Rerun notebook

kevlar-dev · Jul 6, 2017 · 13384a2 · 13384a2
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commit 13384a2
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Showing 10 changed files with 119 additions and 87 deletions.
diff --git a/notebook/human-sim-pico/HumanSimulationPico.ipynb b/notebook/human-sim-pico/HumanSimulationPico.ipynb
@@ -191,29 +191,29 @@
      "text": [
       "[bwa_index] Pack FASTA... 0.03 sec\n",
       "[bwa_index] Construct BWT for the packed sequence...\n",
-      "[bwa_index] 1.01 seconds elapse.\n",
+      "[bwa_index] 0.80 seconds elapse.\n",
       "[bwa_index] Update BWT... 0.03 sec\n",
       "[bwa_index] Pack forward-only FASTA... 0.02 sec\n",
-      "[bwa_index] Construct SA from BWT and Occ... 0.30 sec\n",
+      "[bwa_index] Construct SA from BWT and Occ... 0.23 sec\n",
       "[main] Version: 0.7.15-r1140\n",
       "[main] CMD: bwa index human.random.fa\n",
-      "[main] Real time: 1.423 sec; CPU: 1.383 sec\n",
+      "[main] Real time: 1.131 sec; CPU: 1.114 sec\n",
       "\n",
-      "real\t0m1.435s\n",
-      "user\t0m1.329s\n",
-      "sys\t0m0.058s\n",
+      "real\t0m1.144s\n",
+      "user\t0m1.077s\n",
+      "sys\t0m0.041s\n",
       "\n",
-      "real\t0m36.752s\n",
-      "user\t0m51.304s\n",
-      "sys\t0m0.843s\n",
+      "real\t0m29.926s\n",
+      "user\t0m44.088s\n",
+      "sys\t0m0.666s\n",
       "\n",
-      "real\t0m34.798s\n",
-      "user\t0m49.096s\n",
-      "sys\t0m0.727s\n",
+      "real\t0m30.516s\n",
+      "user\t0m45.150s\n",
+      "sys\t0m0.662s\n",
       "\n",
-      "real\t0m34.500s\n",
-      "user\t0m48.703s\n",
-      "sys\t0m0.749s\n"
+      "real\t0m31.790s\n",
+      "user\t0m46.424s\n",
+      "sys\t0m0.661s\n"
      ]
     }
    ],
@@ -250,13 +250,13 @@
       "[kevlar::counting]     done loading reads; 295877 reads processed, 22485272 k-mers stored; estimated false positive rate is 0.008; saved to \"father.counttable\"\n",
       "[kevlar::counting]     loading sample from mother-reads-dump.fq.gz\n",
       "[kevlar::counting]     done loading reads; 295581 reads processed, 6951229 k-mers stored; estimated false positive rate is 0.180; saved to \"mother.counttable\"\n",
-      "[kevlar::count] 2 samples loaded in 89.47 sec\n",
+      "[kevlar::count] 2 samples loaded in 79.09 sec\n",
       "[kevlar::count] Loading case samples\n",
       "[kevlar::counting]     computing k-mer abundances for 1 samples\n",
       "[kevlar::counting]     loading sample from proband-reads-dump.fq.gz\n",
