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DecodeGenetics / Ratatosk

Hybrid error correction of long reads using colored de Bruijn graphs
BSD 2-Clause "Simplified" License
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Ratatosk::correct(): Corrected read file is not in the same order as input long read file. Abort. #36

Closed kgun12 closed 2 years ago

kgun12 commented 2 years ago

Hi - I'm using ratatosk 0.7.5 to correct nanopore long reads with some Illumina MiSeq data. Things seem to run fine for a few hours, and then terminates on the 2nd pass with

FileParser::FileParser(): Missing input files Ratatosk::correct(): Corrected read file is not in the same order as input long read file. Abort.

A 6.2G {prefix}.2.fastq file is created as output A {prefix}.fastq file is created but it is empty

I'm running it on a single SMP machine w/ 32c/64t and 256G of ram.

Thanks in advance.

Complete log:

nohup: ignoring input Ratatosk::Ratatosk(): Building graph from short reads (1/2). KmerStream::KmerStream(): Start computing k-mer cardinality estimations CompactedDBG::build(): Estimated number of k-mers occurring at least once: 3157246438 CompactedDBG::build(): Estimated number of minimizer occurring at least once: 777395301 CompactedDBG::build(): Estimated number of k-mers occurring twice or more: 338646117 CompactedDBG::build(): Estimated number of minimizers occurring twice or more: 82410049 CompactedDBG::filter(): Closed all fasta/fastq files CompactedDBG::filter(): Processed 4845560557 k-mers in 34559750 reads CompactedDBG::filter(): Found 3180398519 unique k-mers CompactedDBG::filter(): Number of blocks in Bloom filter is 2314964 CompactedDBG::construct(): Extract approximate unitigs CompactedDBG::construct(): Closed all input files

CompactedDBG::construct(): Splitting unitigs (1/2)

CompactedDBG::construct(): Splitting unitigs (2/2) CompactedDBG::construct(): Before split: 14854969 unitigs CompactedDBG::construct(): After split (1/2): 13238017 unitigs CompactedDBG::construct(): After split (2/2): 13433207 unitigs CompactedDBG::construct(): Unitigs split: 228451 CompactedDBG::construct(): Unitigs deleted: 1618906

CompactedDBG::construct(): Joining unitigs CompactedDBG::construct(): After join: 12494356 unitigs CompactedDBG::construct(): Joined 938851 unitigs

CompactedDBG::write(): Writing graph to disk KmerStream::KmerStream(): Start computing k-mer cardinality estimations CompactedDBG::build(): Estimated number of k-mers occurring at least once: 276919512 CompactedDBG::build(): Estimated number of minimizer occurring at least once: 62083602 CompactedDBG::filter(): Closed all fasta/fastq files CompactedDBG::filter(): Processed 730176982 k-mers in 12494356 reads CompactedDBG::filter(): Found 280692060 unique k-mers CompactedDBG::filter(): Number of blocks in Bloom filter is 1893005 CompactedDBG::construct(): Extract approximate unitigs CompactedDBG::construct(): Closed all input files

CompactedDBG::construct(): Splitting unitigs (1/2)

CompactedDBG::construct(): Splitting unitigs (2/2) CompactedDBG::construct(): Before split: 17730668 unitigs CompactedDBG::construct(): After split (1/1): 17730853 unitigs CompactedDBG::construct(): Unitigs split: 92362 CompactedDBG::construct(): Unitigs deleted: 0

