ABYSS -k64 -q3 -v --coverage-hist=coverage.hist -s test-bubbles.fa -o test-1.fa reads1.fq reads2.fq ABySS 1.5.2 ABYSS -k64 -q3 -v --coverage-hist=coverage.hist -s test-bubbles.fa -o test-1.fa reads1.fq reads2.fq Reading `reads1.fq'... Read 28163 reads. Hash load: 5084412 / 1073741824 = 0.00474 using 521 MB `reads1.fq': discarded 7 reads shorter than 64 bases Reading `reads2.fq'... Read 27950 reads. Hash load: 8638068 / 1073741824 = 0.00804 using 633 MB `reads2.fq': discarded 220 reads shorter than 64 bases `reads2.fq': discarded 1 reads containing non-ACGT characters Loaded 8638068 k-mer Hash load: 8638068 / 33554432 = 0.257 using 371 MB Minimum k-mer coverage is 31 Coverage: 31 Reconstruction: 5111 Coverage: 7.07 Reconstruction: 37481 Coverage: 3.16 Reconstruction: 324663 Coverage: 1.73 Reconstruction: 1459078 Coverage: 1.41 Reconstruction: 8638068 Coverage: 1 Reconstruction: 8638068 Using a coverage threshold of 1... The median k-mer coverage is 1 The reconstruction is 8638068 The k-mer coverage threshold is 1 Setting parameter e (erode) to 2 Setting parameter E (erodeStrand) to 0 Setting parameter c (coverage) to 2 Generating adjacency Finding adjacent k-mer: 1000000 Finding adjacent k-mer: 2000000 Finding adjacent k-mer: 3000000 Finding adjacent k-mer: 4000000 Finding adjacent k-mer: 5000000 Finding adjacent k-mer: 6000000 Finding adjacent k-mer: 7000000 Finding adjacent k-mer: 8000000 Added 17241022 edges. Eroding tips Eroded 6367118 tips. Eroded 0 tips. Hash load: 2270950 / 8388608 = 0.271 using 363 MB Pruning tips shorter than 1 bp... Removed 272 marked k-mer. Pruned 272 k-mer in 272 tips. Pruning tips shorter than 2 bp... Removed 402 marked k-mer. Pruned 402 k-mer in 239 tips. Pruning tips shorter than 4 bp... Removed 795 marked k-mer. Pruned 795 k-mer in 314 tips. Pruning tips shorter than 8 bp... Removed 1422 marked k-mer. Pruned 1422 k-mer in 323 tips. Pruning tips shorter than 16 bp... Removed 4806 marked k-mer. Pruned 4806 k-mer in 590 tips. Pruning tips shorter than 32 bp... Removed 11382 marked k-mer. Pruned 11382 k-mer in 776 tips. Pruning tips shorter than 64 bp... Removed 37837 marked k-mer. Pruned 37837 k-mer in 1395 tips. Pruning tips shorter than 64 bp... Removed 60 marked k-mer. Pruned 60 k-mer in 1 tips. Pruning tips shorter than 64 bp... Pruned 3910 tips in 8 rounds. Hash load: 2213974 / 8388608 = 0.264 using 363 MB Splitting: 1000000 Splitting: 2000000 Marked 34265 edges of 16269 ambiguous vertices. Removing low-coverage contigs (mean k-mer coverage < 2) Found 2212692 k-mer in 28888 contigs before removing low-coverage contigs. Removed 1223613 k-mer in 11260 low-coverage contigs. Split 19346 ambigiuous branches. Hash load: 990361 / 4194304 = 0.236 using 361 MB Eroding tips Eroded 627 tips. Eroded 0 tips. Hash load: 989734 / 4194304 = 0.236 using 361 MB Pruning tips shorter than 1 bp... Removed 488 marked k-mer. Pruned 488 k-mer in 488 tips. Pruning tips shorter than 2 bp... Removed 630 marked k-mer. Pruned 630 k-mer in 389 tips. Pruning tips shorter than 4 bp... Removed 1096 marked k-mer. Pruned 1096 k-mer in 464 tips. Pruning tips shorter than 8 bp... Removed 1889 marked k-mer. Pruned 1889 k-mer in 497 tips. Pruning