       "[kevlar::counting]     done loading reads; 296034 reads processed, 6617158 k-mers stored; estimated false positive rate is 0.172; saved to \"proband.counttable\"\n",
-      "[kevlar::count] 1 sample(s) loaded in 56.47 sec\n",
-      "[kevlar::count] Total time: 145.95 seconds\n"
+      "[kevlar::count] 1 sample(s) loaded in 49.21 sec\n",
+      "[kevlar::count] Total time: 128.30 seconds\n"
      ]
     }
    ],
@@ -294,16 +294,16 @@
       "[kevlar::novel]    INFO: counttables for 2 sample(s) provided, any corresponding FASTA/FASTQ input will be ignored for computing k-mer abundances\n",
       "[kevlar::counting]     loading sketchfile \"mother.counttable\"...done! estimated false positive rate is 0.180\n",
       "[kevlar::counting]     loading sketchfile \"father.counttable\"...done! estimated false positive rate is 0.008\n",
-      "[kevlar::novel] Control samples loaded in 0.44 sec\n",
+      "[kevlar::novel] Control samples loaded in 0.38 sec\n",
       "[kevlar::novel] Loading case samples\n",
       "[kevlar::novel]    INFO: counttables for 1 samples provided, any corresponding FASTA/FASTQ input will be ignored for computing k-mer abundances\n",
       "[kevlar::counting]     loading sketchfile \"proband.counttable\"...done! estimated false positive rate is 0.172\n",
-      "[kevlar::novel] Case samples loaded in 0.08 sec\n",
-      "[kevlar::novel] All samples loaded in 0.53 sec\n",
+      "[kevlar::novel] Case samples loaded in 0.06 sec\n",
+      "[kevlar::novel] All samples loaded in 0.45 sec\n",
       "[kevlar::novel] Iterating over reads from 1 case sample(s)\n",
-      "[kevlar::novel] Iterated over 296033 reads in 55.78 seconds\n",
+      "[kevlar::novel] Iterated over 296033 reads in 51.97 seconds\n",
       "[kevlar::novel] Found 22684 instances of 1125 unique novel kmers in 938 reads\n",
-      "[kevlar::novel] Total time: 56.30 seconds\n"
+      "[kevlar::novel] Total time: 52.42 seconds\n"
      ]
     }
    ],
@@ -338,11 +338,11 @@
      "text": [
       "[kevlar::filter] Loading reference genome from human.random.fa\n",
       "    1 sequences and 2499976 k-mers consumed; estimated false positive rate is 0.000\n",
-      "[kevlar::filter] Reference genome loaded in 2.30 sec\n",
+      "[kevlar::filter] Reference genome loaded in 2.07 sec\n",
       "[kevlar::filter] Loading input; recalculate k-mer abundances, de-duplicate reads and merge k-mers\n",
       "    - proband.novel.augfastq.gz\n",
       "    938 instances of 938 reads consumed, annotated with 22684 instances of 1125 distinct \"interesting\" k-mers; estimated false positive rate is 0.000\n",
-      "[kevlar::filter] Input loaded in 0.58 sec\n",