CompactedDBG::construct(): Joining unitigs CompactedDBG::construct(): After join: 15337587 unitigs CompactedDBG::construct(): Joined 2518366 unitigs Ratatosk::Ratatosk(): Adding colors and coverage to graph (1/2). Ratatosk::addCoverage(): Anchoring reads on graph. Ratatosk::addCoverage(): Detecting and removing duplicated reads. Ratatosk::addCoverage(): Coloring graph with reads. Ratatosk::addCoverage(): Processed 1000000 reads. Ratatosk::addCoverage(): Processed 2000000 reads. Ratatosk::addCoverage(): Processed 3000000 reads. Ratatosk::addCoverage(): Processed 4000000 reads. Ratatosk::addCoverage(): Processed 5000000 reads. Ratatosk::addCoverage(): Processed 6000000 reads. Ratatosk::addCoverage(): Processed 7000000 reads. Ratatosk::addCoverage(): Processed 8000000 reads. Ratatosk::addCoverage(): Processed 9000000 reads. Ratatosk::addCoverage(): Processed 10000000 reads. Ratatosk::addCoverage(): Processed 11000000 reads. Ratatosk::addCoverage(): Processed 12000000 reads. Ratatosk::addCoverage(): Processed 13000000 reads. Ratatosk::addCoverage(): Processed 14000000 reads. Ratatosk::addCoverage(): Processed 15000000 reads. Ratatosk::addCoverage(): Processed 16000000 reads. Ratatosk::addCoverage(): Processed 17000000 reads. Ratatosk::addCoverage(): Processed 18000000 reads. Ratatosk::addCoverage(): Processed 19000000 reads. Ratatosk::addCoverage(): Processed 20000000 reads. Ratatosk::addCoverage(): Processed 21000000 reads. Ratatosk::addCoverage(): Processed 22000000 reads. Ratatosk::addCoverage(): Processed 23000000 reads. Ratatosk::addCoverage(): Processed 24000000 reads. Ratatosk::addCoverage(): Processed 25000000 reads. Ratatosk::addCoverage(): Processed 26000000 reads. Ratatosk::addCoverage(): Processed 27000000 reads. Ratatosk::addCoverage(): Processed 28000000 reads. Ratatosk::addCoverage(): Processed 29000000 reads. Ratatosk::addCoverage(): Processed 30000000 reads. Ratatosk::addCoverage(): Processed 31000000 reads. Ratatosk::addCoverage(): Processed 32000000 reads. Ratatosk::addCoverage(): Processed 33000000 reads. Ratatosk::addCoverage(): Processed 34000000 reads. Ratatosk::addCoverage(): Collecting branching information. Ratatosk::addCoverage(): Compacting colors. Ratatosk::Ratatosk(): Adding SNPs candidates to graph (1/2). Ratatosk::detectSNPs(): Scanning graph for k-mers with substitutions (SNPs) Ratatosk::detectSNPs(): Processed 1000448 vertices. Ratatosk::detectSNPs(): Processed 2000896 vertices. Ratatosk::detectSNPs(): Processed 3000320 vertices. Ratatosk::detectSNPs(): Processed 4000768 vertices. Ratatosk::detectSNPs(): Processed 5000192 vertices. Ratatosk::detectSNPs(): Processed 6000640 vertices. Ratatosk::detectSNPs(): Processed 7000064 vertices. Ratatosk::detectSNPs(): Processed 8000512 vertices. Ratatosk::detectSNPs(): Processed 9000960 vertices. Ratatosk::detectSNPs(): Processed 10000384 vertices. Ratatosk::detectSNPs(): Processed 11000832 vertices. Ratatosk::detectSNPs(): Processed 12000256 vertices. Ratatosk::detectSNPs(): Processed 13000704 vertices. Ratatosk::detectSNPs(): Processed 14000128 vertices. Ratatosk::detectSNPs(): Processed 15000576 vertices. Ratatosk::Ratatosk(): Adding micro/mini-satellites motif candidates to graph (1/2). Ratatosk::detectShortCycles(): Detecting unitigs in short cycles Ratatosk::detectShortCycles(): Found 25335 in short cycles. (23975 unique) Ratatosk::Ratatosk(): Correcting long reads (1/2). Ratatosk::correct(): Processed 1000 reads Ratatosk::correct(): Processed 2000 reads Ratatosk::correct(): Processed 3000 reads Ratatosk::correct(): Processed 4000 reads Ratatosk::correct(): Processed 5000 reads Ratatosk::correct(): Processed 6000 reads Ratatosk::correct(): Processed 7000 reads Ratatosk::correct(): Processed 8000 reads Ratatosk::correct(): Processed 9000 reads Ratatosk::correct(): Processed 10000 reads Ratatosk::correct(): Processed 11000 reads Ratatosk::correct(): Processed 12000 reads Ratatosk::correct(): Processed 13000 reads Ratatosk::correct(): Processed 14000 reads Ratatosk::correct(): Processed 15000 reads Ratatosk::correct(): Processed 16000 reads Ratatosk::correct(): Processed 17000 reads Ratatosk::correct(): Processed 18000 reads Ratatosk::correct(): Processed 19000 reads Ratatosk::correct(): Processed 20000 reads Ratatosk::correct(): Processed 21000 reads Ratatosk::correct(): Processed 22000 reads Ratatosk::correct(): Processed 23000 reads Ratatosk::correct(): Processed 24000 reads Ratatosk::correct(): Processed 25000 reads Ratatosk::correct(): Processed 26000 reads Ratatosk::correct(): Processed 27000 reads Ratatosk::correct(): Processed 28000 reads Ratatosk::correct(): Processed 29000 reads Ratatosk::correct(): Processed 30000 reads Ratatosk::correct(): Processed 31000 reads Ratatosk::correct(): Processed 32000 reads Ratatosk::correct(): Processed 33000 reads Ratatosk::correct(): Processed 34000 reads Ratatosk::correct(): Processed 35000 reads Ratatosk::correct(): Processed 36000 reads Ratatosk::correct(): Processed 37000 reads Ratatosk::correct(): Processed 38000 reads Ratatosk::correct(): Processed 39000 reads Ratatosk::correct(): Processed 40000 reads Ratatosk::correct(): Processed 41000 reads Ratatosk::correct(): Processed 42000 reads Ratatosk::correct(): Processed 43000 reads Ratatosk::correct(): Processed 44000 reads Ratatosk::correct(): Processed 45000 reads Ratatosk::correct(): Processed 46000 reads Ratatosk::correct(): Processed 47000 reads Ratatosk::correct(): Processed 48000 reads Ratatosk::correct(): Processed 49000 reads Ratatosk::correct(): Processed 50000 reads Ratatosk::correct(): Processed 51000 reads Ratatosk::correct(): Processed 52000 reads Ratatosk::correct(): Processed 53000 reads Ratatosk::correct(): Processed 54000 reads Ratatosk::correct(): Processed 55000 reads Ratatosk::correct(): Processed 56000 reads Ratatosk::correct(): Processed 57000 reads Ratatosk::correct(): Processed 58000 reads Ratatosk::correct(): Processed 59000 reads Ratatosk::correct(): Processed 60000 reads Ratatosk::correct(): Processed 61000 reads Ratatosk::correct(): Processed 62000 reads Ratatosk::correct(): Processed 63000 reads Ratatosk::correct(): Processed 64000 reads Ratatosk::correct(): Processed 65000 reads Ratatosk::correct(): Processed 66000 reads Ratatosk::correct(): Processed 67000 reads Ratatosk::correct(): Processed 68000 reads Ratatosk::correct(): Processed 69000 reads Ratatosk::correct(): Processed 70000 reads Ratatosk::correct(): Processed 71000 reads Ratatosk::correct(): Processed 72000 reads Ratatosk::correct(): Processed 73000 reads Ratatosk::correct(): Processed 74000 reads Ratatosk::correct(): Processed 75000 reads Ratatosk::correct(): Processed 76000 reads Ratatosk::correct(): Processed 77000 reads