Error occurred while parsing the output of qiime2
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
Reproduce the problem with the listed table.qza, taxonomy.qza, and metadata.tsv inputs, then inspect mp_import_qiime2 and the validityMethod/print.MPSE path shown in the trace. Done means the imported MPSE object passes validation with matching taxonomy tip labels and OTU assays.
Written by the indexing model from the issue text.
Description
Hi Shuangbin,
I met some troubles while parsing the output of qiime2. I've checked the output of qiime2 but I didn't find any reasons of the following error.
running:
otuqza="./table.qza"
taxaqzafile="./taxonomy.qza"
mapfile="./metadata.tsv"
mpse <- mp_import_qiime2(otuqza=otuqzafile, taxaqza=taxaqzafile, mapfilename=mapfile)
mpse
error:
Error in validityMethod():
! The number of tip labels of taxatree is not equal the number of otu in assays.
• Please check the taxatree or assays!
Run rlang::last_trace() to see where the error occurred.
rlang::last_trace()
<error/rlang_error>
Error invalidityMethod():
! The number of tip labels of taxatree is not equal the number of otu in assays.
• Please check the taxatree or assays!
Backtrace:
▆
- ├─methods (local)
<stndrdGn>(<MPSE[,0]>) - ├─MicrobiotaProcess (local)
<stndrdGn>(<MPSE[,0]>) - │ └─object %>% print()
- ├─base::print(.)
- └─MicrobiotaProcess:::print.MPSE(.)
- └─MicrobiotaProcess:::print2.MPSE(...)
-
├─x[seq_len(n), seq_len(min(1, ncol(x))), drop = FALSE] -
└─x[seq_len(n), seq_len(min(1, ncol(x))), drop = FALSE] -
└─methods::validObject(nx) -
├─methods (local) anyStrings(validityMethod(object)) -
│ └─base::isTRUE(x) -
└─MicrobiotaProcess (local) validityMethod(object)
Run rlang::last_trace(drop = FALSE) to see 1 hidden frame.
- Dominant language
- R
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- 195
- Forks
- 36
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