+      "[kevlar::filter] Input loaded in 0.57 sec\n",
       "[kevlar::filter] Validate k-mers and print reads\n",
       "    processed 22684 instances of 1125 distinct \"interesting\" k-mers in 938 reads\n",
       "        838 instances of 95 distinct k-mers masked by the reference genome\n",
@@ -351,8 +351,8 @@
       "        407 reads with no surviving valid k-mers ignored\n",
       "        0 contaminant reads discarded\n",
       "        531 reads written to output\n",
-      "[kevlar::filter] k-mers validated and reads printed in 1.69 sec\n",
-      "[kevlar::filter] Total time: 4.56 seconds\n"
+      "[kevlar::filter] k-mers validated and reads printed in 1.30 sec\n",
+      "[kevlar::filter] Total time: 3.93 seconds\n"
      ]
     }
    ],
@@ -386,13 +386,13 @@
      "output_type": "stream",
      "text": [
       "[kevlar::partition] Loading reads from proband.novel.filtered.augfastq.gz\n",
-      "[kevlar::partition] Reads loaded in 0.64 sec\n",
+      "[kevlar::partition] Reads loaded in 0.49 sec\n",
       "[kevlar::partition] Building read graph in relaxed mode (shared novel k-mer required)\n",
-      "[kevlar::partition] Graph built in 1.09 sec\n",
+      "[kevlar::partition] Graph built in 0.85 sec\n",
       "[kevlar::partition] Writing output to prefix part\n",
       "[kevlar::overlap] grouped 531 reads into 10 connected components\n",
-      "[kevlar::partition] Output written in 0.71 sec\n",
-      "[kevlar::partition] Total time: 1.80 seconds\n"
+      "[kevlar::partition] Output written in 0.57 sec\n",
+      "[kevlar::partition] Total time: 1.42 seconds\n"
      ]
     }
    ],
@@ -426,44 +426,62 @@
       "\n",
       "\n",
       "==== iter 0 ====\n",
-      "[kevlar::assemble] WARNING: assembly graph contains 3 connected components; designated in the output by cc=N\n",
-      "[kevlar::assemble] assembled 67/76 reads from 3 connected component(s) into 3 contig(s)\n",
+      "[kevlar::assemble] loaded 129 reads and 414 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 126 nodes and 1477 edges\n",
+      "[kevlar::assemble] assembled 105/129 reads from 1 connected component(s) into 10 contig(s)\n",
       "\n",
       "\n",
       "==== iter 1 ====\n",
-      "[kevlar::assemble] assembled 107/129 reads from 1 connected component(s) into 9 contig(s)\n",
+      "[kevlar::assemble] loaded 77 reads and 182 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 75 nodes and 971 edges\n",
+      "[kevlar::assemble] assembled 65/77 reads from 1 connected component(s) into 7 contig(s)\n",
       "\n",
       "\n",
       "==== iter 2 ====\n",
