MaestSi
commented
3 years ago Hi, I am not sure but probably yes, it may be due to the RAM, if it happens only when considering a greater amount of reads (across all samples). You may try either reducing the number of reads or the identity threshold for clustering (this will reduce the number of representative sequences used for building the phylogenetic tree)...or, in alternative, you may use Evaluate_diversity_non_phylogenetic.sh script. Let me know if you are able to solve it! Simone
timregan
Most of the time, the Evaluate_diversity.sh script works perfectly for me. However, I am receiving a recurring error on some slightly larger datasets (e.g. 20 samples, subsampled at 20k reads). The script seems to run ok until the "qiime phylogeny align-to-tree-mafft-fasttree" command when I receive the following error:
Plugin error from phylogeny: Command '['mafft', '--preservecase', '--inputorder', '--thread', '8', '/tmp/qiime2-archive-so3u883h/9152bd3d-d8d5-472b-9c98-8c868156dfa3/data/dna-sequences.fasta']' returned non-zero exit status 1.
Debug info has been saved to /tmp/qiime2-q2cli-err-vund61s9.log
$ head -50 /tmp/qiime2-q2cli-err-vund61s9.log
Running external command line application. This may print messages to stdout and/or stderr. The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: mafft --preservecase --inputorder --thread 8 /tmp/qiime2-archive-so3u883h/9152bd3d-d8d5-472b-9c98-8c868156dfa3/data/dna-sequences.fasta
Traceback (most recent call last): File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call results = action(arguments) File "", line 2, in align_to_tree_mafft_fasttree
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/qiime2/sdk/action.py", line 484, in _callableexecutor
outputs = self._callable(scope.ctx, view_args)
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/q2_phylogeny/_align_to_tree_mafft_fasttree.py", line 20, in align_to_tree_mafft_fasttree
parttree=parttree)
File "", line 2, in mafft
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callableexecutor
output_views = self._callable(**view_args)
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 127, in mafft
return _mafft(sequences_fp, None, n_threads, parttree)
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 99, in _mafft
run_command(cmd, result_fp)
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 26, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/anaconda/envs/MetONTIIME_env/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '8', '/tmp/qiime2-archive-so3u883h/9152bd3d-d8d5-472b-9c98-8c868156dfa3/data/dna-sequences.fasta']' returned non-zero exit status 1.
I've tried increasing the number of cores to 12, but the same error appears. Do you think it's RAM or something else? Many thanks, Tim