Ratatosk::correct(): Processed 78000 reads Ratatosk::correct(): Processed 79000 reads Ratatosk::correct(): Processed 80000 reads Ratatosk::correct(): Processed 81000 reads Ratatosk::correct(): Processed 82000 reads Ratatosk::correct(): Processed 83000 reads Ratatosk::correct(): Processed 84000 reads Ratatosk::correct(): Processed 85000 reads Ratatosk::correct(): Processed 86000 reads Ratatosk::correct(): Processed 87000 reads Ratatosk::correct(): Processed 88000 reads Ratatosk::correct(): Processed 89000 reads Ratatosk::correct(): Processed 90000 reads Ratatosk::correct(): Processed 91000 reads Ratatosk::correct(): Processed 92000 reads Ratatosk::correct(): Processed 93000 reads Ratatosk::correct(): Processed 94000 reads Ratatosk::correct(): Processed 95000 reads Ratatosk::correct(): Processed 96000 reads Ratatosk::correct(): Processed 97000 reads Ratatosk::correct(): Processed 98000 reads Ratatosk::correct(): Processed 99000 reads Ratatosk::correct(): Processed 100000 reads Ratatosk::correct(): Processed 101000 reads Ratatosk::correct(): Processed 102000 reads Ratatosk::correct(): Processed 103000 reads Ratatosk::correct(): Processed 104000 reads Ratatosk::correct(): Processed 105000 reads Ratatosk::correct(): Processed 106000 reads Ratatosk::correct(): Processed 107000 reads Ratatosk::correct(): Processed 108000 reads Ratatosk::correct(): Processed 109000 reads Ratatosk::correct(): Processed 110000 reads Ratatosk::correct(): Processed 111000 reads Ratatosk::correct(): Processed 112000 reads Ratatosk::correct(): Processed 113000 reads Ratatosk::correct(): Processed 114000 reads Ratatosk::correct(): Processed 115000 reads Ratatosk::correct(): Processed 116000 reads Ratatosk::correct(): Processed 117000 reads Ratatosk::correct(): Processed 118000 reads Ratatosk::correct(): Processed 119000 reads Ratatosk::correct(): Processed 120000 reads Ratatosk::correct(): Processed 121000 reads Ratatosk::correct(): Processed 122000 reads Ratatosk::correct(): Processed 123000 reads Ratatosk::correct(): Processed 124000 reads Ratatosk::correct(): Processed 125000 reads Ratatosk::correct(): Processed 126000 reads Ratatosk::correct(): Processed 127000 reads Ratatosk::correct(): Processed 128000 reads Ratatosk::correct(): Processed 129000 reads Ratatosk::correct(): Processed 130000 reads Ratatosk::correct(): Processed 131000 reads Ratatosk::correct(): Processed 132000 reads Ratatosk::correct(): Processed 133000 reads Ratatosk::correct(): Processed 134000 reads Ratatosk::correct(): Processed 135000 reads Ratatosk::correct(): Processed 136000 reads Ratatosk::correct(): Processed 137000 reads Ratatosk::correct(): Processed 138000 reads Ratatosk::correct(): Processed 139000 reads Ratatosk::correct(): Processed 140000 reads Ratatosk::correct(): Processed 141000 reads Ratatosk::correct(): Processed 142000 reads Ratatosk::correct(): Processed 143000 reads Ratatosk::correct(): Processed 144000 reads Ratatosk::correct(): Processed 145000 reads Ratatosk::correct(): Processed 146000 reads Ratatosk::correct(): Processed 147000 reads Ratatosk::correct(): Processed 148000 reads Ratatosk::correct(): Processed 149000 reads Ratatosk::correct(): Processed 150000 reads Ratatosk::correct(): Processed 151000 reads Ratatosk::correct(): Processed 152000 reads Ratatosk::correct(): Processed 153000 reads Ratatosk::correct(): Processed 154000 reads Ratatosk::correct(): Processed 155000 reads Ratatosk::correct(): Processed 156000 reads Ratatosk::correct(): Processed 157000 reads Ratatosk::correct(): Processed 158000 reads Ratatosk::correct(): Processed 159000 reads Ratatosk::correct(): Processed 160000 reads Ratatosk::correct(): Processed 161000 reads Ratatosk::correct(): Processed 162000 reads Ratatosk::correct(): Processed 163000 reads Ratatosk::correct(): Processed 164000 reads Ratatosk::correct(): Processed 165000 reads Ratatosk::correct(): Processed 166000 reads Ratatosk::correct(): Processed 167000 reads Ratatosk::correct(): Processed 168000 reads Ratatosk::correct(): Processed 169000 reads Ratatosk::correct(): Processed 170000 reads Ratatosk::correct(): Processed 171000 reads Ratatosk::correct(): Processed 172000 reads Ratatosk::correct(): Processed 173000 reads Ratatosk::correct(): Processed 174000 reads Ratatosk::correct(): Processed 175000 reads Ratatosk::correct(): Processed 176000 reads Ratatosk::correct(): Processed 177000 reads Ratatosk::correct(): Processed 178000 reads Ratatosk::correct(): Processed 179000 reads Ratatosk::correct(): Processed 180000 reads Ratatosk::correct(): Processed 181000 reads Ratatosk::correct(): Processed 182000 reads Ratatosk::correct(): Processed 183000 reads Ratatosk::correct(): Processed 184000 reads Ratatosk::correct(): Processed 185000 reads Ratatosk::correct(): Processed 186000 reads Ratatosk::correct(): Processed 187000 reads Ratatosk::correct(): Processed 188000 reads Ratatosk::correct(): Processed 189000 reads Ratatosk::correct(): Processed 190000 reads Ratatosk::correct(): Processed 191000 reads Ratatosk::correct(): Processed 192000 reads Ratatosk::correct(): Processed 193000 reads Ratatosk::correct(): Processed 194000 reads Ratatosk::correct(): Processed 195000 reads Ratatosk::correct(): Processed 196000 reads Ratatosk::correct(): Processed 197000 reads Ratatosk::correct(): Processed 198000 reads Ratatosk::correct(): Processed 199000 reads Ratatosk::correct(): Processed 200000 reads Ratatosk::correct(): Processed 201000 reads Ratatosk::correct(): Processed 202000 reads Ratatosk::correct(): Processed 203000 reads Ratatosk::correct(): Processed 204000 reads Ratatosk::correct(): Processed 205000 reads Ratatosk::correct(): Processed 206000 reads Ratatosk::correct(): Processed 207000 reads Ratatosk::correct(): Processed 208000 reads Ratatosk::correct(): Processed 209000 reads Ratatosk::correct(): Processed 210000 reads Ratatosk::correct(): Processed 211000 reads Ratatosk::correct(): Processed 212000 reads Ratatosk::correct(): Processed 213000 reads Ratatosk::correct(): Processed 214000 reads Ratatosk::correct(): Processed 215000 reads Ratatosk::correct(): Processed 216000 reads Ratatosk::correct(): Processed 217000 reads Ratatosk::correct(): Processed 218000 reads Ratatosk::correct(): Processed 219000 reads Ratatosk::correct(): Processed 220000 reads Ratatosk::correct(): Processed 221000 reads Ratatosk::correct(): Processed 222000 reads Ratatosk::correct(): Processed 223000 reads Ratatosk::correct(): Processed 224000 reads Ratatosk::correct(): Processed 225000 reads Ratatosk::correct(): Processed 226000 reads Ratatosk::correct(): Processed 227000 reads Ratatosk::correct(): Processed 228000 reads Ratatosk::correct(): Processed 229000 reads Ratatosk::correct(): Processed 230000 reads Ratatosk::correct(): Processed 