-      "[kevlar::assemble] WARNING: assembly graph contains 2 connected components; designated in the output by cc=N\n",
-      "[kevlar::assemble] assembled 60/66 reads from 2 connected component(s) into 3 contig(s)\n",
+      "[kevlar::assemble] loaded 66 reads and 175 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 62 nodes and 600 edges\n",
+      "[kevlar::assemble] assembled 56/66 reads from 1 connected component(s) into 5 contig(s)\n",
       "\n",
       "\n",
       "==== iter 3 ====\n",
-      "[kevlar::assemble] assembled 21/26 reads from 1 connected component(s) into 1 contig(s)\n",
+      "[kevlar::assemble] loaded 42 reads and 85 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 42 nodes and 541 edges\n",
+      "[kevlar::assemble] assembled 37/42 reads from 1 connected component(s) into 1 contig(s)\n",
       "\n",
       "\n",
       "==== iter 4 ====\n",
-      "[kevlar::assemble] assembled 15/16 reads from 1 connected component(s) into 2 contig(s)\n",
+      "[kevlar::assemble] loaded 26 reads and 25 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 26 nodes and 225 edges\n",
+      "[kevlar::assemble] assembled 21/26 reads from 1 connected component(s) into 1 contig(s)\n",
       "\n",
       "\n",
       "==== iter 5 ====\n",
-      "[kevlar::assemble] assembled 37/42 reads from 1 connected component(s) into 1 contig(s)\n",
+      "[kevlar::assemble] loaded 21 reads and 22 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 21 nodes and 175 edges\n",
+      "[kevlar::assemble] assembled 19/21 reads from 1 connected component(s) into 2 contig(s)\n",
       "\n",
       "\n",
       "==== iter 6 ====\n",
-      "[kevlar::assemble] assembled 18/20 reads from 1 connected component(s) into 2 contig(s)\n",
+      "[kevlar::assemble] loaded 21 reads and 24 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 19 nodes and 100 edges\n",
+      "[kevlar::assemble] assembled 16/21 reads from 1 connected component(s) into 1 contig(s)\n",
       "\n",
       "\n",
       "==== iter 7 ====\n",
-      "[kevlar::assemble] assembled 16/21 reads from 1 connected component(s) into 1 contig(s)\n",
+      "[kevlar::assemble] loaded 20 reads and 24 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 18 nodes and 117 edges\n",
+      "[kevlar::assemble] assembled 18/20 reads from 1 connected component(s) into 2 contig(s)\n",
       "\n",
       "\n",
       "==== iter 8 ====\n",
-      "[kevlar::assemble] assembled 19/21 reads from 1 connected component(s) into 2 contig(s)\n",
+      "[kevlar::assemble] loaded 16 reads and 25 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 15 nodes and 88 edges\n",
