search

marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
644 stars 177 forks source link

Strange Error #2321

Open gunjanpandey opened 1 week ago

gunjanpandey commented 1 week ago

I use canu often bit never encountered this error. Could you please help how to resolve it? Please note this is a highly hetrozygous diploid genome with potentially large proportion of repeats. Also that the hifi reads do not show error with other assemblers such as hifiasm.

I ran this command canu -assemble -p Hopper -d ./ genomeSize=8g -pacbio-hifi reads.fq minReadLength=1000 maxInputCoverage=100 correctedErrorRate=0.025 utgOvlErrorRate=0.065 -useGrid=false

And getting this error..

image

Full log is here. 

[UNITIGGING/READS]
--
-- In sequence store './Hopper.seqStore':
--   Found 16787992 reads.
--   Found 110872450238 bases (13.85 times coverage).
--   
--    G=110872450238                     sum of  ||               length     num
--    NG         length     index       lengths  ||                range    seqs
--    ----- ------------ --------- ------------  ||  ------------------- -------
--    00010        12752    774118  11087247590  ||       1000-1720        42172|--
--    00020        11094   1710655  22174494464  ||       1721-2441       620092|-----------------------
--    00030         9911   2769735  33261735760  ||       2442-3162      1670750|------------------------------------------------------------
--    00040         8914   3950001  44348983630  ||       3163-3883      1759766|---------------------------------------------------------------
--    00050         7982   5264168  55436226188  ||       3884-4604      1555742|--------------------------------------------------------
--    00060         7044   6741241  66523476728  ||       4605-5325      1401010|---------------------------------------------------
--    00070         6044   8437091  77610719496  ||       5326-6046      1305108|-----------------------------------------------
--    00080         4948  10457581  88697961548  ||       6047-6767      1236260|---------------------------------------------
--    00090         3744  13020505  99785206174  ||       6768-7488      1171960|------------------------------------------
--    00100         1000  16787991 110872450238  ||       7489-8209      1098806|----------------------------------------
--    001.000x            16787992 110872450238  ||       8210-8930       998360|------------------------------------
--                                               ||       8931-9651       877214|--------------------------------
--                                               ||       9652-10372      737098|---------------------------
--                                               ||      10373-11093      602948|----------------------
--                                               ||      11094-11814      478180|------------------
--                                               ||      11815-12535      366094|--------------
--                                               ||      12536-13256      276862|----------
--                                               ||      13257-13977      202666|--------
--                                               ||      13978-14698      144752|------
--                                               ||      14699-15419       97908|----
--                                               ||      15420-16140       63186|---
--                                               ||      16141-16861       37818|--
--                                               ||      16862-17582       21908|-
--                                               ||      17583-18303       11806|-
--                                               ||      18304-19024        5552|-
--                                               ||      19025-19745        2388|-
--                                               ||      19746-20466         932|-
--                                               ||      20467-21187         266|-
--                                               ||      21188-21908         142|-
--                                               ||      21909-22629          58|-
--                                               ||      22630-23350          60|-
--                                               ||      23351-24071          44|-
--                                               ||      24072-24792          24|-
--                                               ||      24793-25513           8|-
--                                               ||      25514-26234           6|-
--                                               ||      26235-26955          14|-
--                                               ||      26956-27676           8|-
--                                               ||      27677-28397          10|-
--                                               ||      28398-29118           4|-
--                                               ||      29119-29839           0|
--                                               ||      29840-30560           2|-
--                                               ||      30561-31281           0|
--                                               ||      31282-32002           2|-
--                                               ||      32003-32723           2|-
--                                               ||      32724-33444           0|
--                                               ||      33445-34165           0|
--                                               ||      34166-34886           0|
--                                               ||      34887-35607           2|-
--                                               ||      35608-36328           0|
--                                               ||      36329-37049           2|-
--

