skoren
commented
6 years ago Your second attempt did not work, it ended up with only 3x, this would imply the longest reads aren't very high quality but that's not necessarily surprising itself. The k-mer distribution from the corrected reads is consistent with a 2-3mb genome size. However, the 22mb assembly when you increase the coverage and the lack of assembly with the 90x coverage is suspicious.
Are you able to share the data, see the FAQ for instructions to send it to us. Otherwise, you could try running mash screen (https://github.com/marbl/Mash) on it as well as running GenomeScope (http://qb.cshl.edu/genomescope/) on the unitigging/0-*/*.histogram outputs. Have you tried mapping the data to a close reference to estimate identity/coverage? That should provide more information on what's going on with the data.
ml3958
rbartelme
I have been trying to assemble a bacteria genome of 2.5mb with a high coverage 1800X PacBio data, but had no luck. I tried a few parameter suggested, None of them gave me ideal continous contigs.
Attempts:
corOutCoverage=100- it gave me sufficient corrected reads (91X), but discontinuous contigs (67 sequences, total length 2696826 bp including 6 repeats of total length 198541 bp).corMhapSensitivity=high corMinCoverage=0- coverage is also ok (40X), but contigs (total length 246496bp) are only 10% coverage compared to genome size (2.5mb)corOutCoverage=500 ovlErrorRate=0.15 obtErrorRate=0.15to smash hyplotype. This gave me crazy number of contigs (774 sequences, total length 28825721 bp including 180 repeats of total length 10087773 bp) and ran over two days.....I am rerunning Canu with just corOutCoverage=200 now. In the meantime, I am questioning if my samples is contaminated..... any suggestions?
Thank you!!
The report for attempts 1. 2. 3. are below
[CORRECTION/MERS]
-- 16-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 590490024 *****--> 0.3880 0.1283 -- 2- 2 384381114 ** 0.6406 0.2953 -- 3- 4 344538198 ** 0.7861 0.4397 -- 5- 7 132698608 **** 0.9122 0.6215 -- 8- 11 39138405 * 0.9643 0.7368 -- 12- 16 14968864 * 0.9827 0.7986 -- 17- 22 6729681 0.9907 0.8374 -- 23- 29 3222241 0.9945 0.8625 -- 30- 37 1586497 0.9964 0.8789 -- 38- 46 778504 0.9973 0.8895 -- 47- 56 376394 0.9978 0.8960 -- 57- 67 189576 0.9980 0.8999 -- 68- 79 117437 0.9982 0.9023 -- 80- 92 131456 0.9982 0.9042 -- 93- 106 236023 0.9983 0.9068 -- 107- 121 411456 0.9985 0.9121 -- 122- 137 568627 0.9988 0.9227 -- 138- 154 570369 0.9991 0.9390 -- 155- 172 398398 0.9995 0.9569 -- 173- 191 193149 0.9998 0.9706 -- 192- 211 72915 0.9999 0.9778 -- 212- 232 28822 0.9999 0.9808 -- 233- 254 16500 0.9999 0.9822 -- 255- 277 12514 1.0000 0.9830 -- 278- 301 9921 1.0000 0.9838 -- 302- 326 7569 1.0000 0.9844 -- 327- 352 5747 1.0000 0.9849 -- 353- 379 4418 1.0000 0.9853 -- 380- 407 3747 1.0000 0.9857 -- 408- 436 3033 1.0000 0.9860 -- 437- 466 2442 1.0000 0.9862 -- 467- 497 1792 1.0000 0.9865 -- 498- 529 1390 1.0000 0.9867 -- 530- 562 1082 1.0000 0.9868 -- 563- 596 862 1.0000 0.9870 -- 597- 631 680 1.0000 0.9871 -- 632- 667 618 1.0000 0.9871 -- 668- 704 527 1.0000 0.9872 -- 705- 742 530 1.0000 0.9873 -- 743- 781 571 1.0000 0.9874 -- 782- 821 627 1.0000 0.9875
-- 6187952 (max occurrences) -- 4012007789 (total mers, non-unique) -- 931423950 (distinct mers, non-unique) -- 590490024 (unique mers)
[CORRECTION/CORRECTIONS]
-- Reads to be corrected: -- 7742 reads longer than 43630 bp -- 280804813 bp -- Expected corrected reads: -- 7742 reads -- 249007801 bp -- 26861 bp minimum length -- 32163 bp mean length -- 45987 bp n50 length
[TRIMMING/READS]
-- In gatekeeper store 'trimming/hc1_hybrid_cov100.gkpStore': -- Found 7838 reads. -- Found 227633046 bases (91.41 times coverage).