+      "[kevlar::assemble] assembled 15/16 reads from 1 connected component(s) into 2 contig(s)\n",
       "\n",
       "\n",
       "==== iter 9 ====\n",
+      "[kevlar::assemble] loaded 16 reads and 53 interesting k-mers\n",
+      "[kevlar::assemble] initialized \"shared interesting k-mers\" graph with 15 nodes and 68 edges\n",
       "[kevlar::assemble] assembled 13/16 reads from 1 connected component(s) into 1 contig(s)\n"
      ]
     }

diff --git a/notebook/human-sim-pico/part.cc0.fa b/notebook/human-sim-pico/part.cc0.fa
@@ -1,6 +1,20 @@
->contig21;cc=1
-TTACACCCAAGGGGGCGTATAACATGTTACTCAGTTGCGTCGGACCGATTAATAACTCGAATGTAAGGCAGGATATTTGGAATGAGATCACTTGAGGTATCTGTTACTTCAGAGTTGCAGTGATGTGCCCCACTGTGCCTTTATATAAAGAGAGTGGGTCTTGGTCATTGTTGATT
->contig31;cc=2
-TCCCTTTCCTTAAATAACTAGAGGGCTTCCTCATCAAGGCTGGTCCTGGGTCTTGTTTTCTAATTTTTAAATCAAGACAGAGTGGGATTACGTAGGAAATCCGCGGGGCTGTGACATATATTTGTTGACAAGCATATATTGTTCCTAGAGGTCGTTGGGTTCGTTACACCCAAGGGGGCGTATAACATGTTACTCAGTTGCGTCGGACCGATTAATAACTCGAATGTAAGGCAGGATATTTGGAATGAGATCAC
->contig1;cc=3
-CTCATTCCAAATATCCTGCCTTACATTCGAGTTATTAATCGGTCCGACGCAACTGAGTAACATGTTATACGCCCCCTAGGGTGTAACGAACCCAACGACCTCTAGGAACAATA
+>contig87;cc=1
+GTGGTCCGAGTGTATCACATTCGACCCTTTCTATATTTTGATCTGTTCTTTTGTTCGTCGATTTACCCACGACGTCCATCGTAAAACAAACACTTTGTTTTACTGGACTCCGTCCTTAGGAACAGAACTTACGAGTCGGTGACTACCCGGAGTCGGTCGAATATAATAATTTTGCTCGAACCTCGTAGTAAAGATATGGATAGGACACAGAACACAAATAATAAAGTCAATCGAAACAAGAGTTCATAGTCATCAAATTGGTTTTGTTTAGGTCTGGTTTGGTGATCAAAGCTAGAAGGCATAT
+>contig91;cc=1
+TTTTGACAAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGTTTGAAAATTCAATTGATCACCGTTGTCAGAGACCACTCTCACAGTGGTCGGAGTGTATCACATTCGACCCTTTCTATATTTTGATCTGTTCTTTTGTT
+>contig76;cc=1
+GATTCCTTTGTTTTTGTCAAAACTATGAGAAAATTTTGTTCACTCAGCCTTACTTTGGGAAACAAAAAAAAAACTAAGCTTTTGGATTACAGTTGGAAGTCAGGTCTCA
+>contig89;cc=1
+TAGGTTAAATGACCATCTCACTTCATGTGCAGAGGCTGGAATTGAATGGAAGCCCAAATGAGGAGGAAATGCCCATATCCCTTCTAGCTTTGATCACCAAACCAGACCTAAACAAAACCAATTTGATGACTATGAACTCTTGTTTCGATTGACTTTATTATTTGTGTTCTGTG
+>contig88;cc=1
+ACAAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGTTTGAAAATTCAATTGATCACCGTTGTCAGAGACCACTCTCACAGTGGTCCGAGTGTATCACATTCGACCCTTTCTATATTTTGATCTGTTCTTTTGTTCGTCGATTTACCCACGACGTCCATCGTAACACAAACA
+>contig90;cc=1
+TTACATTTATTCGTTTGTGCAGGCTGAGACCTCACTTCCAACTGTAATCCAAAAGCTTAGTTTTTTTTTTGTTTCCCAAAGTAAGGCTGAGTGAACAATATTTTCTCATAGTTTTGACAAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGGTTGAAAATTCAATTGATCACCGTTGTCAG
+>contig16;cc=1
+GAACCTCGTAGTAAAGATATGGATAGGACACAGAACACAAATAATAAAGTCAATCGAAACAAGAGTTCATAGTCATCAAATTGGTTTTGTTTAGGTCTGGT
+>contig17;cc=1