231000 reads Ratatosk::correct(): Processed 232000 reads Ratatosk::correct(): Processed 233000 reads Ratatosk::correct(): Processed 234000 reads Ratatosk::correct(): Processed 235000 reads Ratatosk::correct(): Processed 236000 reads Ratatosk::correct(): Processed 237000 reads Ratatosk::correct(): Processed 238000 reads Ratatosk::correct(): Processed 239000 reads Ratatosk::correct(): Processed 240000 reads Ratatosk::correct(): Processed 241000 reads Ratatosk::correct(): Processed 242000 reads Ratatosk::correct(): Processed 243000 reads Ratatosk::correct(): Processed 244000 reads Ratatosk::correct(): Processed 245000 reads Ratatosk::correct(): Processed 246000 reads Ratatosk::correct(): Processed 247000 reads Ratatosk::correct(): Processed 248000 reads Ratatosk::correct(): Processed 249000 reads Ratatosk::correct(): Processed 250000 reads Ratatosk::correct(): Processed 251000 reads Ratatosk::correct(): Processed 252000 reads Ratatosk::correct(): Processed 253000 reads Ratatosk::correct(): Processed 254000 reads Ratatosk::correct(): Processed 255000 reads Ratatosk::correct(): Processed 256000 reads Ratatosk::correct(): Processed 257000 reads Ratatosk::correct(): Processed 258000 reads Ratatosk::correct(): Processed 259000 reads Ratatosk::correct(): Processed 260000 reads Ratatosk::correct(): Processed 261000 reads Ratatosk::correct(): Processed 262000 reads Ratatosk::correct(): Processed 263000 reads Ratatosk::correct(): Processed 264000 reads Ratatosk::correct(): Processed 265000 reads Ratatosk::correct(): Processed 266000 reads Ratatosk::correct(): Processed 267000 reads Ratatosk::correct(): Processed 268000 reads Ratatosk::correct(): Processed 269000 reads Ratatosk::correct(): Processed 270000 reads Ratatosk::correct(): Processed 271000 reads Ratatosk::correct(): Processed 272000 reads Ratatosk::correct(): Processed 273000 reads Ratatosk::correct(): Processed 274000 reads Ratatosk::correct(): Processed 275000 reads Ratatosk::correct(): Processed 276000 reads Ratatosk::correct(): Processed 277000 reads Ratatosk::correct(): Processed 278000 reads Ratatosk::correct(): Processed 279000 reads Ratatosk::correct(): Processed 280000 reads Ratatosk::correct(): Processed 281000 reads Ratatosk::correct(): Processed 282000 reads Ratatosk::correct(): Processed 283000 reads Ratatosk::correct(): Processed 284000 reads Ratatosk::correct(): Processed 285000 reads Ratatosk::correct(): Processed 286000 reads Ratatosk::correct(): Processed 287000 reads Ratatosk::correct(): Processed 288000 reads Ratatosk::correct(): Processed 289000 reads Ratatosk::correct(): Processed 290000 reads Ratatosk::correct(): Processed 291000 reads Ratatosk::correct(): Processed 292000 reads Ratatosk::correct(): Processed 293000 reads Ratatosk::correct(): Processed 294000 reads Ratatosk::correct(): Processed 295000 reads Ratatosk::correct(): Processed 296000 reads Ratatosk::correct(): Processed 297000 reads Ratatosk::correct(): Processed 298000 reads Ratatosk::correct(): Processed 299000 reads Ratatosk::correct(): Processed 300000 reads Ratatosk::correct(): Processed 301000 reads Ratatosk::correct(): Processed 302000 reads Ratatosk::correct(): Processed 303000 reads Ratatosk::correct(): Processed 304000 reads Ratatosk::correct(): Processed 305000 reads Ratatosk::correct(): Processed 306000 reads Ratatosk::correct(): Processed 307000 reads Ratatosk::correct(): Processed 308000 reads Ratatosk::correct(): Processed 309000 reads Ratatosk::correct(): Processed 310000 reads Ratatosk::correct(): Processed 311000 reads Ratatosk::correct(): Processed 312000 reads Ratatosk::correct(): Processed 313000 reads Ratatosk::correct(): Processed 314000 reads Ratatosk::correct(): Processed 315000 reads Ratatosk::correct(): Processed 316000 reads Ratatosk::correct(): Processed 317000 reads Ratatosk::correct(): Processed 318000 reads Ratatosk::correct(): Processed 319000 reads Ratatosk::correct(): Processed 320000 reads Ratatosk::correct(): Processed 321000 reads Ratatosk::correct(): Processed 322000 reads Ratatosk::correct(): Processed 323000 reads Ratatosk::correct(): Processed 324000 reads Ratatosk::correct(): Processed 325000 reads Ratatosk::correct(): Processed 326000 reads Ratatosk::correct(): Processed 327000 reads Ratatosk::correct(): Processed 328000 reads Ratatosk::correct(): Processed 329000 reads Ratatosk::correct(): Processed 330000 reads Ratatosk::correct(): Processed 331000 reads Ratatosk::correct(): Processed 332000 reads Ratatosk::correct(): Processed 333000 reads Ratatosk::correct(): Processed 334000 reads Ratatosk::correct(): Processed 335000 reads Ratatosk::correct(): Processed 336000 reads Ratatosk::correct(): Processed 337000 reads Ratatosk::correct(): Processed 338000 reads Ratatosk::correct(): Processed 339000 reads Ratatosk::correct(): Processed 340000 reads Ratatosk::correct(): Processed 341000 reads Ratatosk::correct(): Processed 342000 reads Ratatosk::correct(): Processed 343000 reads Ratatosk::correct(): Processed 344000 reads Ratatosk::correct(): Processed 345000 reads Ratatosk::correct(): Processed 346000 reads Ratatosk::correct(): Processed 347000 reads Ratatosk::correct(): Processed 348000 reads Ratatosk::correct(): Processed 349000 reads Ratatosk::correct(): Processed 350000 reads Ratatosk::correct(): Processed 351000 reads Ratatosk::correct(): Processed 352000 reads Ratatosk::correct(): Processed 353000 reads Ratatosk::correct(): Processed 354000 reads Ratatosk::correct(): Processed 355000 reads Ratatosk::correct(): Processed 356000 reads Ratatosk::correct(): Processed 357000 reads Ratatosk::correct(): Processed 358000 reads Ratatosk::correct(): Processed 359000 reads Ratatosk::correct(): Processed 360000 reads Ratatosk::correct(): Processed 361000 reads Ratatosk::correct(): Processed 362000 reads Ratatosk::correct(): Processed 363000 reads Ratatosk::correct(): Processed 364000 reads Ratatosk::correct(): Processed 365000 reads Ratatosk::correct(): Processed 366000 reads Ratatosk::correct(): Processed 367000 reads Ratatosk::correct(): Processed 368000 reads Ratatosk::correct(): Processed 369000 reads Ratatosk::correct(): Processed 370000 reads Ratatosk::correct(): Processed 371000 reads Ratatosk::correct(): Processed 372000 reads Ratatosk::correct(): Processed 373000 reads Ratatosk::correct(): Processed 374000 reads Ratatosk::correct(): Processed 375000 reads Ratatosk::correct(): Processed 376000 reads Ratatosk::correct(): Processed 377000 reads Ratatosk::correct(): Processed 378000 reads Ratatosk::correct(): Processed 379000 reads Ratatosk::correct(): Processed 380000 reads Ratatosk::correct(): Processed 381000 reads Ratatosk::correct(): Processed 382000 reads Ratatosk::correct(): Processed 383000 reads Ratatosk::correct(): Processed 