======== SOAPdenovo2 ========== ['SOAPdenovo-63mer', 'all', '-s', 'SOAPdenovo2.config', '-o', 'SOAPdenovo2', '-K', '31', '-N', '184000000', '-R', '-M', '1', '-L', '200', '-p', '32'] Start time: 2021-06-05 09:07:14.183314 Version 2.04: released on July 13th, 2012 Compile Apr 5 2019 17:00:46 ******************** Pregraph ******************** Parameters: pregraph -s SOAPdenovo2.config -K 31 -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: 305s, 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. 565419804 node(s) allocated, 3852059593 kmer(s) in reads, 3852059593 kmer(s) processed. done hashing nodes 539979845 linear node(s) marked. Time spent on marking linear nodes: 8s. Time spent on pre-graph construction: 315s. Start to remove frequency-one-kmer tips shorter than 62. Total 9304844 tip(s) removed. 32 thread(s) initialized. 5397067 linear node(s) marked. Start to remove tips with minority links. 1552639 tip(s) removed in cycle 1. 7857 tip(s) removed in cycle 2. 25 tip(s) removed in cycle 3. 0 tip(s) removed in cycle 4. Total 1560521 tip(s) removed. 32 thread(s) initialized. 0 linear node(s) marked. Time spent on removing tips: 625s. 24915151 (12460166) edge(s) and 1446253 extra node(s) constructed. Time spent on constructing edges: 677s. 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: 75s, chopping reads to kmers: 35s, searching kmers: 215s, aligning reads to edges: 46s, searching (K+1)mers: 50s, adding pre-arcs: 48s, recording read paths: 64s. 815900868 marker(s) output. Reads alignment done, 3362027 read(s) deleted, 22107335 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: 563s. 9542319 vertex(es) output. Overall time spent on constructing pre-graph: 36m. ******************** Contig ******************** Parameters: contig -g SOAPdenovo2 -M 1 -R -s SOAPdenovo2.config -p 32 There are 9542319 kmer(s) in vertex file. There are 24915151 edge(s) in edge file. Kmers sorted. 24915151 edge(s) input. 30219784 pre-arcs loaded. 403424822 markers overall. 403424822 markers loaded. 6230053 none-palindrome edge(s) swapped, 0 palindrome edge(s) processed. 24915151 edge(s) sorted. Arcs sorted. 50225 repeat(s) are solvable, 100482 more edge(s). 200964 dead arc(s) removed. Time spent on solving repeat: 9s. Start to pinch bubbles, cutoff 0.100000, MAX NODE NUM 3, MAX DIFF NUM 2. .............100000 bubbles merged. 1239172 start points, 19528401 dheap nodes. 5560644 pair(s) found, 229037 pair of path(s) compared, 175902 pair(s) merged. Sequence comparison failed: Path crossing deleted edge 0 Length difference of two paths greater than two 29722 Mismatch score greater than cutoff (2) 10562 Mismatch score ratio greater than cutoff (0.1) 0 Path length shorter than (Kmer-1) 12851 DFibHeap: 902659 node(s) allocated. 798245 edge(s) concatenated in cycle 1. 10342 edge(s) concatenated in cycle 2. 0 edge(s) concatenated in cycle 3. Time spent on pinching bubbles: 73s. Start to destroy weak inner edges. 2037307 weak inner edge(s) destroyed in cycle 1. 6940 weak inner edge(s) destroyed in cycle 2. 37 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. 4071007 dead arc(s) removed. 334453 inner edge(s) with coverage lower than or equal to 1 destroyed. 679755 dead arc(s) removed. 3641346 edge(s) concatenated in cycle 1. 218917 edge(s) concatenated in cycle 2. 1175 edge(s) concatenated in cycle 3. 0 edge(s) concatenated in cycle 4. Before compacting, 25015633 edge(s) existed. After compacting, 10555931 edge(s) left. Strict: 0, cutoff length: 62. 1021549 tips cut in cycle 1. 85616 tips cut in cycle 2. 11013 tips cut in cycle 3. 2667 tips cut in cycle 4. 1146 tips cut in cycle 5. 841 tips cut in cycle 6. 923 tips cut in cycle 7. 597 tips cut in cycle 8. 668 tips cut in cycle 9. 671 tips cut in cycle 10. 312 tips cut in cycle 11. 102 tips cut in cycle 12. 39 tips cut in cycle 13. 21 tips cut in cycle 14. 20 tips cut in cycle 15. 17 tips cut in cycle 16. 7 tips cut in cycle 17. 7 tips cut in cycle 18. 3 tips cut in cycle 19. 1 tips cut in cycle 20. 0 tips cut in cycle 21. 854955 dead arc(s) removed. 632687 edge(s) concatenated in cycle 1. 5151 edge(s) concatenated in cycle 2. 0 edge(s) concatenated in cycle 3. Before compacting, 10555931 edge(s) existed. After compacting, 7027815 edge(s) left. There are 1344532 contig(s) longer than 100, sum up 284887776 bp, with average length 211. The longest length is 5489 bp, contig N50 is 245 bp,contig N90 is 105 bp. 3516092 contig(s) longer than 32 output. Time spent on constructing contig: 7m. ******************** Map ******************** Parameters: map -s SOAPdenovo2.config -g SOAPdenovo2 -p 32 -K 31 Kmer size: 31. Contig length cutoff: 33. 3516092 contig(s), maximum sequence length 5489, minimum sequence length 32, maximum name length 10. Time spent on parsing contigs file: 2s. 32 thread(s) initialized. Time spent on hashing contigs: 28s. 291678272 node(s) allocated, 294974496 kmer(s) in contigs, 294974496 kmer(s) processed. Time spent on graph construction: 30s. Time spent on aligning long reads: 0s. In file: SOAPdenovo2.config, max seq len 100, max name len 256 32 thread(s) initialized. 