Hello,
I assume my problem is similar to this closed topic here:
However, as it does not provide any solution, I would like to ask, what is the state of the issue now. Are there any recommendations, what to do? The only suggestion I found elsewhere was to reinstall everything.
To be more precise:
I run this command on Ubuntu VMware machine using QIIME2 2024.5 Amplicon distribution:
qiime composition ancombc
--i-table qiime2/OUTPUT_manifest/paired-end-table-deblur_woO40O42C.qza
--m-metadata-file qiime2/Buducnost_Qiime2_metadata/Buducnost_metadata_final_Keemei_woO40O42C_allsamples_woextras.tsv
--p-formula 'pH'
--o-differentials qiime2/OUTPUT_manifest/core-metrics-results-filtered-woO40O42C/ANCOM/ancombc-pH.qza
The error is:
If I understand it correctly, it's missing phyloseq package, but installing it additionaly with conda didn't make any difference.
Thank you very much for any help.
Best,
Hana
Details:
n error was encountered while running ANCOM-BC in R (return code 1), please inspect stdout and stderr to learn more.
/home/hana/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/metadata/metadata.py:610: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '[nan]' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
series[missing.index] = missing
/home/hana/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py:77: FutureWarning: Series.getitem treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
term_alpha_value = (metadata.get_column(term)
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/tmpcxp50rq2/input.biom.tsv --inp_metadata_path /tmp/tmpcxp50rq2/input.map.txt --md_column_types {"sample-id-geo": "categorical", "barcode-sequence": "categorical", "NGS": "categorical", "type": "categorical", "location": "categorical", "conductivity [\u00b5S.cm-1]": "numeric", "temperature [\u00b0C]": "numeric", "pH": "numeric", "Ag [mg.kg-1] - liquid": "numeric", "As [mg.kg-1] - liquid": "numeric", "Ca [mg.kg-1] - liquid": "numeric", "Cu [mg.kg-1] - liquid": "numeric", "Fe [mg.kg-1] - liquid": "numeric", "K [mg.kg-1] - liquid": "numeric", "Mg [mg.kg-1] - liquid": "numeric", "Mn [mg.kg-1] - liquid": "numeric", "Ni [mg.kg-1] - liquid": "numeric", "Si [mg.kg-1] - liquid": "numeric", "Sx [mg.kg-1] - liquid": "numeric", "V [mg.kg-1] - liquid": "numeric", "Zn [mg.kg-1] - liquid": "numeric", "Sb [mg.kg-1] - liquid": "numeric", "Sr [mg.kg-1] - liquid": "numeric", "Al [mg.kg-1] - solid": "numeric", "As [mg.kg-1] -solid": "numeric", "Ba [mg.kg-1] -solid": "numeric", "Ca [mg.kg-1] - solid": "numeric", "Co [mg.kg-1] -solid": "numeric", "Cu [mg.kg-1] - solid": "numeric", "Fe [mg.kg-1] -solid": "numeric", "K [mg.kg-1] - solid": "numeric", "Mg [mg.kg-1] -solid": "numeric", "Mn [mg.kg-1] - solid": "numeric", "Ni [mg.kg-1] -solid": "numeric", "Pcel [mg.kg-1] - solid": "numeric", "Scel [mg.kg-1] -solid": "numeric", "Sb [mg.kg-1] - solid": "numeric", "Si [mg.kg-1] -solid": "numeric", "Sr [mg.kg-1] - solid": "numeric", "Ti [mg.kg-1] -solid": "numeric", "Zn [mg.kg-1] - solid": "numeric", "Zr [mg.kg-1] -solid": "numeric", "Mo [mg.kg-1] - solid": "numeric", "Pb [mg.kg-1] -solid": "numeric", "V [mg.kg-1] - solid": "numeric", "Na [mg.kg-1] -solid": "numeric"} --formula pH --p_adj_method holm --prv_cut 0.1 --lib_cut 0 --reference_levels ['pH::2.5'] --tol 1e-05 --max_iter 100 --conserve False --alpha 0.05 --output_loaf /tmp/q2-DataLoafPackageDirFmt-75gt4iff
Error: package or namespace load failed for ‘phyloseq’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/hana/miniconda3/envs/qiime2-amplicon-2024.5/lib/R/library/ade4/libs/ade4.so':
/home/hana/miniconda3/envs/qiime2-amplicon-2024.5/lib/R/bin/exec/../../lib/../.././libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /home/hana/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/hana/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py", line 255, in _ancombc
run_commands([cmd])
File "/home/hana/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/hana/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/tmpcxp50rq2/input.biom.tsv', '--inp_metadata_path', '/tmp/tmpcxp50rq2/input.map.txt', '--md_column_types', '{"sample-id-geo": "categorical", "barcode-sequence": "categorical", "NGS": "categorical", "type": "categorical", "location": "categorical", "conductivity [\u00b5S.cm-1]": "numeric", "temperature [\u00b0C]": "numeric", "pH": "numeric", "Ag [mg.kg-1] - liquid": "numeric", "As [mg.kg-1] - liquid": "numeric", "Ca [mg.kg-1] - liquid": "numeric", "Cu [mg.kg-1] - liquid": "numeric", "Fe [mg.kg-1] - liquid": "numeric", "K [mg.kg-1] - liquid": "numeric", "Mg [mg.kg-1] - liquid": "numeric", "Mn [mg.kg-1] - liquid": "numeric", "Ni [mg.kg-1] - liquid": "numeric", "Si [mg.kg-1] - liquid": "numeric", "Sx [mg.kg-1] - liquid": "numeric", "V [mg.kg-1] - liquid": "numeric", "Zn [mg.kg-1] - liquid": "numeric", "Sb [mg.kg-1] - liquid": "numeric", "Sr [mg.kg-1] - liquid": "numeric", "Al [mg.kg-1] - solid": "numeric", "As [mg.kg-1] -solid": "numeric", "Ba [mg.kg-1] -solid": "numeric", "Ca [mg.kg-1] - solid": "numeric", "Co [mg.kg-1] -solid": "numeric", "Cu [mg.kg-1] - solid": "numeric", "Fe [mg.kg-1] -solid": "numeric", "K [mg.kg-1] - solid": "numeric", "Mg [mg.kg-1] -solid": "numeric", "Mn [mg.kg-1] - solid": "numeric", "Ni [mg.kg-1] -solid": "numeric", "Pcel [mg.kg-1] - solid": "numeric", "Scel [mg.kg-1] -solid": "numeric", "Sb [mg.kg-1] - solid": "numeric", "Si [mg.kg-1] -solid": "numeric", "Sr [mg.kg-1] - solid": "numeric", "Ti [mg.kg-1] -solid": "numeric", "Zn [mg.kg-1] - solid": "numeric", "Zr [mg.kg-1] -solid": "numeric", "Mo [mg.kg-1] - solid": "numeric", "Pb [mg.kg-1] -solid": "numeric", "V [mg.kg-1] - solid": "numeric", "Na [mg.kg-1] -solid": "numeric"}', '--formula', 'pH', '--p_adj_method', 'holm', '--prv_cut', '0.1', '--lib_cut', '0', '--reference_levels', "['pH::2.5']", '--tol', '1e-05', '--max_iter', '100', '--conserve', 'False', '--alpha', '0.05', '--output_loaf', '/tmp/q2-DataLoafPackageDirFmt-75gt4iff']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/hana/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/hana/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/hana/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/hana/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/hana/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_composition/_ancombc.py", line 41, in ancombc
return _ancombc(
File "/home/hana/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.