[CORRECTION/LAYOUT] -- original original -- raw reads raw reads -- category w/overlaps w/o/overlaps -- -------------------- ------------- ------------- -- Number of Reads 15658369 943679 -- Number of Bases 126132641793 3621294469 -- Coverage 31.533 0.905 -- Median 7628 2501 -- Mean 8055 3837 -- N50 8671 6616 -- Minimum 1000 0 -- Maximum 234824 223650 -- -- --------corrected--------- ----------rescued---------- -- evidence expected expected -- category reads raw corrected raw corrected -- -------------------- ------------- ------------- ------------- ------------- ------------- -- Number of Reads 16468680 14357258 14357258 0 0 -- Number of Bases 129517700269 120121047501 112686346990 0 0 -- Coverage 32.379 30.030 28.172 0.000 0.000 -- Median 7538 7787 7578 0 0 -- Mean 7864 8366 7848 0 0 -- N50 8642 8744 8618 0 0 -- Minimum 1000 1000 1 0 0 -- Maximum 234824 225909 225896 0 0 -- -- --------uncorrected-------- -- expected -- category raw corrected -- -------------------- ------------- ------------- -- Number of Reads 2244790 2244790 -- Number of Bases 9632888761 232065 -- Coverage 2.408 0.000 -- Median 3153 0 -- Mean 4291 0 -- N50 6220 0 -- Minimum 0 0 -- Maximum 234824 232065 -- -- Maximum Memory 2941769192 [TRIMMING/READS] -- -- In sequence store './0.070.seqStore': -- Found 12383882 reads. -- Found 95373203011 bases (23.84 times coverage). -- Histogram of corrected reads: -- -- G=95373203011 sum of || length num -- NG length index lengths || range seqs -- ----- ------------ --------- ------------ || ------------------- ------- -- 00010 13907 547606 9537324479 || 1000-4992 2114503|------------------- -- 00020 11122 1325325 19074646028 || 4993-8985 7047062|--------------------------------------------------------------- -- 00030 9823 2242204 28611969436 || 8986-12978 2497709|----------------------- -- 00040 8958 3260919 38149282276 || 12979-16971 515298|----- -- 00050 8285 4369114 47686603075 || 16972-20964 144705|-- -- 00060 7727 5561990 57223924295 || 20965-24957 43232|- -- 00070 7245 6837366 66761243518 || 24958-28950 12548|- -- 00080 6780 8196783 76298567620 || 28951-32943 3636|- -- 00090 5856 9685608 85835885339 || 32944-36936 1365|- -- 00100 1000 12383881 95373203011 || 36937-40929 562|- -- 001.000x 12383882 95373203011 || 40930-44922 418|- -- || 44923-48915 319|- -- || 48916-52908 235|- -- || 52909-56901 233|- -- || 56902-60894 200|- -- || 60895-64887 192|- -- || 64888-68880 181|- -- || 68881-72873 209|- -- || 72874-76866 171|- -- || 76867-80859 168|- -- || 80860-84852 142|- -- || 84853-88845 144|- -- || 88846-92838 98|- -- || 92839-96831 100|- -- || 96832-100824 104|- -- || 100825-104817 79|- -- || 104818-108810 64|- -- || 108811-112803 49|- -- || 112804-116796 37|- -- || 116797-120789 32|- -- || 120790-124782 18|- -- || 124783-128775 19|- -- || 128776-132768 10|- -- || 132769-136761 6|- -- || 136762-140754 5|- -- || 140755-144747 6|- -- || 144748-148740 2|- -- || 148741-152733 4|- -- || 152734-156726 2|- -- || 156727-160719 2|- -- || 160720-164712 4|- -- || 164713-168705 3|- -- || 168706-172698 2|- -- || 172699-176691 0| -- || 176692-180684 1|- -- || 180685-184677 1|- -- || 184678-188670 1|- -- || 188671-192663 0| -- || 192664-196656 0| -- || 196657-200649 1|- -- [TRIMMING/MERS] -- -- 22-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 0 0.0000 0.0000 -- 2- 2 302342024 ********************************************************************** 0.1928 0.0065 -- 3- 4 216287662 ************************************************** 0.2787 0.0108 -- 5- 7 144218728 ********************************* 0.3683 0.0175 -- 8- 11 119717013 *************************** 0.4444 0.0263 -- 12- 16 118409970 *************************** 0.5152 0.0387 -- 17- 22 123616781 **************************** 0.5883 0.0570 -- 23- 29 121274452 **************************** 0.6653 0.0835 -- 30- 37 107516469 ************************ 0.7403 0.1174 -- 38- 46 87508058 ******************** 0.8064 0.1555 -- 47- 56 58741735 ************* 0.8597 0.1937 -- 57- 67 38795879 ******** 0.8953 0.2249 -- 68- 79 25505260 ***** 0.9189 0.2497 -- 80- 92 17441196 **** 0.9345 0.2691 -- 93- 106 12658219 ** 0.9452 0.2848 -- 107- 121 9725697 ** 0.9531 0.2980 -- 122- 137 7778699 * 0.9592 0.3097 -- 138- 154 6388955 * 0.9641 0.3204 -- 155- 172 5341267 * 0.9681 0.3303 -- 173- 191 4509663 * 0.9714 0.3396 -- 192- 211 3855529 0.9743 0.3483 -- 212- 232 3332542 0.9767 0.3566 -- 233- 254 2891943 0.9788 0.3645 -- 255- 277 2517921 0.9806 0.3720 -- 278- 301 2219114 0.9822 0.3791 -- 302- 326 1956051 0.9836 0.3860 -- 327- 352 1740508 0.9849 0.3925 -- 353- 379 1552370 0.9860 0.3988 -- 380- 407 1391006 0.9870 0.4049 -- 408- 436 1252549 0.9879 0.4108 -- 437- 466 1131792 0.9886 0.4164 -- 467- 497 1027220 0.9894 0.4219 -- 498- 529 930389 0.9900 0.4272 -- 530- 562 845840 0.9906 0.4323 -- 563- 596 773996 0.9911 0.4372 -- 597- 631 708200 0.9916 0.4420 -- 632- 667 651874 0.9921 0.4467 -- 668- 704 599996 0.9925 0.4512 -- 705- 742 555442 0.9929 0.4556 -- 743- 781 512733 0.9932 0.4599 -- 782- 821 478028 0.9936 0.4641 -- -- 0 (max occurrences) -- 93288181319 (total mers, non-unique) -- 1568335386 (distinct mers, non-unique) -- 0 (unique mers) [TRIMMING/TRIMMING] -- PARAMETERS: -- ---------- -- 1000 (reads trimmed below this many bases are deleted) -- 0.0700 (use overlaps at or below this fraction error) -- 500 (break region if overlap is less than this long, for 'largest covered' algorithm) -- 2 (break region if overlap coverage is less than this many reads, for 'largest covered' algorithm) -- -- INPUT READS: -- ----------- -- 16602048 reads 95373203011 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: -- ------------ -- 4671057 reads 33277500010 bases (trimmed reads output) -- 7656109 reads 59555870341 bases (reads with no change, kept as is) -- 4237622 reads 106743263 bases (reads with no overlaps, deleted) -- 37260 reads 83519632 bases (reads with short trimmed length, deleted) -- -- TRIMMING DETAILS: -- ---------------- -- 2626526 reads 1157526175 bases (bases trimmed from the 5' end of a read) -- 2895611 reads 1192043590 bases (bases trimmed from the 3' end of a read) [TRIMMING/SPLITTING] -- PARAMETERS: -- ---------- -- 1000 (reads trimmed below this many bases are deleted) -- 0.0700 (use overlaps at or below this fraction error) -- INPUT READS: -- ----------- -- 12327166 reads 95182940116 bases (reads processed) -- 4274882 reads 190262895 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) -- 268 reads 529622 bases (no coverage after adjusting for trimming done already) -- 0 reads 0 bases (processed for chimera) -- 0 reads 0 bases (processed for spur) -- 12326898 reads 95182410494 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) -- 85622 reads 86337 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) -- 86337 reads 31208963 bases (size of subread signal) -- -- TRIMMING: -- -------- -- 43056 reads 326632037 bases (trimmed from the 5' end of the read) -- 42553 reads 327065701 bases (trimmed from the 3' end of the read) [UNITIGGING/READS] -- -- In sequence store './0.070.seqStore': -- Found 12327112 reads. -- Found 92179573151 bases (23.04 times coverage). -- Histogram of corrected-trimmed reads: -- -- G=92179573151 sum of || length num -- NG length index lengths || range seqs -- ----- ------------ --------- ------------ || ------------------- ------- -- 00010 12988 574052 9217958189 || 1000-4545 2015229|---------------------- -- 00020 10696 1366939 18435922841 || 4546-8091 5831091|--------------------------------------------------------------- -- 00030 9561 2281747 27653875586 || 8092-11637 3551526|--------------------------------------- -- 00040 8771 3289930 36871829266 || 11638-15183 664787|-------- -- 00050 8141 4381917 46089794023 || 15184-18729 182316|-- -- 00060 7614 5553508 55307750930 || 18730-22275 54835|- -- 00070 7155 6802946 64525708167 || 22276-25821 17339|- -- 00080 6686 8133450 73743664539 || 25822-29367 5228|- -- 