-- Read length histogram (one '*' equals 10.9 reads): -- 0 999 0 -- 1000 1999 92 **** -- 2000 2999 42 * -- 3000 3999 31 -- 4000 4999 19 -- 5000 5999 12 -- 6000 6999 8 -- 7000 7999 4 -- 8000 8999 7 -- 9000 9999 5 -- 10000 10999 5 -- 11000 11999 7 -- 12000 12999 3 -- 13000 13999 5 -- 14000 14999 6 -- 15000 15999 7 -- 16000 16999 11 -- 17000 17999 14 -- 18000 18999 28 -- 19000 19999 20 * -- 20000 20999 23 -- 21000 21999 52 -- 22000 22999 73 ** -- 23000 23999 117 ** -- 24000 24999 223 **** -- 25000 25999 457 * -- 26000 26999 746 **** -- 27000 27999 722 ** -- 28000 28999 763 ** -- 29000 29999 746 **** -- 30000 30999 658 **** -- 31000 31999 680 ** -- 32000 32999 606 *** -- 33000 33999 581 *** -- 34000 34999 432 * -- 35000 35999 294 ** -- 36000 36999 195 *** -- 37000 37999 67 ** -- 38000 38999 38 * -- 39000 39999 16 * -- 40000 40999 6 -- 41000 41999 4 -- 42000 42999 3 -- 43000 43999 0 -- 44000 44999 1 -- 45000 45999 2 -- 46000 46999 4 -- 47000 47999 2 -- 48000 48999 0 -- 49000 49999 0 -- 50000 50999 0 -- 51000 51999 1
[TRIMMING/MERS]
-- 22-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 21250603 *****--> 0.8027 0.0934 -- 2- 2 1605147 ** 0.8633 0.1075 -- 3- 4 793634 ** 0.8838 0.1147 -- 5- 7 257946 * 0.8983 0.1220 -- 8- 11 77877 0.9042 0.1266 -- 12- 16 23408 0.9063 0.1290 -- 17- 22 10086 0.9069 0.1302 -- 23- 29 28710 * 0.9073 0.1311 -- 30- 37 65284 0.9085 0.1349 -- 38- 46 143680 **** 0.9113 0.1461 -- 47- 56 241228 ** 0.9169 0.1747 -- 57- 67 405156 *** 0.9265 0.2335 -- 68- 79 496940 ** 0.9423 0.3499 -- 80- 92 447531 0.9609 0.5112 -- 93- 106 328006 ** 0.9774 0.6773 -- 107- 121 176200 **** 0.9893 0.8164 -- 122- 137 87187 0.9957 0.9004 -- 138- 154 22102 0.9988 0.9467 -- 155- 172 5221 0.9995 0.9593 -- 173- 191 3770 0.9997 0.9630 -- 192- 211 1365 0.9998 0.9658 -- 212- 232 198 0.9999 0.9669 -- 233- 254 100 0.9999 0.9671 -- 255- 277 81 0.9999 0.9672 -- 278- 301 52 0.9999 0.9673 -- 302- 326 50 0.9999 0.9674 -- 327- 352 42 0.9999 0.9675 -- 353- 379 96 0.9999 0.9675 -- 380- 407 46 0.9999 0.9677 -- 408- 436 96 0.9999 0.9678 -- 437- 466 27 0.9999 0.9679 -- 467- 497 19 0.9999 0.9680 -- 498- 529 19 0.9999 0.9680 -- 530- 562 30 0.9999 0.9681 -- 563- 596 34 0.9999 0.9681 -- 597- 631 8 0.9999 0.9682 -- 632- 667 4 0.9999 0.9683 -- 668- 704 4 0.9999 0.9683 -- 705- 742 4 0.9999 0.9683 -- 743- 781 5 0.9999 0.9683 -- 782- 821 1 0.9999 0.9683
-- 874625 (max occurrences) -- 206217845 (total mers, non-unique) -- 5223583 (distinct mers, non-unique) -- 21250603 (unique mers)
[TRIMMING/TRIMMING] -- PARAMETERS:
-- 1000 (reads trimmed below this many bases are deleted) -- 0.1440 (use overlaps at or below this fraction error) -- 1 (break region if overlap is less than this long, for 'largest covered' algorithm) -- 1 (break region if overlap coverage is less than this many read, for 'largest covered' algorithm) --
-- INPUT READS:
-- 7838 reads 227633046 bases (reads processed) -- 0 reads 0 bases (reads not processed, previously deleted) -- 0 reads 0 bases (reads not processed, in a library where trimming isn't allowed) --
-- OUTPUT READS:
-- 7165 reads 174112663 bases (trimmed reads output) -- 661 reads 17126484 bases (reads with no change, kept as is) -- 10 reads 208473 bases (reads with no overlaps, deleted) -- 2 reads 24621 bases (reads with short trimmed length, deleted) --
-- TRIMMING DETAILS:
-- 5356 reads 18353687 bases (bases trimmed from the 5' end of a read) -- 6178 reads 17807118 bases (bases trimmed from the 3' end of a read)
[TRIMMING/SPLITTING] -- PARAMETERS:
-- 1000 (reads trimmed below this many bases are deleted) -- 0.1440 (use overlaps at or below this fraction error) -- INPUT READS:
-- 7826 reads 227399952 bases (reads processed) -- 12 reads 233094 bases (reads not processed, previously deleted) -- 0 reads 0 bases (reads not processed, in a library where trimming isn't allowed) --
-- PROCESSED:
-- 0 reads 0 bases (no overlaps) -- 0 reads 0 bases (no coverage after adjusting for trimming done already) -- 0 reads 0 bases (processed for chimera) -- 0 reads 0 bases (processed for spur) -- 7826 reads 227399952 bases (processed for subreads) --
-- READS WITH SIGNALS:
-- 0 reads 0 signals (number of 5' spur signal) -- 0 reads 0 signals (number of 3' spur signal) -- 0 reads 0 signals (number of chimera signal) -- 4405 reads 5109 signals (number of subread signal) --
-- SIGNALS:
-- 0 reads 0 bases (size of 5' spur signal) -- 0 reads 0 bases (size of 3' spur signal) -- 0 reads 0 bases (size of chimera signal) -- 5109 reads 419488 bases (size of subread signal) --
-- TRIMMING:
-- 2258 reads 23632933 bases (trimmed from the 5' end of the read) -- 2515 reads 26453072 bases (trimmed from the 3' end of the read)
[UNITIGGING/READS]
-- In gatekeeper store 'unitigging/hc1_hybrid_cov100.gkpStore': -- Found 7826 reads. -- Found 141153142 bases (56.68 times coverage).
