s) processed. Time spent on graph construction: 26s. Time spent on aligning long reads: 0s. In file: SOAPdenovo2-1.config, max seq len 100, max name len 256 32 thread(s) initialized. 1617624 edge(s) in the graph. Import reads from file: /local/genbank/workspace/reads.all3/20090202_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_7_R2.fq Current insert size is 239, map_len is 32. Import reads from file: /local/genbank/workspace/reads.all3/20090202_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/20090202_8_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_6_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_6_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_7_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae6.2_8_R2.fq Current insert size is 239, map_len is 32. Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_6_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_6_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_7_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_7_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_8_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/Algae7.2GB_8_R2.fq Import reads from file: /local/genbank/workspace/reads.all3/AB2kb_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/AB2kb_R2.fq Current insert size is 1600, map_len is 35. --- 100000000th reads. Import reads from file: /local/genbank/workspace/reads.all3/AB4kb_R1.fq Import reads from file: /local/genbank/workspace/reads.all3/AB4kb_R2.fq Current insert size is 2200, map_len is 35. Total reads 160910394 Reads in gaps 40113951 Ratio 24.9% Reads on contigs 126864268 Ratio 78.8% 4 pe insert size, the largest boundary is 160910394. LIB(s) information: [LIB] 0, avg_ins 0, reverse 0. [LIB] 1, avg_ins 239, reverse 0. [LIB] 2, avg_ins 239, reverse 0. [LIB] 3, avg_ins 1600, reverse 0. [LIB] 4, avg_ins 2200, reverse 0. Time spent on aligning reads: 2437s. Overall time spent on alignment: 41m. ******************** 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), 160910394 read(s), max read len 100. Kmer size: 55 There are 1617624 edge(s) in edge file. Mask contigs with coverage lower than 1.1 or higher than 22.0, and strict length 0. Average contig coverage is 11, 268579 contig(s) masked. Mask contigs shorter than 200, 765952 contig(s) masked. 942514 arc(s) loaded, average weight is 9. 809271 contig(s) loaded. Done loading updated edges. Time spent on loading updated edges: 38s. ***************************************************** Start to load paired-end reads information. For insert size: 239 Total PE links 6616637 Normal PE links on same contig 3075459 Incorrect oriented PE links 3169 PE links of too small insert size 520809 PE links of too large insert size 0 Correct PE links 3016831 Accumulated connections 1907644 Use contigs longer than 239 to estimate insert size: PE links 2995320 Average insert size 248 SD 66 953822 new connections. For insert size: 239 Total PE links 17937038 Normal PE links on same contig 10309901 Incorrect oriented PE links 7335 PE links of too small insert size 1113824 PE links of too large insert size 0 Correct PE links 6504835 Accumulated connections 2836138 Use contigs longer than 239 to estimate insert size: PE links 10074692 Average insert size 251 SD 65 1418069 new connections. For insert size: 1600 Total PE links 19634840 Normal PE links on same contig 1084437 Incorrect oriented PE links 3084 PE links of too small insert size 10268372 PE links of too large insert size 0 Correct PE links 7317089 Accumulated connections 12990652 Use contigs longer than 1600 to estimate insert size: PE links 753531 Average insert size 314 SD 346 6495326 new connections. For insert size: 2200 Total PE links 8226130 Normal PE links on same contig 1846440 Incorrect oriented PE links 1612 PE links of too small insert size 906027 PE links of too large insert size 0 Correct PE links 4954323 Accumulated connections 3094246 Use contigs longer than 2200 to estimate insert size: PE links 633645 Average insert size 256 SD 228 1547123 new connections. All paired-end reads information loaded. Time spent on loading paired-end reads information: 260s. ***************************************************** Start to construct scaffolds. *************************** For insert size: 239 Total PE links 2371893 PE links to masked contigs 2195724 On same scaffold PE links 0 Report from smallScaf: 0 scaffolds by smallPE. *************************** For insert size: 1600 Total PE links 6495327 PE links to masked contigs 5072146 On same scaffold PE links 0 *************************** For insert size: 2200 Total PE links 1547123 PE links to masked contigs 1180203 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 3621210 Weak connections 3223768 Weak ratio 89.0% 2896 circles removed. Start to remove transitive connection. Total contigs 1617624 Masked contigs 1046115 Remained contigs 571509 None-outgoing-connection contigs 309695 (54.188995%) Single-outgoing-connection contigs 187003 Multi-outgoing-connection contigs 17403 Cycle 1 Two-outgoing-connection contigs 57408 Potential transitive connections 14486 Transitive connections 6748 Transitive ratio 11.8% Cycle 2 Two-outgoing-connection contigs 50288 Potential transitive connections 7716 Transitive connections 12 Transitive ratio 0.0% Cycle 3 Two-outgoing-connection contigs 50276 Potential transitive connections 7704 Transitive connections 0 Transitive ratio 0.0% Start to linearize sub-graph. Picked sub-graphs 55274 Connection-conflict 909 Significant overlapping 45633 Eligible 86 Bubble structures 0 Mask repeats: Puzzles 29238 Masked contigs 19180 Start to remove transitive connection. Total contigs 1617624 Masked contigs 1084475 Remained contigs 533149 None-outgoing-connection contigs 316037 (59.277428%) Single-outgoing-connection contigs 211447 Multi-outgoing-connection contigs 348 Cycle 1 Two-outgoing-connection contigs 5317 Potential transitive connections 3399 Transitive connections 1786 Transitive ratio 33.6% Cycle 2 Two-outgoing-connection contigs 3494 Potential transitive connections 1622 Transitive connections 5 Transitive ratio 0.1% Cycle 3 Two-outgoing-connection contigs 3489 Potential transitive connections 1617 Transitive connections 0 Transitive ratio 0.0% Start to linearize sub-graph. Picked sub-graphs 3183 Connection-conflict 28 Significant overlapping 1990 Eligible 0 Bubble structures 0 Non-strict linearization. Start to linearize sub-graph. Picked sub-graphs 1704 Connection-conflict 22 Significant overlapping 1270 Eligible 0 Bubble structures 0 Start to mask puzzles. Masked contigs 764 Remained puzzles 1 Freezing done. Recover contigs. Total recovered contigs 179 Single-route cases 163 Multi-route cases 8 All links loaded. Time spent on constructing scaffolds: 79s. The final rank ******************************* Scaffold number 43132 In-scaffold contig number 589607 Total scaffold length 177109373 Average scaffold length 4106 Filled gap number 1028 Longest scaffold 110905 Scaffold and singleton number 482745 Scaffold and singleton length 316308010 Average length 655 N50 3177 N90 184 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. Done with 43132 scaffolds, 0 gaps finished, 107569 gaps overall. Overall time spent on constructing scaffolds: 198m. Time for the whole pipeline: 318m. Finish time: 2021-06-12 15:00:55.961125 Elapsed time: 5:18:36.813362