Dear community, I'm trying to run ANCOM-BC with the qiime2 plugin (thanks for it!!) but I'm having an error. I've tried both in qiime2-2022.11 and qiime2-2023.2 and the error is the same. I understand that there is a problem with the ANCOM-BC R-package, but I don't really know how to deal with it.
Thanks in advance,
(qiime2-2023.2) pgen@pgen:/media/pgen/Disco_2/GEN00452_RaquelCampos_nematodos/8_Study_Samples_filtered/Phylum_Nematodos/DA$ qiime composition ancombc --i-table table_Nematozoa.qza --m-metadata-file metadata_samples_final.csv --p-formula Treatment --p-p-adj-method fdr --p-prv-cut 0.1 --p-lib-cut 0 --p-alpha 0.05 --o-differentials ancombc_feature.qza --verbose
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_ancombc.R --inp_abundances_path /tmp/tmpeccwrndq/input.biom.tsv --inp_metadata_path /tmp/tmpeccwrndq/input.map.txt --formula Treatment --p_adj_method fdr --prv_cut 0.1 --lib_cut 0 --reference_levels --neg_lb False --tol 1e-05 --max_iter 100 --conserve False --alpha 0.05 --output_loaf /tmp/q2-DataLoafPackageDirFmt-3bt89y1_
── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.1 ✔ purrr 1.0.1
✔ tibble 3.1.8 ✔ dplyr 1.1.0
✔ tidyr 1.3.0 ✔ stringr 1.5.0
✔ readr 2.1.4 ✔ forcats 1.0.0
── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
Error: package or namespace load failed for ‘ANCOMBC’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/pgen/anaconda3/envs/qiime2-2023.2/lib/R/library/gsl/libs/gsl.so':
libgsl.so.25: no se puede abrir el archivo del objeto compartido: No existe el archivo o el directorio
8: stop(msg, call. = FALSE, domain = NA)
7: value[[3L]](cond)
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(ANCOMBC)
2: withCallingHandlers(expr, warning = function(w) if (inherits(w,
classes)) tryInvokeRestart("muffleWarning"))
1: suppressWarnings(library(ANCOMBC))
Traceback (most recent call last):
File "/home/pgen/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_composition/_ancombc.py", line 176, in _ancombc
run_commands([cmd])
File "/home/pgen/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_composition/_ancombc.py", line 31, in run_commands
subprocess.run(cmd, check=True)
File "/home/pgen/anaconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_ancombc.R', '--inp_abundances_path', '/tmp/tmpeccwrndq/input.biom.tsv', '--inp_metadata_path', '/tmp/tmpeccwrndq/input.map.txt', '--formula', 'Treatment', '--p_adj_method', 'fdr', '--prv_cut', '0.1', '--lib_cut', '0', '--reference_levels', '', '--neg_lb', 'False', '--tol', '1e-05', '--max_iter', '100', '--conserve', 'False', '--alpha', '0.05', '--output_loaf', '/tmp/q2-DataLoafPackageDirFmt-3bt89y1_']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/pgen/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in __call__
results = action(**arguments)
File "<decorator-gen-36>", line 2, in ancombc
File "/home/pgen/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/home/pgen/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/pgen/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_composition/_ancombc.py", line 40, in ancombc
return _ancombc(
File "/home/pgen/anaconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_composition/_ancombc.py", line 178, 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.
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.
was installing the various plugins. I forget why I set up my