-- Read length histogram (one '*' equals 11.61 reads): -- 0 999 0 -- 1000 1999 100 **** -- 2000 2999 42 -- 3000 3999 30 -- 4000 4999 33 -- 5000 5999 31 -- 6000 6999 26 -- 7000 7999 36 -- 8000 8999 441 ** -- 9000 9999 413 -- 10000 10999 387 ***** -- 11000 11999 327 **** -- 12000 12999 122 ** -- 13000 13999 199 * -- 14000 14999 331 **** -- 15000 15999 443 ** -- 16000 16999 763 ***** -- 17000 17999 813 ** -- 18000 18999 529 * -- 19000 19999 302 ** -- 20000 20999 246 *** -- 21000 21999 194 **** -- 22000 22999 127 ** -- 23000 23999 123 ** -- 24000 24999 184 * -- 25000 25999 281 **** -- 26000 26999 240 **** -- 27000 27999 194 **** -- 28000 28999 134 -- 29000 29999 139 -- 30000 30999 93 **** -- 31000 31999 108 * -- 32000 32999 104 ** -- 33000 33999 88 * -- 34000 34999 72 ** -- 35000 35999 48 ** -- 36000 36999 34 -- 37000 37999 14 -- 38000 38999 13 -- 39000 39999 9 -- 40000 40999 4 -- 41000 41999 3 -- 42000 42999 1 -- 43000 43999 1 -- 44000 44999 0 -- 45000 45999 2 -- 46000 46999 1 -- 47000 47999 1
[UNITIGGING/MERS]
-- 22-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 10093919 *****--> 0.7205 0.0716 -- 2- 2 898914 ** 0.7847 0.0843 -- 3- 4 406953 * 0.8050 0.0904 -- 5- 7 113768 **** 0.8181 0.0961 -- 8- 11 30595 0.8227 0.0991 -- 12- 16 34857 0.8244 0.1008 -- 17- 22 61921 0.8271 0.1048 -- 23- 29 179269 * 0.8323 0.1157 -- 30- 37 368195 **** 0.8461 0.1532 -- 38- 46 562333 *** 0.8743 0.2506 -- 47- 56 542176 ** 0.9143 0.4217 -- 57- 67 401443 *** 0.9522 0.6185 -- 68- 79 209573 **** 0.9793 0.7865 -- 80- 92 75165 * 0.9934 0.8897 -- 93- 106 17688 * 0.9980 0.9288 -- 107- 121 5882 0.9992 0.9405 -- 122- 137 2967 0.9996 0.9449 -- 138- 154 393 0.9998 0.9473 -- 155- 172 145 0.9998 0.9477 -- 173- 191 98 0.9998 0.9479 -- 192- 211 94 0.9998 0.9480 -- 212- 232 56 0.9998 0.9481 -- 233- 254 29 0.9998 0.9482 -- 255- 277 66 0.9998 0.9483 -- 278- 301 42 0.9998 0.9484 -- 302- 326 31 0.9998 0.9485 -- 327- 352 43 0.9998 0.9485 -- 353- 379 79 0.9998 0.9486 -- 380- 407 52 0.9998 0.9488 -- 408- 436 57 0.9998 0.9490 -- 437- 466 18 0.9998 0.9492 -- 467- 497 19 0.9998 0.9492 -- 498- 529 11 0.9998 0.9493 -- 530- 562 30 0.9998 0.9493 -- 563- 596 29 0.9998 0.9494 -- 597- 631 15 0.9998 0.9496 -- 632- 667 3 0.9998 0.9496 -- 668- 704 5 0.9998 0.9496 -- 705- 742 9 0.9998 0.9497 -- 743- 781 12 0.9998 0.9497 -- 782- 821 6 0.9998 0.9498
-- 843946 (max occurrences) -- 130894877 (total mers, non-unique) -- 3915192 (distinct mers, non-unique) -- 10093919 (unique mers)
[UNITIGGING/OVERLAPS] -- category reads % read length feature size or coverage analysis
-- middle-missing 489 6.25 29070.37 +- 5639.63 3275.87 +- 3732.77 (bad trimming) -- middle-hump 0 0.00 0.00 +- 0.00 0.00 +- 0.00 (bad trimming) -- no-5-prime 1 0.01 39957.00 +- 0.00 16246.00 +- 0.00 (bad trimming) -- no-3-prime 1 0.01 27989.00 +- 0.00 1467.00 +- 0.00 (bad trimming) --
-- low-coverage 11 0.14 18916.27 +- 9142.20 4.71 +- 2.11 (easy to assemble, potential for lower quality consensus) -- unique 2968 37.92 13454.04 +- 4834.91 23.83 +- 8.89 (easy to assemble, perfect, yay) -- repeat-cont 192 2.45 18707.28 +- 12170.97 248.06 +- 97.64 (potential for consensus errors, no impact on assembly) -- repeat-dove 25 0.32 37392.24 +- 2983.29 221.19 +- 80.86 (hard to assemble, likely won't assemble correctly or even at all) --
-- span-repeat 3590 45.87 20157.09 +- 5795.09 7406.85 +- 5937.53 (read spans a large repeat, usually easy to assemble) -- uniq-repeat-cont 276 3.53 12146.35 +- 6426.16 (should be uniquely placed, low potential for consensus errors, no impact on assembly) -- uniq-repeat-dove 252 3.22 24134.07 +- 7879.99 (will end contigs, potential to misassemble) -- uniq-anchor 21 0.27 19304.67 +- 11838.94 4755.52 +- 3217.80 (repeat read, with unique section, probable bad read)
[UNITIGGING/ADJUSTMENT] -- No report available.