+AGTTTTTTTTTTGTTTCCCAAAGTAAGGCTGAGTGAACAATATTTTCTCATAGTTTTGACAAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGTTTGA
+>contig92;cc=1
+TGTTCGTCGATTTACCCACTACGTCCATCGTAAAACAAACACTTTGTTTTACTGGACTCCGTCCTTAGGAACAGAACTTACGAGTCGGTGACTACCCGGAGTCGGTCGAATATAATAATTTTGCTCGAACGTCGTAGTAAAGATATGG
+>contig79;cc=1
+CACCACTGTGAGAGTGGTCTCTGACAACGGTGATCAATTGAATTTTCAAACTCCCGAGTTTAATAACTAAGGATTCCTTTGTTTTTGTCAAAACTATGAGAAAATATTGTTCACTCAGCCTTACTTTGGGAAACAAAAAAAA
diff --git a/notebook/human-sim-pico/part.cc1.fa b/notebook/human-sim-pico/part.cc1.fa
@@ -1,18 +1,14 @@
->contig86;cc=1
-CAAACTCCCGAGTTTAATAACTAAGGATTCCTTTGTTTTTGTCAAAACTATGAGAAAATATTGTTCACTCAGCCTTACTTTGGGAAACAAAAAAAAAACTAAGCTTTTGGATTACAGTTGGAAGTGAGGTCTCAGCCTGCACAAACGAATAAATGTAA
->contig92;cc=1
-TTTTGACAAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGTTTGAAAATTCAATTGATCACCGTTGTCAGAGACCACTCTCACAGTGGTCGGAGTGTATCACATTCGACCCTTTCTATATTTTGATCTGTTCTTTTGTT
->contig91;cc=1
-TAGGTTAAATGACCATCTCACTTCATGTGCAGAGGCTGGAATTGAATGGAAGCCCAAATGAGGAGGAAATGCCCATATCCCTTCTAGCTTTGATCACCAAACCAGACCTAAACAAAACCAATTTGATGACTATGAACTCTTGTTTCGATTGACTTTATTATTTGTGTTCTGTG
->contig78;cc=1
-GATTCCTTTGTTTTTGTCAAAACTATGAGAAAATTTTGTTCACTCAGCCTTACTTTGGGAAACAAAAAAAAAACTAAGCTTTTGGATTACAGTTGGAAGTCAGGTCTCA
->contig93;cc=1
-TGTTCGTCGATTTACCCACTACGTCCATCGTAAAACAAACACTTTGTTTTACTGGACTCCGTCCTTAGGAACAGAACTTACGAGTCGGTGACTACCCGGAGTCGGTCGAATATAATAATTTTGCTCGAACGTCGTAGTAAAGATATGG
->contig79;cc=1
-TTTTGCTCGAACCTCGTAGTAAAGATATGGATAGGACACAGAACACAAATAATAAAGTCAATCGAAACAAGAGTTCATAGTCATCAAATTGGTTTTGTTTAGGTCTGGTTTGGTGATCAAAGCTAGAAGGCATAT
->contig89;cc=1
-GTGGTCCGAGTGTATCACATTCGACCCTTTCTATATTTTGATCTGTTCTTTTGTTCGTCGATTTACCCACGACGTCCATCGTAAAACAAACACTTTGTTTTACTGGACTCCGTCCTTAGGAACAGAACTTACGAGTCGGTGACTACCCGGAGTCGGTCGAATATAATAATTTTGCTCGAACCTCGTAGTAAAGATATGGATAGGACACAGAACACAAATAATAAAGTCAATCGAAACAAGAGTTCATAGTCATCAAATTGGTTTTTTTT
->contig85;cc=1
-GTTTTTTTTTTGTTTCCCAAAGTAAGGCTGAGTGAACAATATTTTCTCATAGTTTTGACAAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGTTTGAAAATTCAATTGATCACCGTTGTCAGAGACCACTCTCACAGTGGTG
->contig90;cc=1
-ACAAAAACAAAGGAATCCTTAGTTATTAAACTCGGGAGTTTGAAAATTCAATTGATCACCGTTGTCAGAGACCACTCTCACAGTGGTCCGAGTGTATCACATTCGACCCTTTCTATATTTTGATCTGTTCTTTTGTTCGTCGATTTACCCACGACGTCCATCGTAACACAAACA
+>contig51;cc=1
+CTCAGTTGCGTCGGACCGATTAATAACTCGAATGTAAGGCAGGATATTTGGAATGAGATCACTTGAGGTATCTGTTACTTCAGAGTTGCAGTGATGTGCCCCACTGTGCCTTTATATAAAGAGAGTGGGTCTTGGTCATTGTTGATT
+>contig52;cc=1
+TCCCTTTCCTTAAATAACTAGAGGGCTTCCTCATCAAGGCTGGTCCTGGGTCTTGTTTTCTAATTTTTAAATCAAGACAGAGTGGGATTACGTAGGAAATCCGCGGGGCTGTGACATATATTTGTTGACAAGCATATATTGTTCCTAGAGGTCGTTGGGTTCGTTACACCCAAGGGGGCGTATTA
+>contig48;cc=1
+TGCAACTCTGAAGTAACAGATACCTCAAGTGATCTCATTCCAAATATCCTGCCTTACATTCGAGTTATTAATCGGTCCGACGCAACTGAGTAACATGTTATACGCCCCCTTGGGTGTAACGAACCCAACGACCTCTAGGAACAATATATGCT
