ABYSS -k21 -q3 -e2 -E0 -c2 -v --SS --coverage-hist=coverage.hist -s K21_prova-bubbles.fa -o K21_prova-1.fa prova_R1.fastq prova_R2.fastq ABySS 1.9.0 ABYSS -k21 -q3 -e2 -E0 -c2 -v --SS --coverage-hist=coverage.hist -s K21_prova-bubbles.fa -o K21_prova-1.fa prova_R1.fastq prova_R2.fastq Reading `prova_R1.fastq'... Read 100000 reads. Hash load: 5760131 / 1073741824 = 0.00536 using 624 MB Read 200000 reads. Hash load: 10782817 / 1073741824 = 0.01 using 841 MB Read 300000 reads. Hash load: 15185551 / 1073741824 = 0.0141 using 1.02 GB Read 400000 reads. Hash load: 19045527 / 1073741824 = 0.0177 using 1.17 GB Read 500000 reads. Hash load: 22606104 / 1073741824 = 0.0211 using 1.31 GB Read 600000 reads. Hash load: 25792695 / 1073741824 = 0.024 using 1.44 GB Read 700000 reads. Hash load: 28708683 / 1073741824 = 0.0267 using 1.56 GB Read 800000 reads. Hash load: 31422715 / 1073741824 = 0.0293 using 1.67 GB Read 900000 reads. Hash load: 33840568 / 1073741824 = 0.0315 using 1.77 GB Read 1000000 reads. Hash load: 36070666 / 1073741824 = 0.0336 using 1.86 GB Read 1000000 reads. Hash load: 36070666 / 1073741824 = 0.0336 using 1.86 GB `prova_R1.fastq': reversed 1000000 reads `prova_R1.fastq': discarded 2 reads containing non-ACGT characters Reading `prova_R2.fastq'... Read 100000 reads. Hash load: 37505485 / 1073741824 = 0.0349 using 1.92 GB Read 200000 reads. Hash load: 38809228 / 1073741824 = 0.0361 using 1.97 GB Read 300000 reads. Hash load: 40058412 / 1073741824 = 0.0373 using 2.02 GB Read 400000 reads. Hash load: 41362825 / 1073741824 = 0.0385 using 2.07 GB Read 500000 reads. Hash load: 42568704 / 1073741824 = 0.0396 using 2.12 GB Read 600000 reads. Hash load: 43693675 / 1073741824 = 0.0407 using 2.17 GB Read 700000 reads. Hash load: 44794752 / 1073741824 = 0.0417 using 2.22 GB Read 800000 reads. Hash load: 45927157 / 1073741824 = 0.0428 using 2.26 GB Read 900000 reads. Hash load: 46882846 / 1073741824 = 0.0437 using 2.3 GB Read 1000000 reads. Hash load: 47800009 / 1073741824 = 0.0445 using 2.34 GB Read 1000000 reads. Hash load: 47800009 / 1073741824 = 0.0445 using 2.34 GB `prova_R2.fastq': discarded 68 reads containing non-ACGT characters Loaded 47800009 k-mer Hash load: 47800009 / 134217728 = 0.356 using 2.31 GB Minimum k-mer coverage is 44 Coverage: 44 Reconstruction: 214 Coverage: 8.43 Reconstruction: 1004632 Coverage: 2.83 Reconstruction: 19149053 Coverage: 2 Reconstruction: 30231282 Coverage: 1.73 Reconstruction: 30231282 Using a coverage threshold of 2... The median k-mer coverage is 3 The reconstruction is 30231282 The k-mer coverage threshold is 1.73 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 Finding adjacent k-mer: 9000000 Finding adjacent k-mer: 10000000 Finding adjacent k-mer: 11000000 Finding adjacent k-mer: 12000000 Finding adjacent k-mer: 13000000 Finding adjacent k-mer: 14000000 Finding adjacent k-mer: 15000000 Finding adjacent k-mer: 16000000 Finding adjacent k-mer: 17000000 Finding adjacent k-mer: 18000000 Finding adjacent k-mer: 19000000 Finding adjacent k-mer: 20000000 Finding adjacent k-mer: 21000000 Finding adjacent k-mer: 22000000 Finding adjacent k-mer: 23000000 Finding adjacent k-mer: 24000000 Finding adjacent k-mer: 25000000 Finding adjacent k-mer: 26000000 Finding adjacent k-mer: 27000000 Finding adjacent k-mer: 28000000 Finding adjacent k-mer: 29000000 Finding adjacent k-mer: 30000000 Finding adjacent k-mer: 31000000 Finding adjacent k-mer: 32000000 Finding adjacent k-mer: 33000000 Finding adjacent k-mer: 34000000 