[UNITIGGING/CONTIGS] -- Found, in version 1, after unitig construction: -- contigs: 67 sequences, total length 2626599 bp (including 6 repeats of total length 197551 bp). -- bubbles: 0 sequences, total length 0 bp. -- unassembled: 5621 sequences, total length 109001061 bp.
-- Contig sizes based on genome size -- -- NG (bp) LG (contigs) sum (bp)
-- 10 75162 3 266606 -- 20 64125 7 533093 -- 30 54400 11 770426 -- 40 49697 16 1024873 -- 50 45684 21 1262405 -- 60 41653 27 1522313 -- 70 35424 33 1749108 -- 80 31548 41 2015962 -- 90 27723 49 2252104 -- 100 19148 60 2505107
[UNITIGGING/CONSENSUS] -- Found, in version 2, after consensus generation: -- contigs: 67 sequences, total length 2696826 bp (including 6 repeats of total length 198541 bp). -- bubbles: 0 sequences, total length 0 bp. -- unassembled: 5621 sequences, total length 109152481 bp.
-- Contig sizes based on genome size -- -- NG (bp) LG (contigs) sum (bp)
-- 10 83110 3 286850 -- 20 70479 6 506173 -- 30 60435 10 763059 -- 40 53599 15 1038577 -- 50 46099 20 1279489 -- 60 42838 25 1501972 -- 70 36509 32 1775771 -- 80 33939 39 2020245 -- 90 27940 47 2258007 -- 100 22568 56 2490408
[CORRECTION/MERS]
-- 16-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 594082432 *****--> 0.3924 0.1322 -- 2- 2 383772344 ** 0.6459 0.3031 -- 3- 4 340411799 ** 0.7908 0.4496 -- 5- 7 129208131 * 0.9152 0.6323 -- 8- 11 37410055 ** 0.9660 0.7466 -- 12- 16 13968007 * 0.9836 0.8068 -- 17- 22 6329618 0.9911 0.8437 -- 23- 29 3098351 0.9947 0.8681 -- 30- 37 1534876 0.9965 0.8843 -- 38- 46 748727 0.9974 0.8947 -- 47- 56 359020 0.9978 0.9012 -- 57- 67 178536 0.9981 0.9050 -- 68- 79 110558 0.9982 0.9073 -- 80- 92 127503 0.9982 0.9091 -- 93- 106 234077 0.9983 0.9117 -- 107- 121 411794 0.9985 0.9171 -- 122- 137 568842 0.9988 0.9280 -- 138- 154 567957 0.9992 0.9447 -- 155- 172 392933 0.9995 0.9629 -- 173- 191 188465 0.9998 0.9767 -- 192- 211 70309 0.9999 0.9840 -- 212- 232 27625 0.9999 0.9870 -- 233- 254 15821 1.0000 0.9883 -- 255- 277 11747 1.0000 0.9891 -- 278- 301 8990 1.0000 0.9898 -- 302- 326 6600 1.0000 0.9904 -- 327- 352 4922 1.0000 0.9908 -- 353- 379 3846 1.0000 0.9912 -- 380- 407 3402 1.0000 0.9915 -- 408- 436 2734 1.0000 0.9918 -- 437- 466 2168 1.0000 0.9921 -- 467- 497 1596 1.0000 0.9923 -- 498- 529 1202 1.0000 0.9924 -- 530- 562 913 1.0000 0.9926 -- 563- 596 701 1.0000 0.9927 -- 597- 631 555 1.0000 0.9928 -- 632- 667 476 1.0000 0.9929 -- 668- 704 420 1.0000 0.9929 -- 705- 742 448 1.0000 0.9930 -- 743- 781 474 1.0000 0.9931 -- 782- 821 527 1.0000 0.9931
-- 6187952 (max occurrences) -- 3898198967 (total mers, non-unique) -- 919794736 (distinct mers, non-unique) -- 594082432 (unique mers)
[CORRECTION/CORRECTIONS]
-- Reads to be corrected: -- 57007 reads longer than 30840 bp -- 1601121265 bp -- Expected corrected reads: -- 57007 reads -- 1245006954 bp -- 11879 bp minimum length -- 21840 bp mean length -- 46654 bp n50 length
[TRIMMING/READS]
-- In gatekeeper store 'trimming/hc1_pacbio_smash.gkpStore': -- Found 62585 reads. -- Found 953598509 bases (382.97 times coverage).