+>contig55;cc=1
+CATCACTGCAACTCTGAAGTAACAGATACCTCAATTGATCTCATTCCAAATATCCTGCCTTACATTCGAGTTATTAATCGGTCCGACGCAACTGAGTAACATGTTATTCGCCCCCTTGGGTGTAACGAACCCAACGACCTCTAGGAACAATATATGCTTGTCAACAAATAT
+>contig54;cc=1
+ATCCGCGGGGCTGTGACATATATTTGTTGACAAGCATATATTGTTCCTAGAGGTCGTTGGGTTCGTTACACCCAAGGGGGCGTATAACATGTTACTCAGTTGCGTCGGACCGATTATTAACTCGAATGTAAGGCAGGATATTTGGAATGAGATCACTTGAGGTA
+>contig56;cc=1
+AGACCCACTCTCTTTATAAAAAGGCACAGTGGGGCACATCACTGCAACTCTGAAGTAACAGATACCTCAAGTGATCTCATTCCAAATATCCTGCCTTACATTCGAGTTATTAATCGGTCAGACGCAACTGAGTAACATGTTATACGCCCCCTTGGGTGTAACGAACCCAACGA
+>contig53;cc=1
+TATTGTTCCTAGAGGTCGTTGGGTTCGTTACACCCTAGGGGGCGTATAACATGTTACTCAGTTGCGTCGGACCGATTAATAACTCGAATGTAAGGCAGGATATTTGGAATGAGAACACTTGAGGTATCTGTTACTTC
diff --git a/notebook/human-sim-pico/part.cc2.fa b/notebook/human-sim-pico/part.cc2.fa
@@ -1,6 +1,10 @@
->contig12;cc=1
-GATATAAGCTCCGTGTTCTCAGTTGGTGGGTAACAGAACCCGCAAGCACACCGCTTTCAGTGTGTCACATGCACAGATAAATCAAAAATGGGGTTTCAGTCAGGAAAAAATTACCCTAAATTCTCCATGCCAAATTTTTGTTTTTTTTTAAAGTGACTGATAAGTATGCT
->contig32;cc=2
+>contig41;cc=1
+TTTTTCCTGACTGAAACCCCATTTTTGATTTATCTGTGCATGTGACACACTGAAAGCGGTGTGCTTGCGGGTTCTGTTACCCACCAACTGAGAACACGGAGCTTATATCTACGGCCCCTC
+>contig46;cc=1
+AGCATACTTATCAGTCACTTTAAAAAAAAACAAAAATTTGGCATGGAGAATTTAGGGTAATTTTTTCCTGACTGAAACCCCATTTTTGATTTATCTGTGCATGTGACACACTGAAAGCGGTGTGCTTGCGGGTTCTGTTACCCACCAACTGAGAAAACGGAGCTTATATCTACGGCCCCTCAA
+>contig45;cc=1
+ATTGCGTCTAATTGATGGGCCGTAGATATAAGCTCCGTGTTCTCAGTTGGTGGGTAACAGAACCCGCAAGCACACCGCTTTCAGTGTGTCACATGCACAGATAATTCAAAAATGGGGTTTCAGTCAGGAAAAAATTAC
+>contig47;cc=1
+CTGACTGAAACCCCATTTTTGATTTATCTGTGCATGTGACACACTGAAAGCGGTGTGCATGCGGGTTCTGTTACCCACCAACTGAGAACACGGAGCTTATAACTACGGCCCCTCAATTAGACGCAATTGCGTACGCTAAGCTGTTGCTTAACTTAATCTTAAGTATCACG
+>contig44;cc=1
 TGACACACTGAAAGCGGTGTGCTTGCGGGTTCTGTTACCCACCAACTGAGAACACGGAGCTTATATCTACGGCCCCTCAATTAGACGCAATTGCGTACGCTAAGCTGTTGCTTAACTTAATCTTAAGTATCACGCTGCGTCTCGGCCTGTTAGAAAACGGTGGCAGCCGTGATCTTTCCTTCCCTGAGATGTTCAACGAATCTGCCAAACTCTCATGGTTGCATTCTGGTCTCT
->contig33;cc=2
-ATTTTTGATTTATCTGTGCATGTGACACACTGAAAGCGGTGTGCTTGCGGGTTCTGTTACCCACCAACTGAGAACACGGAGCTTATATCTACGGCCCCTCAATTAGACGCAATTTCGTACG
diff --git a/notebook/human-sim-pico/part.cc3.fa b/notebook/human-sim-pico/part.cc3.fa
@@ -1,2 +1,2 @@
->contig20;cc=1
-CTGATTTTGAAGAAGAAAATCAGTTTAAGTCAAAAGGTTACTTTCCTTGTCCTGAACTGGAGAACTGGGGCCCTGCCATTATAGATGCTAGATTCACATCTTCATTTATTTTTACTTTTTGTCTTGACAGAGTGGGCGCTGGTTTTTTTAATTATTTTTGGCCAATCAAAAAATACTCTCCTTCGTGGGT
+>contig36;cc=1
+GTTTTTATTTCTTTCCCTACCTTCCACAAATGTATGCCACCTACCCTGCGGGGGCACTTTCCTTGGGCCGGGAGGACACATAAACTGTTGTCTCGATCTTGTATATCAAAAATAACTCGACCTTGTGAAATGAGGTCAACGGGATGCTAGACAATACATTTGGATCTCGGCGGATCACATTATATAAATTCTTCAAGCTTTTATATATTAACATCTCAAATATAATAATA