00090 5616 9606083 82961616659 || 29368-32913 1824|- -- 00100 1000 12327111 92179573151 || 32914-36459 631|- -- 001.000x 12327112 92179573151 || 36460-40005 356|- -- || 40006-43551 262|- -- || 43552-47097 237|- -- || 47098-50643 161|- -- || 50644-54189 190|- -- || 54190-57735 168|- -- || 57736-61281 127|- -- || 61282-64827 107|- -- || 64828-68373 111|- -- || 68374-71919 94|- -- || 71920-75465 89|- -- || 75466-79011 60|- -- || 79012-82557 63|- -- || 82558-86103 49|- -- || 86104-89649 45|- -- || 89650-93195 34|- -- || 93196-96741 34|- -- || 96742-100287 20|- -- || 100288-103833 22|- -- || 103834-107379 23|- -- || 107380-110925 16|- -- || 110926-114471 10|- -- || 114472-118017 5|- -- || 118018-121563 7|- -- || 121564-125109 3|- -- || 125110-128655 4|- -- || 128656-132201 1|- -- || 132202-135747 2|- -- || 135748-139293 1|- -- || 139294-142839 3|- -- || 142840-146385 0| -- || 146386-149931 1|- -- || 149932-153477 0| -- || 153478-157023 0| -- || 157024-160569 0| -- || 160570-164115 0| -- || 164116-167661 0| -- || 167662-171207 0| -- || 171208-174753 0| -- || 174754-178299 1|- -- [UNITIGGING/MERS] -- -- 22-mers Fraction -- Occurrences NumMers Unique Total -- 1- 1 0 0.0000 0.0000 -- 2- 2 273895713 ********************************************************************** 0.1829 0.0061 -- 3- 4 199413325 ************************************************** 0.2654 0.0102 -- 5- 7 137160628 *********************************** 0.3531 0.0166 -- 8- 11 117162722 ***************************** 0.4297 0.0254 -- 12- 16 117527458 ****************************** 0.5026 0.0380 -- 17- 22 122892289 ******************************* 0.5787 0.0568 -- 23- 29 119811778 ****************************** 0.6588 0.0840 -- 30- 37 105468082 ************************** 0.7363 0.1185 -- 38- 46 84881564 ********************* 0.8042 0.1571 -- 47- 56 56523939 ************** 0.8582 0.1953 -- 57- 67 37305865 ********* 0.8940 0.2263 -- 68- 79 24537572 ****** 0.9178 0.2509 -- 80- 92 16822554 **** 0.9336 0.2702 -- 93- 106 12228666 *** 0.9444 0.2858 -- 107- 121 9416205 ** 0.9524 0.2990 -- 122- 137 7540787 * 0.9585 0.3108 -- 138- 154 6195768 * 0.9635 0.3214 -- 155- 172 5173583 * 0.9676 0.3314 -- 173- 191 4380166 * 0.9710 0.3406 -- 192- 211 3739919 0.9739 0.3494 -- 212- 232 3232983 0.9763 0.3577 -- 233- 254 2799486 0.9785 0.3656 -- 255- 277 2447395 0.9803 0.3731 -- 278- 301 2149930 0.9820 0.3803 -- 302- 326 1895962 0.9834 0.3871 -- 327- 352 1687498 0.9846 0.3937 -- 353- 379 1506288 0.9858 0.4000 -- 380- 407 1350868 0.9868 0.4061 -- 408- 436 1216422 0.9877 0.4119 -- 437- 466 1099672 0.9885 0.4176 -- 467- 497 994341 0.9892 0.4231 -- 498- 529 903420 0.9899 0.4284 -- 530- 562 819471 0.9905 0.4335 -- 563- 596 750149 0.9910 0.4385 -- 597- 631 686245 0.9915 0.4433 -- 632- 667 630670 0.9920 0.4479 -- 668- 704 581294 0.9924 0.4524 -- 705- 742 536621 0.9928 0.4568 -- 743- 781 498605 0.9931 0.4611 -- 782- 821 462159 0.9935 0.4653 -- -- 0 (max occurrences) -- 90313549959 (total mers, non-unique) -- 1497669418 (distinct mers, non-unique) -- 0 (unique mers) [UNITIGGING/OVERLAPS] -- category reads % read length feature size or coverage analysis -- ---------------- ------- ------- ---------------------- ------------------------ -------------------- -- middle-missing 7018 0.06 8689.48 +- 4844.92 630.64 +- 908.07 (bad trimming) -- middle-hump 2399 0.02 5472.34 +- 3748.85 150.60 +- 391.87 (bad trimming) -- no-5-prime 67615 0.55 7978.33 +- 3255.36 76.72 +- 271.91 (bad trimming) -- no-3-prime 27730 0.22 7557.48 +- 3318.23 104.26 +- 321.63 (bad trimming) -- -- low-coverage 46381 0.38 3490.60 +- 2196.20 4.58 +- 1.61 (easy to assemble, potential for lower quality consensus) -- unique 933141 7.57 6584.20 +- 3434.81 23.06 +- 7.25 (easy to assemble, perfect, yay) -- repeat-cont 4479045 36.33 6324.41 +- 3243.61 9124.14 +- 12916.65 (potential for consensus errors, no impact on assembly) -- repeat-dove 90727 0.74 9918.57 +- 3654.82 3479.79 +- 6862.84 (hard to assemble, likely