-- Read length histogram (one '*' equals 57.91 reads): -- 0 999 0 -- 1000 1999 1669 **** -- 2000 2999 1678 **** -- 3000 3999 1674 **** -- 4000 4999 1672 **** -- 5000 5999 1767 ** -- 6000 6999 1854 **** -- 7000 7999 2040 * -- 8000 8999 2306 ***** -- 9000 9999 2470 ** -- 10000 10999 2888 * -- 11000 11999 4054 ** -- 12000 12999 3517 **** -- 13000 13999 3225 *** -- 14000 14999 3161 ** -- 15000 15999 2779 ** -- 16000 16999 2657 -- 17000 17999 2396 ***** -- 18000 18999 2124 **** -- 19000 19999 1716 * -- 20000 20999 1678 **** -- 21000 21999 1664 **** -- 22000 22999 1667 **** -- 23000 23999 1573 ** -- 24000 24999 1480 -- 25000 25999 1412 **** -- 26000 26999 1256 *** -- 27000 27999 1052 ** -- 28000 28999 902 * -- 29000 29999 852 ** -- 30000 30999 718 **** -- 31000 31999 683 -- 32000 32999 643 -- 33000 33999 501 **** -- 34000 34999 367 ** -- 35000 35999 241 ** -- 36000 36999 133 -- 37000 37999 52 -- 38000 38999 26 -- 39000 39999 17 -- 40000 40999 8 -- 41000 41999 4 -- 42000 42999 1 -- 43000 43999 0 -- 44000 44999 1 -- 45000 45999 0 -- 46000 46999 5 -- 47000 47999 2
[TRIMMING/MERS]
-- 22-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 55231268 *****--> 0.8492 0.0580 -- 2- 2 3685405 ** 0.9059 0.0657 -- 3- 4 2117182 **** 0.9274 0.0701 -- 5- 7 882823 **** 0.9449 0.0754 -- 8- 11 365315 ** 0.9540 0.0796 -- 12- 16 161397 * 0.9583 0.0826 -- 17- 22 73227 0.9604 0.0846 -- 23- 29 34139 0.9613 0.0859 -- 30- 37 16278 0.9618 0.0868 -- 38- 46 8318 0.9620 0.0873 -- 47- 56 4738 0.9621 0.0876 -- 57- 67 2955 0.9622 0.0879 -- 68- 79 1805 0.9622 0.0881 -- 80- 92 1434 0.9623 0.0882 -- 93- 106 964 0.9623 0.0883 -- 107- 121 926 0.9623 0.0884 -- 122- 137 712 0.9623 0.0885 -- 138- 154 2170 0.9623 0.0886 -- 155- 172 6610 0.9624 0.0890 -- 173- 191 8184 0.9625 0.0902 -- 192- 211 13762 0.9626 0.0918 -- 212- 232 30966 0.9628 0.0947 -- 233- 254 76172 0.9633 0.1024 -- 255- 277 139178 0.9645 0.1226 -- 278- 301 224652 ** 0.9667 0.1628 -- 302- 326 350000 ** 0.9702 0.2328 -- 327- 352 448360 **** 0.9757 0.3503 -- 353- 379 465122 **** 0.9826 0.5111 -- 380- 407 361448 ** 0.9897 0.6896 -- 408- 436 215609 *** 0.9952 0.8367 -- 437- 466 76080 0.9984 0.9294 -- 467- 497 8483 0.9995 0.9635 -- 498- 529 457 0.9996 0.9673 -- 530- 562 716 0.9997 0.9675 -- 563- 596 2053 0.9997 0.9680 -- 597- 631 4324 0.9997 0.9692 -- 632- 667 4047 0.9998 0.9721 -- 668- 704 2073 0.9998 0.9748 -- 705- 742 2174 0.9999 0.9763 -- 743- 781 3307 0.9999 0.9780 -- 782- 821 1127 0.9999 0.9806
-- 5458608 (max occurrences) -- 897052951 (total mers, non-unique) -- 9807648 (distinct mers, non-unique) -- 55231268 (unique mers)
[TRIMMING/TRIMMING] -- PARAMETERS:
-- 1000 (reads trimmed below this many bases are deleted) -- 0.1500 (use overlaps at or below this fraction error) -- 1 (break region if overlap is less than this long, for 'largest covered' algorithm) -- 1 (break region if overlap coverage is less than this many read, for 'largest covered' algorithm) --
-- INPUT READS:
-- 62585 reads 953598509 bases (reads processed) -- 0 reads 0 bases (reads not processed, previously deleted) -- 0 reads 0 bases (reads not processed, in a library where trimming isn't allowed) --
-- OUTPUT READS:
-- 54254 reads 797345148 bases (trimmed reads output) -- 8195 reads 116372849 bases (reads with no change, kept as is) -- 89 reads 462733 bases (reads with no overlaps, deleted) -- 47 reads 79304 bases (reads with short trimmed length, deleted) --
-- TRIMMING DETAILS:
-- 38763 reads 23269896 bases (bases trimmed from the 5' end of a read) -- 42441 reads 16068579 bases (bases trimmed from the 3' end of a read)
[TRIMMING/SPLITTING] -- PARAMETERS:
-- 1000 (reads trimmed below this many bases are deleted) -- 0.1500 (use overlaps at or below this fraction error) -- INPUT READS:
-- 62449 reads 953056472 bases (reads processed) -- 136 reads 542037 bases (reads not processed, previously deleted) -- 0 reads 0 bases (reads not processed, in a library where trimming isn't allowed) --
-- PROCESSED:
-- 0 reads 0 bases (no overlaps) -- 0 reads 0 bases (no coverage after adjusting for trimming done already) -- 0 reads 0 bases (processed for chimera) -- 0 reads 0 bases (processed for spur) -- 62449 reads 953056472 bases (processed for subreads) --
-- READS WITH SIGNALS:
-- 0 reads 0 signals (number of 5' spur signal) -- 0 reads 0 signals (number of 3' spur signal) -- 0 reads 0 signals (number of chimera signal) -- 19659 reads 21848 signals (number of subread signal) --
-- SIGNALS:
-- 0 reads 0 bases (size of 5' spur signal) -- 0 reads 0 bases (size of 3' spur signal) -- 0 reads 0 bases (size of chimera signal) -- 21848 reads 6289853 bases (size of subread signal) --
-- TRIMMING:
-- 8938 reads 53461841 bases (trimmed from the 5' end of the read) -- 12082 reads 64183872 bases (trimmed from the 3' end of the read)
[UNITIGGING/READS]
-- In gatekeeper store 'unitigging/hc1_pacbio_smash.gkpStore': -- Found 62449 reads. -- Found 796072284 bases (319.7 times coverage).