384000 reads Ratatosk::correct(): Processed 385000 reads Ratatosk::correct(): Processed 386000 reads Ratatosk::correct(): Processed 387000 reads Ratatosk::correct(): Processed 388000 reads Ratatosk::correct(): Processed 389000 reads Ratatosk::correct(): Processed 390000 reads Ratatosk::correct(): Processed 391000 reads Ratatosk::correct(): Processed 392000 reads Ratatosk::correct(): Processed 393000 reads Ratatosk::correct(): Processed 394000 reads Ratatosk::correct(): Processed 395000 reads Ratatosk::correct(): Processed 396000 reads Ratatosk::correct(): Processed 397000 reads Ratatosk::correct(): Processed 398000 reads Ratatosk::correct(): Processed 399000 reads Ratatosk::correct(): Processed 400000 reads Ratatosk::correct(): Processed 401000 reads Ratatosk::correct(): Processed 402000 reads Ratatosk::correct(): Processed 403000 reads Ratatosk::correct(): Processed 404000 reads Ratatosk::correct(): Processed 405000 reads Ratatosk::correct(): Processed 406000 reads Ratatosk::correct(): Processed 407000 reads Ratatosk::correct(): Processed 408000 reads Ratatosk::correct(): Processed 409000 reads Ratatosk::correct(): Processed 410000 reads Ratatosk::correct(): Processed 411000 reads Ratatosk::correct(): Processed 412000 reads Ratatosk::correct(): Processed 413000 reads Ratatosk::correct(): Processed 414000 reads Ratatosk::correct(): Processed 415000 reads Ratatosk::correct(): Processed 416000 reads Ratatosk::correct(): Processed 417000 reads Ratatosk::correct(): Processed 418000 reads Ratatosk::correct(): Processed 419000 reads Ratatosk::correct(): Processed 420000 reads Ratatosk::correct(): Processed 421000 reads Ratatosk::correct(): Processed 422000 reads Ratatosk::correct(): Processed 423000 reads Ratatosk::correct(): Processed 424000 reads Ratatosk::correct(): Processed 425000 reads Ratatosk::correct(): Processed 426000 reads Ratatosk::correct(): Processed 427000 reads Ratatosk::correct(): Processed 428000 reads Ratatosk::correct(): Processed 429000 reads Ratatosk::correct(): Processed 430000 reads Ratatosk::correct(): Processed 431000 reads Ratatosk::correct(): Processed 432000 reads Ratatosk::correct(): Processed 433000 reads Ratatosk::correct(): Processed 434000 reads Ratatosk::correct(): Processed 435000 reads Ratatosk::correct(): Processed 436000 reads Ratatosk::correct(): Processed 437000 reads Ratatosk::correct(): Processed 438000 reads Ratatosk::correct(): Processed 439000 reads Ratatosk::correct(): Processed 440000 reads Ratatosk::correct(): Processed 441000 reads Ratatosk::correct(): Processed 442000 reads Ratatosk::correct(): Processed 443000 reads Ratatosk::correct(): Processed 444000 reads Ratatosk::correct(): Processed 445000 reads Ratatosk::correct(): Processed 446000 reads Ratatosk::correct(): Processed 447000 reads Ratatosk::correct(): Processed 448000 reads Ratatosk::correct(): Processed 449000 reads Ratatosk::correct(): Processed 450000 reads Ratatosk::correct(): Processed 451000 reads Ratatosk::correct(): Processed 452000 reads Ratatosk::correct(): Processed 453000 reads Ratatosk::correct(): Processed 454000 reads Ratatosk::correct(): Processed 455000 reads Ratatosk::correct(): Processed 456000 reads Ratatosk::correct(): Processed 457000 reads Ratatosk::correct(): Processed 458000 reads Ratatosk::correct(): Processed 459000 reads Ratatosk::correct(): Processed 460000 reads Ratatosk::correct(): Processed 461000 reads Ratatosk::correct(): Processed 462000 reads Ratatosk::correct(): Processed 463000 reads Ratatosk::correct(): Processed 464000 reads Ratatosk::correct(): Processed 465000 reads Ratatosk::correct(): Processed 466000 reads Ratatosk::correct(): Processed 467000 reads Ratatosk::correct(): Processed 468000 reads Ratatosk::correct(): Processed 469000 reads Ratatosk::correct(): Processed 470000 reads Ratatosk::correct(): Processed 471000 reads Ratatosk::correct(): Processed 472000 reads Ratatosk::correct(): Processed 473000 reads Ratatosk::correct(): Processed 474000 reads Ratatosk::correct(): Processed 475000 reads Ratatosk::correct(): Processed 476000 reads Ratatosk::correct(): Processed 477000 reads Ratatosk::correct(): Processed 478000 reads Ratatosk::correct(): Processed 479000 reads Ratatosk::correct(): Processed 480000 reads Ratatosk::correct(): Processed 481000 reads Ratatosk::correct(): Processed 482000 reads Ratatosk::correct(): Processed 483000 reads Ratatosk::correct(): Processed 484000 reads Ratatosk::correct(): Processed 485000 reads Ratatosk::correct(): Processed 486000 reads Ratatosk::correct(): Processed 487000 reads Ratatosk::correct(): Processed 488000 reads Ratatosk::correct(): Processed 489000 reads Ratatosk::correct(): Processed 490000 reads Ratatosk::correct(): Processed 491000 reads Ratatosk::correct(): Processed 492000 reads Ratatosk::correct(): Processed 493000 reads Ratatosk::correct(): Processed 494000 reads Ratatosk::correct(): Processed 495000 reads Ratatosk::correct(): Processed 496000 reads Ratatosk::correct(): Processed 497000 reads Ratatosk::correct(): Processed 498000 reads Ratatosk::correct(): Processed 499000 reads Ratatosk::correct(): Processed 500000 reads Ratatosk::correct(): Processed 501000 reads Ratatosk::correct(): Processed 502000 reads Ratatosk::correct(): Processed 503000 reads Ratatosk::correct(): Processed 504000 reads Ratatosk::correct(): Processed 505000 reads Ratatosk::correct(): Processed 506000 reads Ratatosk::correct(): Processed 507000 reads Ratatosk::correct(): Processed 508000 reads Ratatosk::correct(): Processed 509000 reads Ratatosk::correct(): Processed 510000 reads Ratatosk::correct(): Processed 511000 reads Ratatosk::correct(): Processed 512000 reads Ratatosk::correct(): Processed 513000 reads Ratatosk::correct(): Processed 514000 reads Ratatosk::correct(): Processed 515000 reads Ratatosk::correct(): Processed 516000 reads Ratatosk::correct(): Processed 517000 reads Ratatosk::correct(): Processed 518000 reads Ratatosk::correct(): Processed 519000 reads Ratatosk::correct(): Processed 520000 reads Ratatosk::correct(): Processed 521000 reads Ratatosk::correct(): Processed 522000 reads Ratatosk::correct(): Processed 523000 reads Ratatosk::correct(): Processed 524000 reads Ratatosk::correct(): Processed 525000 reads Ratatosk::correct(): Processed 526000 reads Ratatosk::correct(): Processed 527000 reads Ratatosk::correct(): Processed 528000 reads Ratatosk::correct(): Processed 529000 reads Ratatosk::correct(): Processed 530000 reads Ratatosk::correct(): Processed 531000 reads Ratatosk::correct(): Processed 532000 reads Ratatosk::correct(): Processed 533000 reads Ratatosk::correct(): Processed 534000 reads Ratatosk::correct(): Processed 535000 reads Ratatosk::correct(): Processed 536000 reads