tips shorter than 16 bp... Removed 5715 marked k-mer. Pruned 5715 k-mer in 824 tips. Pruning tips shorter than 32 bp... Removed 14018 marked k-mer. Pruned 14018 k-mer in 1030 tips. Pruning tips shorter than 64 bp... Removed 30786 marked k-mer. Pruned 30786 k-mer in 1163 tips. Pruning tips shorter than 64 bp... Pruned 4855 tips in 7 rounds. Hash load: 935112 / 4194304 = 0.223 using 361 MB Popping bubbles Removed 76 bubbles. Removed 76 bubbles Marked 4197 edges of 1982 ambiguous vertices. Left 7790 unassembled k-mer in circular contigs. Assembled 921514 k-mer in 7118 contigs. Removed 7702956 k-mer. The signal-to-noise ratio (SNR) is -9.16 dB. AdjList -v -k64 -m50 test-1.fa >test-1.adj Reading `test-1.fa'... Finding overlaps of exactly k-1 bp... V=14236 E=7364 E/V=0.517 Degree: █▂▁ 01234 0: 64% 1: 22% 2-4: 14% 5+: 0% max: 4 Finding overlaps of fewer than k-1 bp... V=14236 E=7372 E/V=0.518 Degree: █▂▁ 01234 0: 64% 1: 22% 2-4: 14% 5+: 0% max: 4 abyss-filtergraph -v -k64 -g test-2.adj test-1.adj >test-1.path Loading graph from file: test-1.adj Graph stats before: V=14236 E=7372 E/V=0.518 Degree: █▂▁ 01234 0: 64% 1: 22% 2-4: 14% 5+: 0% max: 4 Removing shim contigs from the graph... Pass 1: Checking 1678 contigs. Pass 2: Checking 196 contigs. Pass 3: Checking 2 contigs. Shim removal stats: Removed: 807 Too Complex: 1345 Tails: 4816 Too Long: 142 Self Adjacent: 8 Parallel Edges: 0 Graph stats after: V=12622 E=5758 E/V=0.456 Degree: █▁ 01234 0: 72% 1: 19% 2-4: 8.6% 5+: 0.7% max: 188 PopBubbles -v -j2 -k64 -p0.9 -g test-3.adj test-1.fa test-2.adj >test-2.path Reading `test-2.adj'... V=12622 E=5758 E/V=0.456 Degree: █▁ 01234 0: 72% 1: 19% 2-4: 8.6% 5+: 0.7% max: 188 Reading `test-1.fa'... Bubbles: 7 Popped: 3 Scaffolds: 0 Complex: 2 Too long: 0 Too many: 1 Dissimilar: 1 V=12596 E=5726 E/V=0.455 Degree: █▁ 01234 0: 72% 1: 19% 2-4: 8.6% 5+: 0.7% max: 188 MergeContigs -v -k64 -o test-3.fa test-1.fa test-2.adj test-2.path Reading `test-2.adj'... Read 12622 vertices. Using 1.52 MB of memory. Reading `test-1.fa'... Read 6311 sequences. Using 3.6 MB of memory. Reading `test-2.path'... Read 10 paths. Using 3.6 MB of memory. The minimum coverage of single-end contigs is 2. The minimum coverage of merged contigs is 2. n n:200 n:N50 min N80 N50 N20 E-size max sum name 6298 2869 1063 200 236 277 469 418 4507 865655 test-3.fa awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \ test-2.path test-1.fa >test-indel.fa ln -sf test-3.fa test-unitigs.fa abyss-map -v -j2 -l64 reads1.fq reads2.fq test-3.fa \ |abyss-fixmate -v -l64 -h test-3.hist \ |sort -snk3 -k4 \ |DistanceEst -v -j2 -k64 -l64 -s200 -n10 -o test-3.dist test-3.hist Reading `test-3.fa'... Reading from standard input... Using 913 kB of memory and 145 B/sequence. Reading `test-3.fa'... Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Read 1.4 MB in 6298 contigs. Using 13.2 MB of memory and 9.4 B/bp. Read 0 alignments Mateless 0 Unaligned 0 Singleton 0 FR 0 RF 0 FF 0 Different 0 Total 0 abyss-fixmate: error: All reads are mateless. This can happen when first and second read IDs do not match. error: `test-3.hist': No such file or directory make: *** [test-3.dist] Error 1 make: *** Deleting file `test-3.dist'