ABYSS -k27 -q3 --coverage-hist=coverage.hist -s Tdiscoideus2-bubbles.fa -o Tdiscoideus2-1.fa /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R1_001.trimmed.fastq.gz /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R2_001.trimmed.fastq.gz ABySS 2.0.2 ABYSS -k27 -q3 --coverage-hist=coverage.hist -s Tdiscoideus2-bubbles.fa -o Tdiscoideus2-1.fa /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R1_001.trimmed.fastq.gz /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R2_001.trimmed.fastq.gz Reading `/home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R1_001.trimmed.fastq.gz'... Reading `/home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R2_001.trimmed.fastq.gz'... Loaded 1373388111 k-mer Minimum k-mer coverage is 5 Using a coverage threshold of 4... The median k-mer coverage is 18 The reconstruction is 541215521 The k-mer coverage threshold is 4.24264 Setting parameter e (erode) to 4 Setting parameter E (erodeStrand) to 1 Setting parameter c (coverage) to 4.24264 Generating adjacency Added 2829256567 edges. Eroding tips Eroded 349815993 tips. Eroded 0 tips. Pruning tips shorter than 1 bp... Pruned 1790 k-mer in 1790 tips. Pruning tips shorter than 2 bp... Pruned 3011 k-mer in 1656 tips. Pruning tips shorter than 4 bp... Pruned 8989 k-mer in 2878 tips. Pruning tips shorter than 8 bp... Pruned 29011 k-mer in 4952 tips. Pruning tips shorter than 16 bp... Pruned 89723 k-mer in 8085 tips. Pruning tips shorter than 27 bp... Pruned 140700 k-mer in 7333 tips. Pruning tips shorter than 27 bp... Pruned 90 k-mer in 8 tips. Pruning tips shorter than 27 bp... Pruned 26702 tips in 7 rounds. Marked 141246315 edges of 62528695 ambiguous vertices. Removing low-coverage contigs (mean k-mer coverage < 4.24264) Found 1023285082 k-mer in 67538652 contigs before removing low-coverage contigs. Removed 487806783 k-mer in 26322028 low-coverage contigs. Split 52613741 ambigiuous branches. Eroding tips Eroded 1747403 tips. Eroded 0 tips. Pruning tips shorter than 1 bp... Pruned 56641 k-mer in 56641 tips. Pruning tips shorter than 2 bp... Pruned 68505 k-mer in 48505 tips. Pruning tips shorter than 4 bp... Pruned 152163 k-mer in 63677 tips. Pruning tips shorter than 8 bp... Pruned 302218 k-mer in 66562 tips. Pruning tips shorter than 16 bp... Pruned 525705 k-mer in 56781 tips. Pruning tips shorter than 27 bp... Pruned 551826 k-mer in 31495 tips. Pruning tips shorter than 27 bp... Pruned 458 k-mer in 41 tips. Pruning tips shorter than 27 bp... Pruned 323702 tips in 7 rounds. Popping bubbles Removed 236107 bubbles. Removed 236107 bubbles Marked 31047942 edges of 13312687 ambiguous vertices. Left 18681 unassembled k-mer in circular contigs. Assembled 525355674 k-mer in 13077481 contigs. Removed 841301009 k-mer. The signal-to-noise ratio (SNR) is -1.98969 dB. AdjList -k27 -m50 --dot Tdiscoideus2-1.fa >Tdiscoideus2-1.dot abyss-filtergraph --dot -k27 -g Tdiscoideus2-2.dot1 Tdiscoideus2-1.dot Tdiscoideus2-1.fa >Tdiscoideus2-1.path MergeContigs -k27 -g Tdiscoideus2-2.dot -o Tdiscoideus2-2.fa Tdiscoideus2-1.fa Tdiscoideus2-2.dot1 Tdiscoideus2-1.path PopBubbles --dot -j2 -k27 -p0.9 -g Tdiscoideus2-3.dot Tdiscoideus2-2.fa Tdiscoideus2-2.dot >Tdiscoideus2-2.path MergeContigs -k27 -o Tdiscoideus2-3.fa Tdiscoideus2-2.fa Tdiscoideus2-2.dot Tdiscoideus2-2.path awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \ Tdiscoideus2-2.path