-- Read length histogram (one '*' equals 81.4 reads): -- 0 999 0 -- 1000 1999 1775 * -- 2000 2999 1881 *** -- 3000 3999 2033 **** -- 4000 4999 2412 * -- 5000 5999 2855 *** -- 6000 6999 3166 ** -- 7000 7999 3519 *** -- 8000 8999 5698 ** -- 9000 9999 3949 **** -- 10000 10999 3475 ** -- 11000 11999 3025 * -- 12000 12999 2020 **** -- 13000 13999 2243 * -- 14000 14999 2434 *** -- 15000 15999 2546 *** -- 16000 16999 2939 **** -- 17000 17999 2778 ** -- 18000 18999 2051 * -- 19000 19999 1491 ** -- 20000 20999 1391 ** -- 21000 21999 1278 -- 22000 22999 1054 **** -- 23000 23999 941 -- 24000 24999 900 -- 25000 25999 911 ** -- 26000 26999 733 -- 27000 27999 595 ** -- 28000 28999 464 -- 29000 29999 437 * -- 30000 30999 342 ** -- 31000 31999 319 * -- 32000 32999 258 -- 33000 33999 206 -- 34000 34999 132 -- 35000 35999 90 * -- 36000 36999 46 -- 37000 37999 19 -- 38000 38999 14 -- 39000 39999 12 -- 40000 40999 6 -- 41000 41999 5 -- 42000 42999 1 -- 43000 43999 1 -- 44000 44999 0 -- 45000 45999 2 -- 46000 46999 1 -- 47000 47999 1
[UNITIGGING/MERS]
-- 22-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 30278566 *****--> 0.7935 0.0381 -- 2- 2 2785278 ** 0.8665 0.0451 -- 3- 4 1568706 * 0.8940 0.0491 -- 5- 7 627265 ***** 0.9156 0.0536 -- 8- 11 248535 ** 0.9265 0.0571 -- 12- 16 106525 0.9314 0.0595 -- 17- 22 46308 0.9337 0.0611 -- 23- 29 20091 0.9347 0.0621 -- 30- 37 10535 0.9352 0.0627 -- 38- 46 5740 0.9354 0.0631 -- 47- 56 3196 0.9356 0.0634 -- 57- 67 1654 0.9357 0.0636 -- 68- 79 1311 0.9357 0.0637 -- 80- 92 1275 0.9357 0.0638 -- 93- 106 1533 0.9358 0.0640 -- 107- 121 6774 0.9358 0.0642 -- 122- 137 10652 0.9360 0.0652 -- 138- 154 10920 0.9363 0.0670 -- 155- 172 23410 0.9366 0.0690 -- 173- 191 56187 0.9372 0.0742 -- 192- 211 91811 0.9387 0.0875 -- 212- 232 150802 * 0.9412 0.1118 -- 233- 254 227477 * 0.9452 0.1550 -- 255- 277 325041 **** 0.9512 0.2258 -- 278- 301 383536 ***** 0.9599 0.3367 -- 302- 326 395184 *** 0.9700 0.4773 -- 327- 352 337569 **** 0.9803 0.6329 -- 353- 379 243903 ** 0.9890 0.7757 -- 380- 407 121281 * 0.9953 0.8859 -- 408- 436 39520 0.9984 0.9439 -- 437- 466 3670 0.9993 0.9636 -- 467- 497 1727 0.9994 0.9655 -- 498- 529 2184 0.9995 0.9665 -- 530- 562 4971 0.9995 0.9680 -- 563- 596 2437 0.9997 0.9714 -- 597- 631 1985 0.9997 0.9731 -- 632- 667 2579 0.9998 0.9747 -- 668- 704 2665 0.9998 0.9768 -- 705- 742 650 0.9999 0.9791 -- 743- 781 182 0.9999 0.9796 -- 782- 821 118 0.9999 0.9798
-- 4625539 (max occurrences) -- 764482287 (total mers, non-unique) -- 7877581 (distinct mers, non-unique) -- 30278566 (unique mers)
[UNITIGGING/OVERLAPS] -- category reads % read length feature size or coverage analysis
-- middle-missing 46 0.07 29493.83 +- 7307.73 1491.52 +- 1824.50 (bad trimming) -- middle-hump 0 0.00 0.00 +- 0.00 0.00 +- 0.00 (bad trimming) -- no-5-prime 1 0.00 41272.00 +- 0.00 17545.00 +- 0.00 (bad trimming) -- no-3-prime 2 0.00 18903.00 +- 7237.95 14211.00 +- 9907.98 (bad trimming) --
-- low-coverage 1 0.00 41272.00 +- 0.00 6.16 +- 1.70 (easy to assemble, potential for lower quality consensus) -- unique 8 0.01 2984.62 +- 1054.95 30.17 +- 9.86 (easy to assemble, perfect, yay) -- repeat-cont 48546 77.74 10090.60 +- 5030.80 173.61 +- 79.98 (potential for consensus errors, no impact on assembly) -- repeat-dove 2835 4.54 19077.12 +- 3669.65 123.21 +- 51.63 (hard to assemble, likely won't assemble correctly or even at all) --
-- span-repeat 31 0.05 21499.13 +- 11354.69 12121.97 +- 7868.00 (read spans a large repeat, usually easy to assemble) -- uniq-repeat-cont 277 0.44 15073.83 +- 7756.64 (should be uniquely placed, low potential for consensus errors, no impact on assembly) -- uniq-repeat-dove 788 1.26 23463.74 +- 6199.11 (will end contigs, potential to misassemble) -- uniq-anchor 9914 15.88 22927.00 +- 6416.16 9132.49 +- 6470.79 (repeat read, with unique section, probable bad read)