diff --git a/notebook/human-sim-pico/part.cc4.fa b/notebook/human-sim-pico/part.cc4.fa
@@ -1,4 +1,2 @@
->contig1;cc=1
-TGACTTTAAATGATTTATGATAAAAAAGAGACATGTAAATGTCATTCAACATTCTCCAGGAAGTCAAGTCCTTCTGCAAAAGGAACCCTGTAATAAATGC
->contig12;cc=1
-TTACTTCAAATGTGCAGTGTTGGGAGCTAAGCATGGGGTGCGTTTGGATAAAAATAGCACGCTAGAGGTTTTCTCTGTTAAGTAAGAAGTCCTGACTTTAAATGATTTATGATAAAAAAGAGACATGTAAATGTCATTCAACATTCTCCAGGAAGTCAATTCCTTCTGCAAAAGGA
+>contig20;cc=1
+CTGATTTTGAAGAAGAAAATCAGTTTAAGTCAAAAGGTTACTTTCCTTGTCCTGAACTGGAGAACTGGGGCCCTGCCATTATAGATGCTAGATTCACATCTTCATTTATTTTTACTTTTTGTCTTGACAGAGTGGGCGCTGGTTTTTTTAATTATTTTTGGCCAATCAAAAAATACTCTCCTTCGTGGGT
diff --git a/notebook/human-sim-pico/part.cc5.fa b/notebook/human-sim-pico/part.cc5.fa
@@ -1,2 +1,4 @@
->contig36;cc=1
-GTTTTTATTTCTTTCCCTACCTTCCACAAATGTATGCCACCTACCCTGCGGGGGCACTTTCCTTGGGCCGGGAGGACACATAAACTGTTGTCTCGATCTTGTATATCAAAAATAACTCGACCTTGTGAAATGAGGTCAACGGGATGCTAGACAATACATTTGGATCTCGGCGGATCACATTATATAAATTCTTCAAGCTTTTATATATTAACATCTCAAATATAATAATA
+>contig17;cc=1
+TGACACCCTATAGACAGTGGTTTTAGTTAAACTAATCTCCAGAAAAACATACACCCTCACATGTGGTGATTAGGTTAGAATGAAACCTACTGGAATTAATTGGCAGACTTTCTACAAATAAATTAATTTATTTACTTATAATTTTCCTCC
+>contig16;cc=1
+TCCTGCTTAGTTTTAGGTAAAGGGAAAGTGACACCCTATAGACAGTGGTTTTAGTTAAACTAATCTCCAGAAAAACATACACCCTCACATGTGGTGATTAGGTTAGAATGAAACCTACTGGAATA
diff --git a/notebook/human-sim-pico/part.cc6.fa b/notebook/human-sim-pico/part.cc6.fa
@@ -1,4 +1,2 @@
 >contig13;cc=1
-AAAGTACAGATGGTCTTAATATTTTGTATTACCAGAATACCACCATGTTCCAGGTTGGGAGGCCAGGCTCAGCTAAGGACAGAATTCAACATGTTCCCCCAAGCTCTGAAAACACACACTTTTCACTTCAAAAA
->contig14;cc=1
-TGCCCCCAGGTCCAGGTATGCTTGTTAGGACGCCTGTAACCATACAAAGTACAGATGGTCTTAATATTTTGTATTACCAGAATACCACCATGTTCCAGGTTGGGAGGCCAGGCTCAGCTAAGGACAGAATTCAACATGGTCCCCC
+TCTGGTGTTTGAGGCAAAAAGGCAGACTTAAATTCTAAATCACACCTGTGCTTCCAGCACTACCTTCAAGCGCAGGTTCGAGCCAGTCAGGACTGCTCCCCCACTTCCTCAAGTCTCATCGTGTTTTTTTTAGAGCTAGTTTCTTAGTCTCATTAGGCTTCAGTCACCATCATTTCTTATAGGAATACCA
diff --git a/notebook/human-sim-pico/part.cc7.fa b/notebook/human-sim-pico/part.cc7.fa
@@ -1,2 +1,4 @@
+>contig14;cc=1
+TGCCCCCAGGTCCAGGTATGCTTGTTAGGACGCCTGTAACCATACAAAGTACAGATGGTCTTAATATTTTGTATTACCAGAATACCACCATGTTCCAGGTTGGGAGGCCAGGCTCAGCTAAGGACAGAATTCAACATGGTCCCCC
 >contig13;cc=1
-TCTGGTGTTTGAGGCAAAAAGGCAGACTTAAATTCTAAATCACACCTGTGCTTCCAGCACTACCTTCAAGCGCAGGTTCGAGCCAGTCAGGACTGCTCCCCCACTTCCTCAAGTCTCATCGTGTTTTTTTTAGAGCTAGTTTCTTAGTCTCATTAGGCTTCAGTCACCATCATTTCTTATAGGAATACCA
+AAAGTACAGATGGTCTTAATATTTTGTATTACCAGAATACCACCATGTTCCAGGTTGGGAGGCCAGGCTCAGCTAAGGACAGAATTCAACATGTTCCCCCAAGCTCTGAAAACACACACTTTTCACTTCAAAAA