`/local/genbank/workspace/reads.all/454.corrected.fq': discarded 103000 reads shorter than 32 bases The minimum coverage of single-end contigs is 1.12281. The minimum coverage of merged contigs is 2.64706. Consider increasing the coverage threshold parameter, c, to 2.64706. Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 11471816 61.6% Unaligned 515688 2.77% Singleton 786219 4.22% FR 768485 4.12% RF 5248 0.0282% FF 477 0.00256% Different 5090186 27.3% Total 18638119 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 826231 11.8% Singleton 1294697 18.5% FR 826970 11.8% RF 3545 0.0508% FF 491 0.00703% Different 4029536 57.7% Total 6981470 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 158290 31.9% Singleton 115419 23.2% FR 71884 14.5% RF 8 0.00161% FF 8 0.00161% Different 151246 30.4% Total 496855 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 238732 31.1% Unaligned 154865 20.2% Singleton 116352 15.2% FR 88814 11.6% RF 12 0.00156% FF 6 0.000782% Different 168696 22% Total 767477 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 291293 29% Singleton 211131 21% FR 185739 18.5% RF 31 0.00309% FF 18 0.00179% Different 315639 31.4% Total 1003851 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 422328 25.3% Singleton 326143 19.6% FR 369071 22.1% RF 52 0.00312% FF 51 0.00306% Different 550300 33% Total 1667945 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 510758 23.8% Singleton 402022 18.7% FR 511956 23.8% RF 74 0.00344% FF 76 0.00354% Different 723557 33.7% Total 2148443 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 817582 18.5% Singleton 760216 17.2% FR 1253927 28.3% RF 178 0.00402% FF 67 0.00151% Different 1593133 36% Total 4425103 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 216554 28.2% Singleton 166696 21.7% FR 141842 18.5% RF 12 0.00156% FF 7 0.000912% Different 242172 31.6% Total 767283 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 748759 18.6% Singleton 691491 17.2% FR 1136527 28.2% RF 165 0.0041% FF 52 0.00129% Different 1448998 36% Total 4025992 Running with max stack size of 65536 KB: SimpleGraph -s1000 -n10 -j32 -k32 -o abyss1-4.path1 abyss1-4.dot abyss1-3.dist Reading `abyss1-3.fa'... Writing `abyss1-3.fa.fai'... Reading `abyss1-4.fa'... Writing `abyss1-4.fa.fai'... n n:1000 L50 min N75 N50 N25 E-size max sum name 2058477 20341 7728 1000 1150 1374 1786 1652 13586 29.06e6 abyss1-4.path2 Running with max stack size of 65536 KB: PathConsensus --dot -k32 -p0.9 -o abyss1-5.path -s abyss1-5.fa -g abyss1-5.dot - abyss1-4.dot abyss1-4.path3 Ambiguous paths: 20 Merged: 6 No paths: 0 Too many paths: 0 Too complex: 0 Dissimilar: 14 The minimum coverage of single-end contigs is 1.12281. The minimum coverage of merged contigs is 2.66667. Consider increasing the coverage threshold parameter, c, to 2.66667. Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 11471816 61.6% Unaligned 515688 2.77% Singleton 786214 4.22% FR 775519 4.16% RF 6248 0.0335% FF 481 0.00258% Different 5082153 27.3% Total 18638119 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 826231 11.8% Singleton 1294692 18.5% FR 829512 11.9% RF 4267 0.0611% FF 497 0.00712% Different 4026271 57.7% Total 6981470 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 158290 31.9% Singleton 115419 23.2% FR 72572 14.6% RF 8 0.00161% FF 8 0.00161% Different 150558 30.3% Total 496855 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 238732 31.1% Unaligned 154865 20.2% Singleton 116349 15.2% FR 89769 11.7% RF 12 0.00156% FF 6 0.000782% Different 167744 21.9% Total 767477 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 291293 29% Singleton 211132 21% FR 187031 18.6% RF 32 0.00319% FF 18 0.00179% Different 314345 31.3% Total 1003851 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 422327 25.3% Singleton 326147 19.6% FR 371736 22.3% RF 53 0.00318% FF 51 0.00306% Different 547631 32.8% Total 1667945 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 510758 23.8% Singleton 402023 18.7% FR 515508 24% RF 77 0.00358% FF 76 0.00354% Different 720001 33.5% Total 2148443 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 817582 18.5% Singleton 760215 17.2% FR 1264537 28.6% RF 184 0.00416% FF 67 0.00151% Different 1582518 35.8% Total 4425103 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 216554 28.2% Singleton 166697 21.7% FR 143169 18.7% RF 12 0.00156% FF 7 0.000912% Different 240844 31.4% Total 767283 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... Mateless 0 Unaligned 748758 18.6% Singleton 691495 17.2% FR 1146116 28.5% RF 170 0.00422% FF 53 0.00132% Different 1439400 35.8% Total 4025992 warning: Removed 13472 invalid edges. n n:1000 L50 min N75 N50 N25 E-size max sum name 2057738 21457 8085 1000 1151 1385 1821 1666 13617 30.87e6 n=10 s=1000 2058437 22156 8462 1000 1146 1366 1772 1639 13617 31.51e6 n=10 s=2000 2058464 22183 8464 1000 1147 1367 1775 1639 13617 31.56e6 n=10 s=5000 2058464 22183 8464 1000 1147 1367 1775 1639 13617 31.56e6 n=10 s=10000 Best scaffold N50 is 1385 at n=10 s=1000. n n:1000 L50 min N75 N50 N25 E-size max sum name 2057738 21457 8085 1000 1151 1385 1821 1666 13617 30.87e6 n=10 s=1000 Running with max stack size of 65536 KB: PathConsensus --dot -k32 -p0.9 -s abyss1-7.fa -g abyss1-7.dot -o abyss1-7.path abyss1-6.fa abyss1-6.dot abyss1-6.path Ambiguous paths: 709 Merged: 45 No paths: 659 Too many paths: 0 Too complex: 4 Dissimilar: 1 The minimum coverage of single-end contigs is 1.12281. The minimum coverage of merged contigs is 2.7. Consider increasing the coverage threshold parameter, c, to 2.7.