Ratatosk::correct(): Processed 537000 reads Ratatosk::correct(): Processed 538000 reads Ratatosk::correct(): Processed 539000 reads Ratatosk::correct(): Processed 540000 reads Ratatosk::correct(): Processed 541000 reads Ratatosk::correct(): Processed 542000 reads Ratatosk::correct(): Processed 543000 reads Ratatosk::correct(): Processed 544000 reads Ratatosk::correct(): Processed 545000 reads Ratatosk::correct(): Processed 546000 reads Ratatosk::correct(): Processed 547000 reads Ratatosk::correct(): Processed 548000 reads Ratatosk::correct(): Processed 549000 reads Ratatosk::correct(): Processed 550000 reads Ratatosk::correct(): Processed 551000 reads Ratatosk::correct(): Processed 552000 reads Ratatosk::correct(): Processed 553000 reads Ratatosk::correct(): Processed 554000 reads Ratatosk::correct(): Processed 555000 reads Ratatosk::correct(): Processed 556000 reads Ratatosk::correct(): Processed 557000 reads Ratatosk::correct(): Processed 558000 reads Ratatosk::correct(): Processed 559000 reads Ratatosk::correct(): Processed 560000 reads Ratatosk::correct(): Processed 561000 reads Ratatosk::correct(): Processed 562000 reads Ratatosk::correct(): Processed 563000 reads Ratatosk::correct(): Processed 564000 reads Ratatosk::correct(): Processed 565000 reads Ratatosk::correct(): Processed 566000 reads Ratatosk::correct(): Processed 567000 reads Ratatosk::correct(): Processed 568000 reads Ratatosk::correct(): Processed 569000 reads Ratatosk::correct(): Processed 570000 reads Ratatosk::correct(): Processed 571000 reads Ratatosk::correct(): Processed 572000 reads Ratatosk::correct(): Processed 573000 reads Ratatosk::correct(): Processed 574000 reads Ratatosk::correct(): Processed 575000 reads Ratatosk::correct(): Processed 576000 reads Ratatosk::correct(): Processed 577000 reads Ratatosk::correct(): Processed 578000 reads Ratatosk::correct(): Processed 579000 reads Ratatosk::correct(): Processed 580000 reads Ratatosk::correct(): Processed 581000 reads Ratatosk::correct(): Processed 582000 reads Ratatosk::correct(): Processed 583000 reads Ratatosk::correct(): Processed 584000 reads Ratatosk::correct(): Processed 585000 reads Ratatosk::correct(): Processed 586000 reads Ratatosk::correct(): Processed 587000 reads Ratatosk::correct(): Processed 588000 reads Ratatosk::correct(): Processed 589000 reads Ratatosk::correct(): Processed 590000 reads Ratatosk::correct(): Processed 591000 reads Ratatosk::correct(): Processed 592000 reads Ratatosk::correct(): Processed 593000 reads Ratatosk::correct(): Processed 594000 reads Ratatosk::correct(): Processed 595000 reads Ratatosk::correct(): Processed 596000 reads Ratatosk::correct(): Processed 597000 reads Ratatosk::correct(): Processed 598000 reads Ratatosk::correct(): Processed 599000 reads Ratatosk::correct(): Processed 600000 reads Ratatosk::correct(): Processed 601000 reads Ratatosk::correct(): Processed 602000 reads Ratatosk::correct(): Processed 603000 reads Ratatosk::correct(): Processed 604000 reads Ratatosk::correct(): Processed 605000 reads Ratatosk::correct(): Processed 606000 reads Ratatosk::correct(): Processed 607000 reads Ratatosk::correct(): Processed 608000 reads Ratatosk::correct(): Processed 609000 reads Ratatosk::correct(): Processed 610000 reads Ratatosk::correct(): Processed 611000 reads Ratatosk::correct(): Processed 612000 reads Ratatosk::correct(): Processed 613000 reads Ratatosk::correct(): Processed 614000 reads Ratatosk::correct(): Processed 615000 reads Ratatosk::correct(): Processed 616000 reads Ratatosk::correct(): Processed 617000 reads Ratatosk::correct(): Processed 618000 reads Ratatosk::correct(): Processed 619000 reads Ratatosk::correct(): Processed 620000 reads Ratatosk::correct(): Processed 621000 reads Ratatosk::correct(): Processed 622000 reads Ratatosk::correct(): Processed 623000 reads Ratatosk::correct(): Processed 624000 reads Ratatosk::correct(): Processed 625000 reads Ratatosk::correct(): Processed 626000 reads Ratatosk::correct(): Processed 627000 reads Ratatosk::correct(): Processed 628000 reads Ratatosk::correct(): Processed 629000 reads Ratatosk::correct(): Processed 630000 reads Ratatosk::correct(): Processed 631000 reads Ratatosk::correct(): Processed 632000 reads Ratatosk::correct(): Processed 633000 reads Ratatosk::correct(): Processed 634000 reads Ratatosk::correct(): Processed 635000 reads Ratatosk::correct(): Processed 636000 reads Ratatosk::correct(): Processed 637000 reads Ratatosk::correct(): Processed 638000 reads Ratatosk::correct(): Processed 639000 reads Ratatosk::correct(): Processed 640000 reads Ratatosk::correct(): Processed 641000 reads Ratatosk::correct(): Processed 642000 reads Ratatosk::correct(): Processed 643000 reads Ratatosk::correct(): Processed 644000 reads Ratatosk::correct(): Processed 645000 reads Ratatosk::correct(): Processed 646000 reads Ratatosk::correct(): Processed 647000 reads Ratatosk::correct(): Processed 648000 reads Ratatosk::correct(): Processed 649000 reads Ratatosk::correct(): Processed 650000 reads Ratatosk::correct(): Processed 651000 reads Ratatosk::correct(): Processed 652000 reads Ratatosk::correct(): Processed 653000 reads Ratatosk::correct(): Processed 654000 reads Ratatosk::correct(): Processed 655000 reads Ratatosk::correct(): Processed 656000 reads Ratatosk::correct(): Processed 657000 reads Ratatosk::correct(): Processed 658000 reads Ratatosk::correct(): Processed 659000 reads Ratatosk::correct(): Processed 660000 reads Ratatosk::correct(): Processed 661000 reads Ratatosk::correct(): Processed 662000 reads Ratatosk::correct(): Processed 663000 reads Ratatosk::correct(): Processed 664000 reads Ratatosk::correct(): Processed 665000 reads Ratatosk::correct(): Processed 666000 reads Ratatosk::correct(): Processed 667000 reads Ratatosk::correct(): Processed 668000 reads Ratatosk::correct(): Processed 669000 reads Ratatosk::correct(): Processed 670000 reads Ratatosk::correct(): Processed 671000 reads Ratatosk::correct(): Processed 672000 reads Ratatosk::correct(): Processed 673000 reads Ratatosk::correct(): Processed 674000 reads Ratatosk::correct(): Processed 675000 reads Ratatosk::correct(): Processed 676000 reads Ratatosk::correct(): Processed 677000 reads Ratatosk::correct(): Processed 678000 reads Ratatosk::correct(): Processed 679000 reads Ratatosk::correct(): Processed 680000 reads Ratatosk::correct(): Processed 681000 reads Ratatosk::correct(): Processed 682000 reads Ratatosk::correct(): Processed 683000 reads Ratatosk::correct(): Processed 684000 reads Ratatosk::correct(): Processed 685000 reads Ratatosk::correct(): Processed 686000 reads Ratatosk::correct(): Processed 687000 reads Ratatosk::correct(): Processed 688000 reads Ratatosk::correct(): Processed 689000 reads