Hi qiime2 team,
I'm trying to run ANCOMBC on my data through the q2-composition plugin. This is through WSL in a qiime2-2024.5 environment. This was all set up within the last month and I followed the installation guide for setting this up, nothing else has been installed. This looks to be the same error as mentioned in this [post] (ANCOM-BC plugin error) and here. After troubleshooting by making sure my .condarc file was blank which did not fix the error, I tried the moving pictures tutorial data to see if it could be a problem with my personal metadata file and I received the same error.
Is there anything I can do to fix this error? The latter forum post suggests deleting miniconda and installing everything again. I don't know if this would work for me since everything is a recent install. More details below.
Thanks in advance!
The command:
qiime composition ancombc
--i-table gut-table.qza
--m-metadata-file sample-metadata.tsv
--p-formula 'subject'
--o-differentials ancombc-subject.qza
--verbose
I'm receiving an error that says the following:
Plugin error from composition:
An error was encountered while running ANCOM-BC in R (return code 1), please inspect
stdout and stderr to learn more.
See above for debug info.
Verbose gets me:
Command: run_ancombc.R --inp_abundances_path /tmp/tmpvnk28nv4/input.biom.tsv --inp_metadata_path /tmp/tmpvnk28nv4/input.map.txt --md_column_types {"barcode-sequence": "categorical", "body-site": "categorical", "year": "numeric", "month": "numeric", "day": "numeric", "subject": "categorical", "reported-antibiotic-usage": "categorical", "days-since-experiment-start": "numeric"} --formula subject --p_adj_method holm --prv_cut 0.1 --lib_cut 0 --reference_levels ['subject::subject-1'] --tol 1e-05 --max_iter 100 --conserve False --alpha 0.05 --output_loaf /tmp/q2-DataLoafPackageDirFmt-e67rpj0b
Error: package or namespace load failed for ‘phyloseq’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/R/library/ade4/libs/ade4.so':
/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/R/library/ade4/libs/ade4.so)
8: stop(msg, call. = FALSE, domain = NA)
7: value[3L]
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
4: tryCatch({
attr(package, "LibPath") <- which.lib.loc
ns <- loadNamespace(package, lib.loc)
env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
}, error = function(e) {
P <- if (!is.null(cc <- conditionCall(e)))
paste(" in", deparse(cc)[1L])
else ""
msg <- gettextf("package or namespace load failed for %s%s:\n %s",
sQuote(package), P, conditionMessage(e))
if (logical.return && !quietly)
message(paste("Error:", msg), domain = NA)
else stop(msg, call. = FALSE, domain = NA)
})
3: library(phyloseq)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(library(phyloseq))
Traceback (most recent call last):
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py", line 255, in _ancombc
run_commands([cmd])
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py", line 32, in run_commands
subprocess.run(cmd, check=True)
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_ancombc.R', '--inp_abundances_path', '/tmp/tmpvnk28nv4/input.biom.tsv', '--inp_metadata_path', '/tmp/tmpvnk28nv4/input.map.txt', '--md_column_types', '{"barcode-sequence": "categorical", "body-site": "categorical", "year": "numeric", "month": "numeric", "day": "numeric", "subject": "categorical", "reported-antibiotic-usage": "categorical", "days-since-experiment-start": "numeric"}', '--formula', 'subject', '--p_adj_method', 'holm', '--prv_cut', '0.1', '--lib_cut', '0', '--reference_levels', "['subject::subject-1']", '--tol', '1e-05', '--max_iter', '100', '--conserve', 'False', '--alpha', '0.05', '--output_loaf', '/tmp/q2-DataLoafPackageDirFmt-e67rpj0b']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in ancombc
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in callable_executor
output_views = self._callable(**view_args)
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py", line 41, in ancombc
return _ancombc(
File "/home/mahasti2/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py", line 257, in _ancombc
raise Exception('An error was encountered while running ANCOM-BC'
Exception: An error was encountered while running ANCOM-BC in R (return code 1), please inspect stdout and stderr to learn more.