7027815 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 31659257 Ratio 45.1% Reads on contigs 58257119 Ratio 83.1% 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: 815s. Overall time spent on alignment: 14m. ******************** 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: 31 There are 7027815 edge(s) in edge file. Mask contigs with coverage lower than 0.7 or higher than 14.0, and strict length 100. Average contig coverage is 7, 2472230 contig(s) masked. Mask contigs shorter than 200, 3874762 contig(s) masked. 7068022 arc(s) loaded, average weight is 6. 3516092 contig(s) loaded. Done loading updated edges. Time spent on loading updated edges: 41s. ***************************************************** Start to load paired-end reads information. For insert size: 339 Total PE links 3212813 Normal PE links on same contig 626956 Incorrect oriented PE links 260 PE links of too small insert size 32350 PE links of too large insert size 0 Correct PE links 2553141 Accumulated connections 2385846 Use contigs longer than 339 to estimate insert size: PE links 494328 Average insert size 239 SD 68 1192923 new connections. For insert size: 339 Total PE links 9762317 Normal PE links on same contig 2660355 Incorrect oriented PE links 394 PE links of too small insert size 32816 PE links of too large insert size 0 Correct PE links 7068297 Accumulated connections 4429814 Use contigs longer than 339 to estimate insert size: PE links 2060733 Average insert size 242 SD 68 2214907 new connections. For insert size: 2000 Total PE links 8750728 Normal PE links on same contig 144400 Incorrect oriented PE links 116 PE links of too small insert size 523 PE links of too large insert size 0 Correct PE links 8605596 Accumulated connections 16135382 Use contigs longer than 2000 to estimate insert size: PE links 184 Average insert size 339 SD 222 8067691 new connections. For insert size: 4000 Total PE links 4126296 Normal PE links on same contig 649968 Incorrect oriented PE links 805 PE links of too small insert size 185 PE links of too large insert size 0 Correct PE links 3474464 Accumulated connections 2924254 Use contigs longer than 4000 to estimate insert size: PE links 128 Average insert size 264 SD 64 1462127 new connections. All paired-end reads information loaded. Time spent on loading paired-end reads information: 86s. ***************************************************** Start to construct scaffolds. *************************** For insert size: 339 Total PE links 3407832 PE links to masked contigs 3231153 On same scaffold PE links 0 Report from smallScaf: 0 scaffolds by smallPE. *************************** For insert size: 2000 Total PE links 8067692 PE links to masked contigs 7478329 On same scaffold PE links 0 *************************** For insert size: 4000 Total PE links 1462127 PE links to masked contigs 1191479 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 1838422 Weak connections 1610642 Weak ratio 87.6% 75 circles removed. Start to remove transitive connection. Total contigs 7027815 Masked contigs 6347292 Remained contigs 680523 None-outgoing-connection contigs 478695 (70.342224%) Single-outgoing-connection contigs 177423 Multi-outgoing-connection contigs 2374 Cycle 1 Two-outgoing-connection contigs 22031 Potential transitive connections 14231 Transitive connections 8683 Transitive ratio 39.4% Cycle 2 Two-outgoing-connection contigs 12961 Potential transitive connections 5533 Transitive connections 74 Transitive ratio 0.6% Cycle 3 Two-outgoing-connection contigs 12886 Potential transitive connections 5460 Transitive connections 0 Transitive ratio 0.0% Start to linearize sub-graph. Picked sub-graphs 10719 Connection-conflict 325 Significant overlapping 6746 Eligible 2 Bubble structures 0 Mask repeats: Puzzles 5053 Masked contigs 2997 Start to remove transitive connection. Total contigs 7027815 Masked contigs 6353286 Remained contigs 674529 None-outgoing-connection contigs 470523 (69.755783%) Single-outgoing-connection contigs 202677 Multi-outgoing-connection contigs 77 Cycle 1 Two-outgoing-connection contigs 1252 Potential transitive connections 922 Transitive connections 316 Transitive ratio 25.2% Cycle 2 Two-outgoing-connection contigs 927 Potential transitive connections 610 Transitive connections 5 Transitive ratio 0.5% Cycle 3 Two-outgoing-connection contigs 922 Potential transitive connections 605 Transitive connections 0 Transitive ratio 0.0% Start to linearize sub-graph. Picked sub-graphs 891 Connection-conflict 52 Significant overlapping 688 Eligible 0 Bubble structures 0 Non-strict linearization. Start to linearize sub-graph. Picked sub-graphs 601 Connection-conflict 48 Significant overlapping 428 Eligible 0 Bubble structures 0 Start to mask puzzles. Masked contigs 267 Remained puzzles 0 Freezing done. Recover contigs. Total recovered contigs 220 Single-route cases 215 Multi-route cases 0 All links loaded. Time spent on constructing scaffolds: 41s. The final rank ******************************* Scaffold number 49172 In-scaffold contig number 1344267 Total scaffold length 179946889 Average scaffold length 3659 Filled gap number 6575 Longest scaffold 59843 Scaffold and singleton number 1244727 Scaffold and singleton length 359395243 Average length 288 N50 856 N90 95 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. 48000 scaffolds processed. 49000 scaffolds processed. Done with 49172 scaffolds, 0 gaps finished, 100333 gaps overall. Overall time spent on constructing scaffolds: 131m. Time for the whole pipeline: 189m. Finish time: 2021-06-05 12:16:56.354663 Elapsed time: 3:09:42.171349