Ratatosk::correct(): Processed 690000 reads Ratatosk::correct(): Processed 691000 reads Ratatosk::correct(): Processed 692000 reads Ratatosk::correct(): Processed 693000 reads Ratatosk::correct(): Processed 694000 reads Ratatosk::correct(): Processed 695000 reads Ratatosk::correct(): Processed 696000 reads Ratatosk::correct(): Processed 697000 reads Ratatosk::correct(): Processed 698000 reads Ratatosk::correct(): Processed 699000 reads Ratatosk::correct(): Processed 700000 reads Ratatosk::correct(): Processed 701000 reads Ratatosk::correct(): Processed 702000 reads Ratatosk::correct(): Processed 703000 reads Ratatosk::correct(): Processed 704000 reads Ratatosk::correct(): Processed 705000 reads Ratatosk::correct(): Processed 706000 reads Ratatosk::correct(): Processed 707000 reads Ratatosk::correct(): Processed 708000 reads Ratatosk::correct(): Processed 709000 reads Ratatosk::correct(): Processed 710000 reads Ratatosk::correct(): Processed 711000 reads Ratatosk::correct(): Processed 712000 reads Ratatosk::correct(): Processed 713000 reads Ratatosk::correct(): Processed 714000 reads Ratatosk::correct(): Processed 715000 reads Ratatosk::correct(): Processed 716000 reads Ratatosk::correct(): Processed 717000 reads Ratatosk::correct(): Processed 718000 reads Ratatosk::correct(): Processed 719000 reads Ratatosk::correct(): Processed 720000 reads Ratatosk::correct(): Processed 721000 reads Ratatosk::correct(): Processed 722000 reads Ratatosk::correct(): Processed 723000 reads Ratatosk::correct(): Processed 724000 reads Ratatosk::correct(): Processed 725000 reads Ratatosk::correct(): Processed 726000 reads Ratatosk::correct(): Processed 727000 reads Ratatosk::correct(): Processed 728000 reads Ratatosk::correct(): Processed 729000 reads Ratatosk::correct(): Processed 730000 reads Ratatosk::correct(): Processed 731000 reads Ratatosk::correct(): Processed 732000 reads Ratatosk::correct(): Processed 733000 reads Ratatosk::correct(): Processed 734000 reads Ratatosk::correct(): Processed 735000 reads Ratatosk::correct(): Processed 736000 reads Ratatosk::correct(): Processed 737000 reads Ratatosk::correct(): Processed 738000 reads Ratatosk::correct(): Processed 739000 reads Ratatosk::correct(): Processed 740000 reads Ratatosk::correct(): Processed 741000 reads Ratatosk::correct(): Processed 742000 reads Ratatosk::correct(): Processed 743000 reads Ratatosk::correct(): Processed 744000 reads Ratatosk::correct(): Processed 745000 reads Ratatosk::correct(): Processed 746000 reads Ratatosk::correct(): Processed 747000 reads Ratatosk::correct(): Processed 748000 reads Ratatosk::correct(): Processed 749000 reads Ratatosk::correct(): Processed 750000 reads Ratatosk::correct(): Processed 751000 reads Ratatosk::correct(): Processed 752000 reads Ratatosk::correct(): Processed 753000 reads Ratatosk::correct(): Processed 754000 reads Ratatosk::correct(): Processed 755000 reads Ratatosk::correct(): Processed 756000 reads Ratatosk::correct(): Processed 757000 reads Ratatosk::correct(): Processed 758000 reads Ratatosk::correct(): Processed 759000 reads Ratatosk::correct(): Processed 760000 reads Ratatosk::correct(): Processed 761000 reads Ratatosk::correct(): Processed 762000 reads Ratatosk::correct(): Processed 763000 reads Ratatosk::correct(): Processed 764000 reads Ratatosk::correct(): Processed 765000 reads Ratatosk::correct(): Processed 766000 reads Ratatosk::correct(): Processed 767000 reads Ratatosk::correct(): Processed 768000 reads Ratatosk::correct(): Processed 769000 reads Ratatosk::correct(): Processed 770000 reads Ratatosk::correct(): Processed 771000 reads Ratatosk::correct(): Processed 772000 reads Ratatosk::correct(): Processed 773000 reads Ratatosk::correct(): Processed 774000 reads Ratatosk::correct(): Processed 775000 reads Ratatosk::correct(): Processed 776000 reads Ratatosk::correct(): Processed 777000 reads Ratatosk::correct(): Processed 778000 reads Ratatosk::correct(): Processed 779000 reads Ratatosk::correct(): Processed 780000 reads Ratatosk::correct(): Processed 781000 reads Ratatosk::correct(): Processed 782000 reads Ratatosk::correct(): Processed 783000 reads Ratatosk::correct(): Processed 784000 reads Ratatosk::correct(): Processed 785000 reads Ratatosk::correct(): Processed 786000 reads Ratatosk::correct(): Processed 787000 reads Ratatosk::correct(): Processed 788000 reads Ratatosk::correct(): Processed 789000 reads Ratatosk::correct(): Processed 790000 reads Ratatosk::correct(): Processed 791000 reads Ratatosk::correct(): Processed 792000 reads Ratatosk::correct(): Processed 793000 reads Ratatosk::correct(): Processed 794000 reads Ratatosk::correct(): Processed 795000 reads Ratatosk::correct(): Processed 796000 reads Ratatosk::correct(): Processed 797000 reads Ratatosk::correct(): Processed 798000 reads Ratatosk::correct(): Processed 799000 reads Ratatosk::correct(): Processed 800000 reads Ratatosk::correct(): Processed 801000 reads Ratatosk::correct(): Processed 802000 reads Ratatosk::correct(): Processed 803000 reads Ratatosk::correct(): Processed 804000 reads Ratatosk::correct(): Processed 805000 reads Ratatosk::correct(): Processed 806000 reads Ratatosk::correct(): Processed 807000 reads Ratatosk::correct(): Processed 808000 reads Ratatosk::correct(): Processed 809000 reads Ratatosk::correct(): Processed 810000 reads Ratatosk::correct(): Processed 811000 reads Ratatosk::correct(): Processed 812000 reads Ratatosk::correct(): Processed 813000 reads Ratatosk::correct(): Processed 814000 reads Ratatosk::correct(): Processed 815000 reads Ratatosk::correct(): Processed 816000 reads Ratatosk::correct(): Processed 817000 reads Ratatosk::correct(): Processed 818000 reads Ratatosk::correct(): Processed 819000 reads Ratatosk::correct(): Processed 820000 reads Ratatosk::correct(): Processed 821000 reads Ratatosk::correct(): Processed 822000 reads Ratatosk::correct(): Processed 823000 reads Ratatosk::correct(): Processed 824000 reads Ratatosk::correct(): Processed 825000 reads Ratatosk::correct(): Processed 826000 reads Ratatosk::correct(): Processed 827000 reads Ratatosk::correct(): Processed 828000 reads Ratatosk::correct(): Processed 829000 reads Ratatosk::correct(): Processed 830000 reads Ratatosk::correct(): Processed 831000 reads Ratatosk::correct(): Processed 832000 reads Ratatosk::correct(): Processed 833000 reads Ratatosk::correct(): Processed 834000 reads Ratatosk::correct(): Processed 835000 reads Ratatosk::correct(): Processed 836000 reads Ratatosk::correct(): Processed 837000 reads Ratatosk::correct(): Processed 838000 reads Ratatosk::correct(): Processed 839000 reads Ratatosk::correct(): Processed 840000 reads Ratatosk::search(): Reordering reads Ratatosk::Ratatosk(): Building graph (2/2).