[UNITIGGING/ADJUSTMENT] -- No report available.
[UNITIGGING/CONTIGS] -- Found, in version 1, after unitig construction: -- contigs: 774 sequences, total length 28825721 bp (including 180 repeats of total length 10087773 bp). -- bubbles: 0 sequences, total length 0 bp. -- unassembled: 27967 sequences, total length 467652040 bp.
-- Contig sizes based on genome size -- -- NG (bp) LG (contigs) sum (bp)
-- 10 154794 2 338981 -- 20 148422 4 637556 -- 30 145749 5 783305 -- 40 138518 7 1062580 -- 50 130357 9 1328482 -- 60 129479 11 1588102 -- 70 126396 13 1841286 -- 80 124727 15 2090918 -- 90 122469 17 2336194 -- 100 113677 19 2564092 -- 110 108082 21 2783983 -- 120 104973 23 2994243 -- 130 101000 26 3301631 -- 140 100034 28 3502455 -- 150 97748 31 3798249 -- 160 94684 33 3990519 -- 170 92653 36 4269074 -- 180 90201 39 4542453 -- 190 88536 42 4810047 -- 200 87275 44 4985097 -- 210 86877 47 5245906 -- 220 85192 50 5501815 -- 230 82650 53 5750599 -- 240 80918 56 5995944 -- 250 79379 59 6234829 -- 260 77458 63 6546969 -- 270 74500 66 6772693 -- 280 73254 69 6994323 -- 290 71418 73 7283288 -- 300 70495 76 7495508 -- 310 69738 80 7776030 -- 320 68511 83 7982794 -- 330 67627 87 8254692 -- 340 65652 91 8521122 -- 350 64665 94 8716320 -- 360 64072 98 8973481 -- 370 62565 102 9226959 -- 380 61543 106 9474586 -- 390 60067 110 9717579 -- 400 59586 115 10016434 -- 410 57157 119 10250579 -- 420 56041 123 10476983 -- 430 55078 128 10754430 -- 440 53690 132 10970991 -- 450 52979 137 11237718 -- 460 52262 142 11500811 -- 470 51627 146 11707805 -- 480 50988 151 11963946 -- 490 50277 156 12216841 -- 500 49237 161 12464805 -- 510 48306 166 12707304 -- 520 47671 172 12995191 -- 530 46893 177 13231443 -- 540 46407 182 13464206 -- 550 45829 188 13740551 -- 560 45420 193 13968772 -- 570 44801 198 14193995 -- 580 44345 204 14461249 -- 590 43386 210 14723495 -- 600 41842 216 14977929 -- 610 41405 222 15227512 -- 620 40677 228 15472925 -- 630 40161 234 15714745 -- 640 39543 240 15953710 -- 650 38616 246 16187173 -- 660 37911 253 16454724 -- 670 37122 260 16717158 -- 680 36850 266 16939049 -- 690 35966 273 17193483 -- 700 35505 280 17443357 -- 710 34914 287 17689227 -- 720 34494 294 17932188 -- 730 33858 302 18204752 -- 740 33547 309 18440489 -- 750 33049 317 18706818 -- 760 32763 324 18936825 -- 770 32468 332 19197593 -- 780 32108 339 19423522 -- 790 31523 347 19677608 -- 800 31078 355 19927805 -- 810 30665 363 20174634 -- 820 30213 371 20418218 -- 830 29594 380 20686317 -- 840 29183 388 20921491 -- 850 28756 397 21182694 -- 860 28141 406 21437913 -- 870 27777 415 21689494 -- 880 27250 424 21936525 -- 890 26935 433 22180422 -- 900 26516 442 22420465 -- 910 26063 452 22683561 -- 920 25788 461 22916707 -- 930 25301 471 23172223 -- 940 24787 481 23423021 -- 950 24486 491 23669106 -- 960 24030 501 23911583 -- 970 23406 512 24173091 -- 980 22623 522 24403028 -- 990 22053 534 24670704 -- 000 21815 545 24911957 -- 010 21516 556 25150516 -- 020 20860 568 25404468 -- 030 20227 580 25650906 -- 040 19854 593 25911110 -- 050 19684 605 26148260 -- 060 19463 618 26402836 -- 070 18856 631 26651276 -- 080 18384 644 26893024 -- 090 18232 658 27149058 -- 100 17459 672 27397834 -- 110 17102 686 27639666 -- 120 16584 701 27892555 -- 130 16070 717 28152959 -- 140 15404 732 28389103 -- 150 11744 750 28639894
[UNITIGGING/CONSENSUS] -- Found, in version 2, after consensus generation: -- contigs: 774 sequences, total length 28496592 bp (including 180 repeats of total length 9776968 bp). -- bubbles: 0 sequences, total length 0 bp. -- unassembled: 27967 sequences, total length 467802133 bp.