Finding adjacent k-mer: 35000000 Finding adjacent k-mer: 36000000 Finding adjacent k-mer: 37000000 Finding adjacent k-mer: 38000000 Finding adjacent k-mer: 39000000 Finding adjacent k-mer: 40000000 Finding adjacent k-mer: 41000000 Finding adjacent k-mer: 42000000 Finding adjacent k-mer: 43000000 Finding adjacent k-mer: 44000000 Finding adjacent k-mer: 45000000 Finding adjacent k-mer: 46000000 Finding adjacent k-mer: 47000000 Added 95526490 edges. Eroding tips Eroded 13008220 tips. Eroded 0 tips. Hash load: 34791789 / 134217728 = 0.259 using 2.31 GB Pruning tips shorter than 1 bp... Removed 1811 marked k-mer. Pruned 1811 k-mer in 1811 tips. Pruning tips shorter than 2 bp... Removed 3280 marked k-mer. Pruned 3280 k-mer in 2118 tips. Pruning tips shorter than 4 bp... Removed 11595 marked k-mer. Pruned 11595 k-mer in 4283 tips. Pruning tips shorter than 8 bp... Removed 41623 marked k-mer. Pruned 41623 k-mer in 8550 tips. Pruning tips shorter than 16 bp... Removed 138839 marked k-mer. Pruned 138839 k-mer in 15622 tips. Pruning tips shorter than 21 bp... Removed 107598 marked k-mer. Pruned 107598 k-mer in 8591 tips. Pruning tips shorter than 21 bp... Removed 5 marked k-mer. Pruned 5 k-mer in 2 tips. Pruning tips shorter than 21 bp... Pruned 40977 tips in 7 rounds. Hash load: 34487038 / 134217728 = 0.257 using 2.31 GB Splitting: 1000000 Splitting: 2000000 Splitting: 3000000 Splitting: 4000000 Splitting: 5000000 Splitting: 6000000 Splitting: 7000000 Splitting: 8000000 Splitting: 9000000 Splitting: 10000000 Splitting: 11000000 Splitting: 12000000 Splitting: 13000000 Splitting: 14000000 Splitting: 15000000 Splitting: 16000000 Splitting: 17000000 Splitting: 18000000 Splitting: 19000000 Splitting: 20000000 Splitting: 21000000 Splitting: 22000000 Splitting: 23000000 Splitting: 24000000 Splitting: 25000000 Splitting: 26000000 Splitting: 27000000 Splitting: 28000000 Splitting: 29000000 Splitting: 30000000 Splitting: 31000000 Splitting: 32000000 Splitting: 33000000 Splitting: 34000000 Marked 714517 edges of 348850 ambiguous vertices. Removing low-coverage contigs (mean k-mer coverage < 2) Found 34478236 k-mer in 596193 contigs before removing low-coverage contigs. Removed 4643987 k-mer in 143655 low-coverage contigs. Split 258356 ambigiuous branches. Hash load: 29843051 / 134217728 = 0.222 using 2.31 GB Eroding tips Eroded 20080 tips. Eroded 0 tips. Hash load: 29822971 / 134217728 = 0.222 using 2.31 GB Pruning tips shorter than 1 bp... Removed 1470 marked k-mer. Pruned 1470 k-mer in 1470 tips. Pruning tips shorter than 2 bp... Removed 2065 marked k-mer. Pruned 2065 k-mer in 1648 tips. Pruning tips shorter than 4 bp... Removed 5889 marked k-mer. Pruned 5889 k-mer in 2827 tips. Pruning tips shorter than 8 bp... Removed 16319 marked k-mer. Pruned 16319 k-mer in 4224 tips. Pruning tips shorter than 16 bp... Removed 47417 marked k-mer. Pruned 47417 k-mer in 6326 tips. Pruning tips shorter than 21 bp... Removed 42081 marked k-mer. Pruned 42081 k-mer in 3326 tips. Pruning tips shorter than 21 bp... Removed 116 marked k-mer. Pruned 116 k-mer in 17 tips. Pruning tips shorter than 21 bp... Pruned 19838 tips in 7 rounds. Hash load: 29707614 / 134217728 = 0.221 using 2.31 GB Popping bubbles Removed 11695 bubbles. Removed 11695 bubbles Splitting: 1000000 Splitting: 2000000 Splitting: 3000000 Splitting: 4000000 Splitting: 5000000 Splitting: 6000000 Splitting: 7000000 Splitting: 8000000 Splitting: 9000000 Splitting: 10000000 Splitting: 11000000 Splitting: 12000000 