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ropensci / phylotaR

An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
https://docs.ropensci.org/phylotaR
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TAXISE error: no applicable method for `@` applied to an object of class "NULL" #76

Open esmacp opened 3 weeks ago

esmacp commented 3 weeks ago

Running old code from February that used to work without issue-- I am having problems with the following error during the TAXISE stage, just after downloading:

Generating taxonomic dictionary ...
Unexpected Error in recs[[x]]@prnt : 
  no applicable method for `@` applied to an object of class "NULL"

Occurred [2024-10-08 10:36:27.361617]
Contact package maintainer for help.
Error in stages_run(wd = wd, frm = 1, to = nstages, stgs_msg = stgs_msg) : 
  Unexpected Error in recs[[x]]@prnt : 
  no applicable method for `@` applied to an object of class "NULL"

Occurred [2024-10-08 10:36:27.361617]
Contact package maintainer for help.

Taxon ID is 8092. Would you be able to assist me with this, or is it possibly an issue on the GenBank end?

ShixiangWang commented 3 weeks ago

The code has not been modified for a long time. It seems the data or the R version issue.

Thanks for your report, I will take a look.

GRyan-geophy commented 1 week ago

Hi, I just wanted to highlight I am having the same issue for multiple NCBI IDs (703407,3650, 41773). I am wondering if there could be a way to skip problematic records.

Searching taxonomic IDs ... Downloading taxonomic records ... . [1-100] . [101-200] . [201-300] . [301-335] Generating taxonomic dictionary ... Unexpected Error in recs[[x]]@prnt : no applicable method for @ applied to an object of class "NULL"

Occurred [2024-10-19 02:17:16.845128] Contact package maintainer for help. Error in stages_run(wd = wd, frm = 1, to = nstages, stgs_msg = stgs_msg) : Unexpected Error in recs[[x]]@prnt : no applicable method for @ applied to an object of class "NULL"

Occurred [2024-10-19 02:17:16.845128] Contact package maintainer for help.

Many Thanks, George

ShixiangWang commented 1 week ago

Thanks for reporting. I will take a look this week and see if I can provide a solution or walkaround.

ShixiangWang commented 1 week ago

today I run a test with preset example and it works well. I need to replay it with problematic ids (https://github.com/ropensci/phylotaR/blob/master/test.R), and see how to make it more robust.

--------------------------------------------------
Completed pipeline at [2024-10-23 17:44:28.881593]
--------------------------------------------------
Phylota Table (Termitoidae)
- [1749] clusters
- [17219] sequences
- [2065] source taxa
[1] 1749
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00   10.91    4.00 1265.00 
[1] 239
Phylota Table (Termitoidae)
- [239] clusters
- [14640] sequences
- [2060] source taxa
ShixiangWang commented 6 days ago

I cannot reproduce the error with id 8092 (log.txt), could you guys make sure you are using the latest code from GitHub? If so, could you please share the R code for reproducing the issue?

ShixiangWang commented 6 days ago

Quite strange. I got a different error when testing 3650. As the whole process are querying and processing data from internet, I think I need to take some time to check all functions during the process as I am not the original developer.

. . . [2801-2900]
. . . [2901-3000]
Unexpected Error in locus[["date"]] : subscript out of bounds

Occurred [2024-10-24 15:19:51.352589]
Contact package maintainer for help.
Error in stages_run(wd = wd, frm = 1, to = nstages, stgs_msg = stgs_msg) : 
  Unexpected Error in locus[["date"]] : subscript out of bounds

Occurred [2024-10-24 15:19:51.352589]