-- Contig sizes based on genome size -- -- NG (bp) LG (contigs) sum (bp)
-- 10 168250 2 364776 -- 20 159014 3 523790 -- 30 148469 5 826603 -- 40 141945 7 1116021 -- 50 141613 8 1257634 -- 60 138364 10 1536890 -- 70 129790 12 1802246 -- 80 122975 14 2050864 -- 90 119871 16 2293387 -- 100 117421 18 2529906 -- 110 114422 20 2758949 -- 120 108874 23 3092649 -- 130 106612 25 3306802 -- 140 104252 27 3516981 -- 150 96660 30 3817342 -- 160 95103 32 4008943 -- 170 94597 35 4292877 -- 180 92707 38 4572494 -- 190 90405 40 4754955 -- 200 89227 43 5023285 -- 210 87188 46 5285676 -- 220 85548 49 5543836 -- 230 81605 52 5792880 -- 240 79794 55 6034323 -- 250 78005 58 6271317 -- 260 76956 61 6503085 -- 270 76390 64 6733181 -- 280 74465 68 7035950 -- 290 72103 71 7254907 -- 300 70339 75 7539006 -- 310 68860 78 7746148 -- 320 68174 82 8019873 -- 330 66658 85 8220335 -- 340 65629 89 8484218 -- 350 63065 93 8739663 -- 360 62757 97 8991038 -- 370 61424 101 9238412 -- 380 59421 105 9477853 -- 390 58960 109 9714284 -- 400 57806 114 10004773 -- 410 56523 118 10231870 -- 420 55112 123 10510643 -- 430 54702 127 10729884 -- 440 53711 132 10999058 -- 450 53146 136 11212430 -- 460 52797 141 11477159 -- 470 52017 146 11738469 -- 480 51786 151 11998103 -- 490 51289 155 12203868 -- 500 50374 160 12458204 -- 510 48871 165 12706892 -- 520 47939 170 12948401 -- 530 46774 176 13232492 -- 540 46291 181 13464642 -- 550 45400 187 13738715 -- 560 44629 192 13963332 -- 570 44051 198 14229562 -- 580 43441 203 14448302 -- 590 42348 209 14704435 -- 600 41952 215 14956968 -- 610 40730 221 15204065 -- 620 40214 227 15446638 -- 630 39983 233 15687168 -- 640 39468 240 15965159 -- 650 39209 246 16201079 -- 660 38447 253 16471122 -- 670 37697 259 16698522 -- 680 36530 266 16956893 -- 690 35997 273 17210759 -- 700 35376 280 17460816 -- 710 34717 287 17705125 -- 720 34249 294 17946699 -- 730 33785 301 18184038 -- 740 32839 309 18450707 -- 750 32456 316 18679070 -- 760 31990 324 18937486 -- 770 31151 332 19189970 -- 780 30739 340 19437541 -- 790 30320 348 19681742 -- 800 29779 356 19922876 -- 810 29507 365 20189728 -- 820 29310 373 20424711 -- 830 28716 382 20685837 -- 840 28212 391 20942015 -- 850 27822 399 21166462 -- 860 27272 408 21414867 -- 870 27069 418 21686349 -- 880 26450 427 21926218 -- 890 26217 436 22163109 -- 900 25775 446 22422589 -- 910 25275 456 22678502 -- 920 24957 466 22930256 -- 930 24377 476 23176038 -- 940 23806 486 23416931 -- 950 22837 497 23673753 -- 960 22101 508 23920590 -- 970 21792 519 24162262 -- 980 21175 531 24419312 -- 990 20691 543 24670202 -- 000 20225 555 24915702 -- 010 19860 567 25155368 -- 020 19691 580 25412156 -- 030 19379 593 25665995 -- 040 18825 606 25913517 -- 050 18436 619 26155142 -- 060 18192 633 26411142 -- 070 17708 646 26644021 -- 080 17307 661 26905976 -- 090 16961 675 27145248 -- 100 16539 690 27397136 -- 110 16150 705 27642026 -- 120 15628 721 27896549 -- 130 14768 737 28141500 -- 140 10555 757 28391723