touala
commented
11 months ago Hello @monxac,
Sorry for the massive delay. It looks like the coverage is quite low for the couple contigs you showed. Could you produce the summary for the complete difference dataset with summary(readRDS(<path_to_rds>))?
Thank you,
Alan
monxac
Hi,
i'm trying to run the nanodisco motif script but i get this error,
[2023-05-31 13:21:36] Prepare output folder. [2023-05-31 13:21:36] Load supplied current differences. [2023-05-31 13:21:37] Detect motifs. [2023-05-31 13:21:37] Processing statistical signal. Error in do.ply(i) : task 12 failed - "wrong sign in 'by' argument" Calls: wrapper.motif.detection ... ddply -> ldply -> llply -> ->
Execution halted
the current difference file looks normal, it has lots of NA, but there is data for some chunks, here are the first lines as an example
1 | megahit_805628 | 1 | rev | t | 0 | 0 | NA | NA | NA 2 | megahit_3546264 | 1 | rev | t | 0 | 0 | NA | NA | NA 3 | megahit_3546264 | 5001 | rev | t | 0 | 0 | NA | NA | NA 4 | megahit_7415660 | 1 | rev | t | 0 | 0 | NA | NA | NA 5 | megahit_3033896 | 1 | rev | t | 0 | 0 | NA | NA | NA 6 | megahit_3033896 | 5001 | rev | t | 0 | 0 | NA | NA | NA 7 | megahit_3033896 | 12402 | fwd | t | 0 | 0 | NA | NA | NA 8 | megahit_3033896 | 12404 | fwd | t | 0 | 0 | NA | NA | NA 9 | megahit_3033896 | 12405 | fwd | t | 0 | 0 | NA | NA | NA 10 | megahit_3033896 | 12406 | fwd | t | 0 | 0 | NA | NA | NA 11 | megahit_3033896 | 12411 | fwd | t | 0 | 0 | NA | NA | NA 12 | megahit_3033896 | 12415 | fwd | t | 0 | 0 | NA | NA | NA 13 | megahit_3033896 | 12416 | fwd | t | 0 | 0 | NA | NA | NA 14 | megahit_3033896 | 12420 | fwd | t | 0 | 0 | NA | NA | NA 15 | megahit_3033896 | 12423 | fwd | t | 0 | 0 | NA | NA | NA 16 | megahit_3033896 | 12424 | fwd | t | 0 | 0 | NA | NA | NA 17 | megahit_3033896 | 12427 | fwd | t | 0 | 0 | NA | NA | NA 18 | megahit_3033896 | 12428 | fwd | t | 0 | 0 | NA | NA | NA 19 | megahit_3033896 | 12429 | fwd | t | 0 | 0 | NA | NA | NA 20 | megahit_3033896 | 12430 | fwd | t | 0 | 0 | NA | NA | NA 21 | megahit_3033896 | 12431 | fwd | t | 0 | 0 | NA | NA | NA 22 | megahit_3033896 | 12432 | fwd | t | 0 | 0 | NA | NA | NA 23 | megahit_3033896 | 12433 | fwd | t | 0 | 0 | NA | NA | NA 24 | megahit_3033896 | 12434 | fwd | t | 0 | 0 | NA | NA | NA 25 | megahit_3033896 | 12435 | fwd | t | 0 | 0 | NA | NA | NA 26 | megahit_3033896 | 12436 | fwd | t | 0 | 0 | NA | NA | NA 27 | megahit_3033896 | 12437 | fwd | t | 0 | 0 | NA | NA | NA 28 | megahit_3033896 | 12438 | fwd | t | 0 | 0 | NA | NA | NA 29 | megahit_3033896 | 12439 | fwd | t | 0 | 0 | NA | NA | NA 30 | megahit_3033896 | 12440 | fwd | t | 0 | 0 | NA | NA | NA 31 | megahit_3033896 | 12441 | fwd | t | 0 | 0 | NA | NA | NA 32 | megahit_3033896 | 12442 | fwd | t | 0 | 0 | NA | NA | NA 33 | megahit_3033896 | 12443 | fwd | t | 0 | 0 | NA | NA | NA 34 | megahit_3033896 | 12444 | fwd | t | 0 | 0 | NA | NA | NA 35 | megahit_3033896 | 12445 | fwd | t | 0 | 0 | NA | NA | NA 36 | megahit_3033896 | 12446 | fwd | t | 6 | 16 | -1.8615509 | 0.0615589 | 0.070095 37 | megahit_3033896 | 12447 | fwd | t | 8 | 9 | -7.3153943 | 0.0147895 | 0.0206499 38 | megahit_3033896 | 12448 | fwd | t | 0 | 0 | NA | NA | NA
i've tried looking at the functions the error message is reffering to, to understand what is causing the errror, i think it's in this part of rollingFunction, called within the wrapper.motif.detection function:
genomic_position_range <- seq(min(genomic_position),max(genomic_position))
, but i don't see what is causing the problem,
would someone know what the problem is?
thank you in advance,