[UNITIGGING/MERS]
--
--  22-mers                                                                                           Fraction
--    Occurrences   NumMers                                                                         Unique Total
--       1-     1         0                                                                        0.0000 0.0000
--       2-     2 108469007 **********                                                             0.0416 0.0028
--       3-     4  77596234 *******                                                                0.0714 0.0068
--       5-     7 138243036 ************                                                           0.1245 0.0174
--       8-    11 457706056 ******************************************                             0.2027 0.0384
--      12-    16 759195331 ********************************************************************** 0.4052 0.1133
--      17-    22 428090780 ***************************************                                0.6611 0.2484
--      23-    29 209224406 *******************                                                    0.7882 0.3406
--      30-    37 156962972 **************                                                         0.8550 0.4028
--      38-    46  97303790 ********                                                               0.9065 0.4625
--      47-    56  49418023 ****                                                                   0.9387 0.5093
--      57-    67  28613814 **                                                                     0.9555 0.5395
--      68-    79  21043250 *                                                                      0.9655 0.5608
--      80-    92  15285708 *                                                                      0.9730 0.5794
--      93-   106  10015695                                                                        0.9785 0.5955
--     107-   121   7021895                                                                        0.9821 0.6079
--     122-   137   5866323                                                                        0.9847 0.6179
--     138-   154   4961717                                                                        0.9868 0.6274
--     155-   172   3835107                                                                        0.9887 0.6365
--     173-   191   2970304                                                                        0.9901 0.6444
--     192-   211   2554849                                                                        0.9912 0.6513
--     212-   232   2159211                                                                        0.9922 0.6578
--     233-   254   1717616                                                                        0.9930 0.6638
--     255-   277   1407037                                                                        0.9936 0.6691
--     278-   301   1277169                                                                        0.9942 0.6739
--     302-   326   1149153                                                                        0.9947 0.6786
--     327-   352    963686                                                                        0.9951 0.6832
--     353-   379    821739                                                                        0.9955 0.6874
--     380-   407    761170                                                                        0.9958 0.6912
--     408-   436    700809                                                                        0.9961 0.6951
--     437-   466    607394                                                                        0.9963 0.6988
--     467-   497    534114                                                                        0.9966 0.7023
--     498-   529    501900                                                                        0.9968 0.7056
--     530-   562    471387                                                                        0.9969 0.7089
--     563-   596    416040                                                                        0.9971 0.7122
--     597-   631    370680                                                                        0.9973 0.7153
--     632-   667    350593                                                                        0.9974 0.7182
--     668-   704    331023                                                                        0.9976 0.7212
--     705-   742    299345                                                                        0.9977 0.7241
--     743-   781    269915                                                                        0.9978 0.7268
--     782-   821    257255                                                                        0.9979 0.7295
--
--           0 (max occurrences)
-- 77757560844 (total mers, non-unique)
--  2604958441 (distinct mers, non-unique)
--           0 (unique mers)

[UNITIGGING/OVERLAPS]
--   category            reads     %          read length        feature size or coverage  analysis
--   ----------------  -------  -------  ----------------------  ------------------------  --------------------
--   middle-missing          2    0.00     6289.00 +- 0.00          1698.00 +- 0.00       (bad trimming)
--   middle-hump             0    0.00        0.00 +- 0.00             0.00 +- 0.00       (bad trimming)
--   no-5-prime              0    0.00        0.00 +- 0.00             0.00 +- 0.00       (bad trimming)
--   no-3-prime              0    0.00        0.00 +- 0.00             0.00 +- 0.00       (bad trimming)
--  
--   low-coverage        66487    0.40     2982.78 +- 1670.16          1.79 +- 0.98       (easy to assemble, potential for lower quality consensus)
--   unique            7273460   43.33     4170.95 +- 2067.23         12.81 +- 3.76       (easy to assemble, perfect, yay)
--   repeat-cont       1472265    8.77     3688.76 +- 1877.77        731.45 +- 1188.87    (potential for consensus errors, no impact on assembly)
--   repeat-dove             2    0.00     6446.00 +- 0.00           188.53 +- 117.00     (hard to assemble, likely won't assemble correctly or even at all)
--  
--   span-repeat       2450159   14.59     5808.29 +- 2329.16       1772.11 +- 1694.99    (read spans a large repeat, usually easy to assemble)
--   uniq-repeat-cont  4818823   28.70     5027.15 +- 2264.80                             (should be uniquely placed, low potential for consensus errors, no impact on assembly)
--   uniq-repeat-dove        4    0.00     7130.00 +- 150.11                              (will end contigs, potential to misassemble)
--   uniq-anchor        548986    3.27     5701.73 +- 2218.67       2195.96 +- 1928.96    (repeat read, with unique section, probable bad read)
skoren commented 1 week ago

The line reporting the error looks like an I/O issue on your system or perhaps a quota issue. It's trying to open a log file and fails. Check that you're not out of space and the canu-logs file log folder exists and is writable.