CompactedDBG::read(): Reading graph from disk KmerStream::KmerStream(): Start computing k-mer cardinality estimations

CompactedDBG::read(): Finished reading graph from disk Ratatosk::Ratatosk(): Adding colors and coverage to graph (2/2). Ratatosk::addCoverage(): Anchoring reads on graph. Ratatosk::addCoverage(): Detecting and removing duplicated reads. Ratatosk::addCoverage(): Coloring graph with reads. Ratatosk::addCoverage(): Collecting branching information. Ratatosk::addCoverage(): Compacting colors. Ratatosk::Ratatosk(): Adding SNPs candidates to graph (2/2). Ratatosk::detectSNPs(): Scanning graph for k-mers with substitutions (SNPs) Ratatosk::detectSNPs(): Processed 1000448 vertices. Ratatosk::detectSNPs(): Processed 2000896 vertices. Ratatosk::detectSNPs(): Processed 3000320 vertices. Ratatosk::detectSNPs(): Processed 4000768 vertices. Ratatosk::detectSNPs(): Processed 5000192 vertices. Ratatosk::detectSNPs(): Processed 6000640 vertices. Ratatosk::detectSNPs(): Processed 7000064 vertices. Ratatosk::detectSNPs(): Processed 8000512 vertices. Ratatosk::detectSNPs(): Processed 9000960 vertices. Ratatosk::detectSNPs(): Processed 10000384 vertices. Ratatosk::detectSNPs(): Processed 11000832 vertices. Ratatosk::detectSNPs(): Processed 12000256 vertices. Ratatosk::Ratatosk(): Adding micro/mini-satellites motif candidates to graph (2/2). Ratatosk::detectShortCycles(): Detecting unitigs in short cycles Ratatosk::detectShortCycles(): Found 15107 in short cycles. (14792 unique) Ratatosk::Ratatosk(): Correcting long reads (2/2). FileParser::FileParser(): Missing input files Ratatosk::correct(): Corrected read file is not in the same order as input long read file. Abort.

kgun12 commented 2 years ago

Update: looks like the problem here was that I sent the output to a subdirectory i.e., -o OUTPUT/output that may not have been properly parsed at the outset of the 2nd pass. I copied the output.2.fastq file to cwd, restarted from pass 2 with -L and it seems to have finished.

GuillaumeHolley commented 2 years ago

Hi @kgun12,

Thanks for notifying me of the issue, it has been fixed in the latest commit I believe if you want to try it. I am on holidays at the moment so I did the very bad thing of pushing a quick fix I haven't even tried directly to production. I like to live dangerously. The issue at hand was that by default, the -L parameter should be the same as -l for the single command usage but it was left empty instead. So on the second correction pass, Ratatosk was trying to read an empty file which obviously couldn't be in the same order as the -l file.

Closing the issue now, feel free to reopen if my quick fix ended up on a catastrophic cascade of bugs.

Guillaume