won't assemble correctly or even at all) -- -- span-repeat 970806 7.88 8598.75 +- 3232.87 4449.00 +- 3711.71 (read spans a large repeat, usually easy to assemble) -- uniq-repeat-cont 3651411 29.62 7745.40 +- 2469.80 (should be uniquely placed, low potential for consensus errors, no impact on assembly) -- uniq-repeat-dove 731962 5.94 9438.32 +- 2884.84 (will end contigs, potential to misassemble) -- uniq-anchor 1318041 10.69 9319.63 +- 3233.24 3204.92 +- 3050.47 (repeat read, with unique section, probable bad read) [UNITIGGING/ADJUSTMENT] -- No report available. [UNITIGGING/ERROR RATES] -- -- ERROR RATES -- ----------- -- --------threshold------ -- 13554508 fraction error fraction percent -- samples (1e-5) error error -- -------------------------- -------- -------- -- command line (-eg) -> 7000.00 7.0000% -- command line (-ef) -> -----.-- ---.----% -- command line (-eM) -> 7000.00 7.0000% -- mean + std.dev 822.94 +- 12 * 1390.15 -> 17504.77 17.5048% -- median + mad 238.00 +- 12 * 198.00 -> 3760.66 3.7607% (enabled) -- 90th percentile -> 2856.00 2.8560% -- -- BEST EDGE FILTERING -- ------------------- -- At graph threshold 7.0000%, reads: -- available to have edges: 1560390 -- with at least one edge: 1485878 -- -- At max threshold 7.0000%, reads: (not computed) -- available to have edges: 0 -- with at least one edge: 0 -- -- At tight threshold 3.7607%, reads with: -- both edges below error threshold: 1288891 (80.00% minReadsBest threshold = 1188702) -- one edge above error threshold: 189899 -- both edges above error threshold: 7088 -- at least one edge: 1485878 -- -- At loose threshold 7.0000%, reads with: -- both edges below error threshold: 1485878 (80.00% minReadsBest threshold = 1188702) -- one edge above error threshold: 0 -- both edges above error threshold: 0 -- at least one edge: 1485878 -- -- -- INITIAL EDGES -- -------- ---------------------------------------- -- 8724148 reads are contained -- 6327756 reads have no best edges (singleton) -- 285903 reads have only one best edge (spur) -- 275070 are mutual best -- 1264241 reads have two best edges -- 113830 have one mutual best edge -- 1142395 have two mutual best edges -- -- -- FINAL EDGES -- -------- ---------------------------------------- -- 8724148 reads are contained -- 6366305 reads have no best edges (singleton) -- 311685 reads have only one best edge (spur) -- 294930 are mutual best -- 1199910 reads have two best edges -- 91266 have one mutual best edge -- 1102321 have two mutual best edges -- -- -- EDGE FILTERING -- -------- ------------------------------------------ -- 0 reads are ignored -- 1175957 reads have a gap in overlap coverage -- 19991 reads have lopsided best edges [UNITIGGING/CONTIGS] -- Found, in version 1, after unitig construction: -- contigs: 144791 sequences, total length 3144758708 bp (including 16034 repeats of total length 202794970 bp). -- bubbles: 21305 sequences, total length 244043295 bp. -- unassembled: 1997935 sequences, total length 14699244493 bp. -- -- Contig sizes based on genome size 4gbp: -- -- NG (bp) LG (contigs) sum (bp) -- ---------- ------------ ---------- -- 10 54362 5757 400018380 -- 20 40466 14384 800002206 -- 30 31972 25558 1200031767 -- 40 25716 39548 1600020974 -- 50 20709 56911 2000010136 -- 60 16338 78667 2400001733 -- 70 12039 106968 2800008162 -- [UNITIGGING/CONSENSUS] -- Found, in version 2, after consensus generation: -- contigs: 144791 sequences, total length 3131174949 bp (including 16034 repeats of total length 200881056 bp). -- bubbles: 21305 sequences, total length 242816037 bp. -- unassembled: 1997935 sequences, total length 14699236525 bp. -- -- Contig sizes based on genome size 4gbp: -- -- NG (bp) LG (contigs) sum (bp) -- ---------- ------------ ---------- -- 10 54196 5772 400050773 -- 20 40327 14430 800036095 -- 30 31827 25651 1200024909 -- 40 25551 39718 1600009779 -- 50 20553 57203 2000016745 -- 60 16155 79162 2400001078 -- 70 11814 107852 2800004677 --