Tdiscoideus2-1.fa >Tdiscoideus2-indel.fa ln -sf Tdiscoideus2-3.fa Tdiscoideus2-unitigs.fa abyss-map -j2 -l40 /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R1_001.trimmed.fastq.gz /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R2_001.trimmed.fastq.gz Tdiscoideus2-3.fa \ |abyss-fixmate -l40 -h Tdiscoideus2-3.hist \ |sort -snk3 -k4 \ |DistanceEst -j2 -k27 -l40 -s1000 -n10 -o Tdiscoideus2-3.dist Tdiscoideus2-3.hist Overlap --dot -k27 -g Tdiscoideus2-4.dot -o Tdiscoideus2-4.fa Tdiscoideus2-3.fa Tdiscoideus2-3.dot Tdiscoideus2-3.dist Overlap: 23 Scaffold: 16 No overlap: 11 Insignificant (<5bp): 5 Homopolymer: 3 Motif: 0 Ambiguous: 0 SimpleGraph -j2 -k27 -o Tdiscoideus2-4.path1 Tdiscoideus2-4.dot Tdiscoideus2-3.dist Total paths attempted: 28262 Unique path: 15148 No possible paths: 790 No valid paths: 0 Repetitive: 0 Multiple valid paths: 3300 Too many solutions: 59 Too complex: 8965 The minimum number of pairs in a distance estimate is 10. The minimum number of pairs used in a path is 10. abyss-index --fai Tdiscoideus2-3.fa abyss-index --fai Tdiscoideus2-4.fa cat Tdiscoideus2-3.fa.fai Tdiscoideus2-4.fa.fai \ |MergePaths -j2 -k27 -o Tdiscoideus2-4.path2 - Tdiscoideus2-4.path1 PathOverlap --assemble -k27 Tdiscoideus2-4.dot Tdiscoideus2-4.path2 >Tdiscoideus2-4.path3 cat Tdiscoideus2-3.fa Tdiscoideus2-4.fa \ |PathConsensus --dot -k27 -p0.9 -o Tdiscoideus2-5.path -s Tdiscoideus2-5.fa -g Tdiscoideus2-5.dot - Tdiscoideus2-4.dot Tdiscoideus2-4.path3 cat Tdiscoideus2-3.fa Tdiscoideus2-4.fa Tdiscoideus2-5.fa |MergeContigs -k27 -o Tdiscoideus2-6.fa - Tdiscoideus2-5.dot Tdiscoideus2-5.path ln -sf Tdiscoideus2-6.fa Tdiscoideus2-contigs.fa PathOverlap --overlap -k27 --dot Tdiscoideus2-5.dot Tdiscoideus2-5.path >Tdiscoideus2-6.dot ln -sf Tdiscoideus2-6.dot Tdiscoideus2-contigs.dot abyss-map -j2 -l40 /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R1_001.trimmed.fastq.gz /home/ngutierrez/nas4/abyss/trimgalore_output/Tdiscoideus2_R2_001.trimmed.fastq.gz Tdiscoideus2-6.fa \ |abyss-fixmate -l40 -h Tdiscoideus2-6.hist \ |sort -snk3 -k4 \ |DistanceEst --dot --mean -j2 -k27 -l40 -s1000 -n10 -o Tdiscoideus2-6.dist.dot Tdiscoideus2-6.hist abyss-scaffold -k27 -s1000-10000 -n10 -g Tdiscoideus2-6.path.dot Tdiscoideus2-6.dot Tdiscoideus2-6.dist.dot >Tdiscoideus2-6.path PathConsensus --dot -k27 -p0.9 -s Tdiscoideus2-7.fa -g Tdiscoideus2-7.dot -o Tdiscoideus2-7.path Tdiscoideus2-6.fa Tdiscoideus2-6.dot Tdiscoideus2-6.path cat Tdiscoideus2-6.fa Tdiscoideus2-7.fa \ |MergeContigs -k27 -o Tdiscoideus2-8.fa - Tdiscoideus2-7.dot Tdiscoideus2-7.path ln -sf Tdiscoideus2-8.fa Tdiscoideus2-scaffolds.fa PathOverlap --overlap -k27 --dot Tdiscoideus2-7.dot Tdiscoideus2-7.path >Tdiscoideus2-8.dot ln -sf Tdiscoideus2-8.dot Tdiscoideus2-scaffolds.dot abyss-fac Tdiscoideus2-unitigs.fa Tdiscoideus2-contigs.fa Tdiscoideus2-scaffolds.fa |tee Tdiscoideus2-stats.tab n n:500 L50 min N80 N50 N20 E-size max sum name 7839167 258311 76210 500 780 1254 2096 1539 18967 293e6 Tdiscoideus2-unitigs.fa 7796392 253190 72429 500 790 1315 2232 1623 18967 295.5e6 Tdiscoideus2-contigs.fa 7795681 252703 71916 500 790 1318 2251 1635 18967 295.5e6 Tdiscoideus2-scaffolds.fa ln -sf Tdiscoideus2-stats.tab Tdiscoideus2-stats tr '\t' , Tdiscoideus2-stats.csv abyss-tabtomd Tdiscoideus2-stats.tab >Tdiscoideus2-stats.md pandoc Tdiscoideus2-stats.md >Tdiscoideus2-stats.html