Splitting: 13000000 Splitting: 14000000 Splitting: 15000000 Splitting: 16000000 Splitting: 17000000 Splitting: 18000000 Splitting: 19000000 Splitting: 20000000 Splitting: 21000000 Splitting: 22000000 Splitting: 23000000 Splitting: 24000000 Splitting: 25000000 Splitting: 26000000 Splitting: 27000000 Splitting: 28000000 Splitting: 29000000 Marked 207407 edges of 99661 ambiguous vertices. Left 12898 unassembled k-mer in circular contigs. Assembled 29412231 k-mer in 252740 contigs. Removed 18092395 k-mer. The signal-to-noise ratio (SNR) is 2.15 dB. AdjList -v --SS -k21 -m50 --dot K21_prova-1.fa >K21_prova-1.dot Reading `K21_prova-1.fa'... Finding overlaps of exactly k-1 bp... V=505480 E=326814 E/V=0.647 Degree: █▃▂ 01234 0: 57% 1: 24% 2-4: 20% 5+: 0% max: 4 abyss-filtergraph -v --dot -k21 -g K21_prova-2.dot1 K21_prova-1.dot K21_prova-1.fa >K21_prova-1.path Loading graph from file: K21_prova-1.dot Graph stats before: V=505480 E=326814 E/V=0.647 Degree: █▃▂ 01234 0: 57% 1: 24% 2-4: 20% 5+: 0% max: 4 Removing shim contigs from the graph... Pass 1: Checking 30536 contigs. Pass 2: Checking 656 contigs. Shim removal stats: Removed: 14500 Too Complex: 21593 Tails: 175234 Too Long: 41001 Self Adjacent: 412 Parallel Edges: 13 Reading `K21_prova-1.fa'... Edge removal stats: Removed: 0 Graph stats after: V=476480 E=297760 E/V=0.625 Degree: █▂▁ 01234 0: 60% 1: 21% 2-4: 19% 5+: 0.15% max: 19 MergeContigs -v -k21 -g K21_prova-2.dot -o K21_prova-2.fa K21_prova-1.fa K21_prova-2.dot1 K21_prova-1.path Reading `K21_prova-2.dot1'... Read 476480 vertices. Using 42.9 MB of memory. Reading `K21_prova-1.fa'... Read 238240 sequences. Using 103 MB of memory. Reading `K21_prova-1.path'... Read 0 paths. Using 103 MB of memory. Writing `K21_prova-2.dot'... V=476480 E=297760 E/V=0.625 Degree: █▂▁ 01234 0: 60% 1: 21% 2-4: 19% 5+: 0.15% max: 19 PopBubbles -v --dot -j16 -k21 --SS -p0.9 -g K21_prova-3.dot K21_prova-2.fa K21_prova-2.dot >K21_prova-2.path Reading `K21_prova-2.dot'... V=476480 E=297760 E/V=0.625 Degree: █▂▁ 01234 0: 60% 1: 21% 2-4: 19% 5+: 0.15% max: 19 Reading `K21_prova-2.fa'... Bubbles: 4960 Popped: 2328 Scaffolds: 0 Complex: 810 Too long: 0 Too many: 48 Dissimilar: 1775 V=462472 E=279094 E/V=0.603 Degree: █▂▁ 01234 0: 62% 1: 20% 2-4: 18% 5+: 0.16% max: 19 MergeContigs -v -k21 -o K21_prova-3.fa K21_prova-2.fa K21_prova-2.dot K21_prova-2.path Reading `K21_prova-2.dot'... Read 476480 vertices. Using 42.9 MB of memory. Reading `K21_prova-2.fa'... Read 238240 sequences. Using 103 MB of memory. Reading `K21_prova-2.path'... Read 4506 paths. Using 104 MB of memory. The minimum coverage of single-end contigs is 2. The minimum coverage of merged contigs is 2. n n:200 L50 min N80 N50 N20 E-size max sum name 231236 50838 16422 200 263 391 630 466 2358 18.98e6 K21_prova-3.fa awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \ K21_prova-2.path K21_prova-1.fa >K21_prova-indel.fa ln -sf K21_prova-3.fa K21_prova-unitigs.fa abyss-map -v -j16 -l21 --SS pe K21_prova-3.fa \ |abyss-fixmate -v -l21 -h pe-3.hist \ |sort -snk3 -k4 \ |DistanceEst -v -j16 -k21 -l21 -s200 -n10 -o pe-3.dist pe-3.hist /bin/bash: line 1: abyss-fixmate: command not found Reading `K21_prova-3.fa'... error: `pe-3.hist': No such file or directory Using 17.8 MB of memory and 77.1 B/sequence. Reading `K21_prova-3.fa'... Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Read 37.6 MB in 231236 contigs. Using 348 MB of memory and 9.26 B/bp. make: *** [pe-3.dist] Error 1 make: *** Deleting file `pe-3.dist'