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_dada_paired.R /tmp/tmp9c8tdwez/forward /tmp/tmp9c8tdwez/reverse /tmp/tmp9c8tdwez/output.tsv.biom /tmp/tmp9c8tdwez/filt_f /tmp/tmp9c8tdwez/filt_r 0 0 0 0 2.0 2 consensus 1.0 3 1000000 R version 3.3.1 (2016-06-21) Loading required package: Rcpp Warning messages: 1: multiple methods tables found for ‘arbind’ 2: multiple methods tables found for ‘acbind’ 3: replacing previous import ‘IRanges::arbind’ by ‘SummarizedExperiment::arbind’ when loading ‘GenomicAlignments’ 4: replacing previous import ‘IRanges::acbind’ by ‘SummarizedExperiment::acbind’ when loading ‘GenomicAlignments’ 5: multiple methods tables found for ‘left’ 6: multiple methods tables found for ‘right’ DADA2 R package version: 1.4.0 1) Filtering ..... 2) Learning Error Rates 2a) Forward Reads Initializing error rates to maximum possible estimate. Sample 1 - 1 reads in 1 unique sequences. Sample 2 - 8 reads in 8 unique sequences. Sample 3 - 21 reads in 21 unique sequences. Sample 4 - 30 reads in 30 unique sequences. Sample 5 - 13 reads in 12 unique sequences. selfConsist step 2 Convergence after 2 rounds. 2b) Reverse Reads Initializing error rates to maximum possible estimate. Sample 1 - 1 reads in 1 unique sequences. Sample 2 - 8 reads in 8 unique sequences. Sample 3 - 21 reads in 19 unique sequences. Sample 4 - 30 reads in 30 unique sequences. Sample 5 - 13 reads in 13 unique sequences. selfConsist step 2 Convergence after 2 rounds. 3) Denoise remaining samples 4) Remove chimeras (method = consensus) Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : Input must be a valid sequence table. Calls: removeBimeraDenovo -> isBimeraDenovoTable In addition: Warning message: In is.na(colnames(unqs[[i]])) : is.na() applied to non-(list or vector) of type 'NULL' Execution halted Traceback (most recent call last): File "/opt/conda/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired run_commands([cmd]) File "/opt/conda/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands subprocess.run(cmd, check=True) File "/opt/conda/lib/python3.5/subprocess.py", line 398, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp9c8tdwez/forward', '/tmp/tmp9c8tdwez/reverse', '/tmp/tmp9c8tdwez/output.tsv.biom', '/tmp/tmp9c8tdwez/filt_f', '/tmp/tmp9c8tdwez/filt_r', '0', '0', '0', '0', '2.0', '2', 'consensus', '1.0', '3', '1000000']' returned non-zero exit status 1 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/conda/lib/python3.5/site-packages/q2cli/commands.py", line 222, in __call__ results = action(**arguments) File "", line 2, in denoise_paired File "/opt/conda/lib/python3.5/site-packages/qiime2/sdk/action.py", line 201, in callable_wrapper output_types, provenance) File "/opt/conda/lib/python3.5/site-packages/qiime2/sdk/action.py", line 334, in _callable_executor_ output_views = callable(**view_args) File "/opt/conda/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 194, in denoise_paired " and stderr to learn more." % e.returncode) Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.