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moold / paf2dotplot

Draw a dot plot from a paf alignment
GNU General Public License v3.0
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Error while resolving a reads against contig file. #2

Open laijirong opened 2 hours ago

laijirong commented 2 hours ago

The command of minimap2 is:

minimap2 -t 16 -x map-ont ../hifi_ctg.fa ../hifi_ont.reads.fa > hifi_ctgXhifi_ont.reads.paf

While plotting with paf2dotplot:

Rscript ~/common/paf2dotplot.R hifi_ctgXhifi_ont.reads.paf

And it returns with:


Number of alignments: 1926
Number of query sequences: 230

After filtering... Number of alignments: 0
After filtering... Number of query sequences: 0

Error in alignments$refStart + sapply(as.character(alignments$refID),  :
  non-numeric argument to binary operator
No traceback available
Error in alignments$refEnd + sapply(as.character(alignments$refID), function(x) ifelse(x ==  :
  non-numeric argument to binary operator
No traceback available
Error in alignments$queryStart + sapply(as.character(alignments$queryID),  :
  non-numeric argument to binary operator
No traceback available
Error in alignments$queryEnd + sapply(as.character(alignments$queryID),  :
  non-numeric argument to binary operator
No traceback available
Error in `geom_point()`:
! Problem while computing aesthetics.
ℹ Error occurred in the 3rd layer.
Caused by error:
! object 'refStart2' not found
Backtrace:
     ▆
  1. ├─ggplot2::ggsave(...)
  2. │ ├─grid::grid.draw(plot)
  3. │ └─ggplot2:::grid.draw.ggplot(plot)
  4. │   ├─base::print(x)
  5. │   └─ggplot2:::print.ggplot(x)
  6. │     ├─ggplot2::ggplot_build(x)
  7. │     └─ggplot2:::ggplot_build.ggplot(x)
  8. │       └─ggplot2:::by_layer(...)
  9. │         ├─rlang::try_fetch(...)
 10. │         │ ├─base::tryCatch(...)
 11. │         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12. │         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 14. │         │ └─base::withCallingHandlers(...)
 15. │         └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 16. │           └─l$compute_aesthetics(d, plot)
 17. │             └─ggplot2 (local) compute_aesthetics(..., self = self)
 18. │               └─base::lapply(aesthetics, eval_tidy, data = data, env = env)
 19. │                 └─rlang (local) FUN(X[[i]], ...)
 20. └─base::.handleSimpleError(...)
 21.   └─rlang (local) h(simpleError(msg, call))
 22.     └─handlers[[1L]](cnd)
 23.       └─cli::cli_abort(...)
 24.         └─rlang::abort(...)
No traceback available

The file is look like this:

8ce7c0be-bb90-48f4-bb34-a10efc5df467    76540   43780   75355   -       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  49472   108861  29127   60976   60      NM:i:31849      ms:i:49537      AS:i:19332>
8ce7c0be-bb90-48f4-bb34-a10efc5df467    76540   15192   43776   -       hifi_gt10k.asm.bp.p_ctg_ptg000055l      85163   45547   85163   19297   48232   1       NM:i:28935      ms:i:32122      AS:i:4330 >
8ce7c0be-bb90-48f4-bb34-a10efc5df467    76540   15157   35276   -       hifi_gt10k.asm.bp.p_ctg_ptg000055l      85163   22142   42180   18004   21662   0       NM:i:3658       ms:i:31145      AS:i:28401>
8ce7c0be-bb90-48f4-bb34-a10efc5df467    76540   26      6867    +       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  28497   35386   6644    6956    60      NM:i:312        ms:i:11999      AS:i:11936>
8ce7c0be-bb90-48f4-bb34-a10efc5df467    76540   26      6872    -       hifi_gt10k.asm.bp.p_ctg_ptg000055l      85163   48793   55084   5976    6938    0       NM:i:962        ms:i:10384      AS:i:9748 >
8ce7c0be-bb90-48f4-bb34-a10efc5df467    76540   13408   16279   +       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  41117   48416   2785    7336    14      NM:i:4551       ms:i:5054       AS:i:602  >
8ce7c0be-bb90-48f4-bb34-a10efc5df467    76540   75135   76514   -       hifi_gt10k.asm.bp.p_ctg_ptg000056l      172400  171005  172400  1228    1426    60      NM:i:198        ms:i:1727       AS:i:1676 >
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  85744   119451  -       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  92721   131815  33001   39462   60      NM:i:6461       ms:i:61148      AS:i:55564>
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  21      25912   -       hifi_gt10k.asm.bp.p_ctg_ptg000056l      172400  102385  146297  25174   44260   60      NM:i:19086      ms:i:45818      AS:i:27563>
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  73260   95606   +       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  75081   108774  20623   34964   60      NM:i:14341      ms:i:37053      AS:i:23503>
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  108     25912   +       hifi_gt10k.asm.bp.p_ctg_ptg000055l      85163   41058   61443   19839   26089   0       NM:i:6250       ms:i:36534      AS:i:30841>
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  57983   71359   +       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  49465   68487   12984   19142   60      NM:i:6158       ms:i:23554      AS:i:17848>
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  51505   62985   -       hifi_gt10k.asm.bp.p_ctg_ptg000055l      85163   46590   63434   10366   17050   60      NM:i:6684       ms:i:14833      AS:i:9268 >
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  28140   36376   -       hifi_gt10k.asm.bp.p_ctg_ptg000056l      172400  85239   100066  7873    14988   34      NM:i:7115       ms:i:13801      AS:i:7038 >
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  28140   36376   -       hifi_gt10k.asm.bp.p_ctg_ptg000056l      172400  66760   81574   7810    14976   0       NM:i:7166       ms:i:13417      AS:i:6665 >
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  28450   36376   +       hifi_gt10k.asm.bp.p_ctg_ptg000055l      85163   64058   78606   7567    14664   0       NM:i:7097       ms:i:13239      AS:i:6506 >
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  28140   36377   -       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  35385   53079   7787    17850   0       NM:i:10063      ms:i:13220      AS:i:3605 >
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  42950   45044   +       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  35385   37480   2069    2104    3       NM:i:35 ms:i:3990       AS:i:3984       nn>
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  42951   45044   -       hifi_gt10k.asm.bp.p_ctg_ptg000055l      85163   64595   66689   2068    2103    0       NM:i:35 ms:i:3988       AS:i:3982       nn>
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  37333   40118   -       hifi_gt10k.asm.bp.p_ctg_ptg000045l      81087   49392   52173   2158    2863    14      NM:i:705        ms:i:1479       AS:i:1420 >
0de7d053-8bc7-4037-bb82-e3653de28c4e    119459  40718   42632   +       hifi_gt10k.asm.bp.p_ctg_ptg000045l      81087   50888   52748   1417    2009    33      NM:i:592        ms:i:885        AS:i:617  >
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  25      24875   +       hifi_gt10k.asm.bp.p_ctg_ptg000056l      172400  9360    24137   10150   29303   60      NM:i:19153      ms:i:18419      AS:i:-421 >
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  69045   74271   +       hifi_gt10k.asm.bp.p_ctg_ptg000056l      172400  57198   62331   4727    5344    1       NM:i:617        ms:i:7449       AS:i:7229 >
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  65118   68670   -       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  93327   97014   3321    3733    34      NM:i:412        ms:i:5452       AS:i:5267 >
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  54952   57658   -       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  105932  108649  2631    2740    37      NM:i:109        ms:i:4811       AS:i:4792 >
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  126462  129139  +       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  115920  118599  2528    2711    2       NM:i:183        ms:i:4307       AS:i:4284 >
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  37489   40085   -       hifi_gt10k.asm.bp.p_ctg_ptg000052l      131815  116448  118595  2071    2628    29      NM:i:557        ms:i:3760       AS:i:3269 >
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  88545   90847   -       hifi_gt10k.asm.bp.p_ctg_ptg000045l      81087   50650   53022   2116    2416    1       NM:i:300        ms:i:3257       AS:i:3138 >
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  139812  140111  -       hifi_gt10k.asm.bp.p_ctg_ptg000056l      172400  29156   29450   284     299     1       NM:i:15 ms:i:508        AS:i:506        nn>
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  115833  116037  +       hifi_gt10k.asm.bp.p_ctg_ptg000045l      81087   9713    9918    178     208     1       NM:i:30 ms:i:237        AS:i:234        nn>
bcb91625-c2fd-4178-b9cc-0c43a58ab90c    142712  86269   86455   -       hifi_gt10k.asm.bp.p_ctg_ptg000055l      85163   70168   70353   164     187     1       NM:i:23 ms:i:230        AS:i:230        nn>

I don't know what's happening, other alignments is available.😭

moold commented 2 hours ago

paf2dotplot is designed for assembly vs assembly, so it will filter short alignments. You must adjust the default parameter to keep all alignments.