Dear Forum:
I have a plugin error that I can't solve. I am trying to run qiime diversity alpha-correlation with
System versions
Python version: 3.6.7
QIIME 2 release: 2019.10
QIIME 2 version: 2019.10.0
q2cli version: 2019.10.0
(I know these aren't the latest version but I have successfully run it on this version.)
This is installed via conda
Commands:
#!/bin/bash
#SBATCH --account=skimble5
#SBATCH -A tow107
#SBATCH --partition=compute
#SBATCH --time 00:30:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24
#SBATCH --export=ALL
#SBATCH --no-requeue
#SBATCH --job-name="alpha-correlation"
#SBATCH --output="alpha-correlation.o%j.%N"
export TMPDIR=/scratch/$USER/$SLURM_JOBID
MODULEPATH=/share/apps/compute/modulefiles/applications:$MODULEPATH
module load anaconda
source activate qiime2
qiime diversity alpha-correlation
--i-alpha-diversity ./diversity_metrics/core-metrics-results_ITS_wo_recaps/shannon_vector_ITS_wo_recaps.qza
--m-metadata-file ./denoised_without_recaps/TurtleMapITS_without_recapsTurtleMapITS_without_recaps_metadata.tsv (114.6 KB) _metadata.tsv
--p-method spearman
--o-visualization ITS_wo_recaps_shannon_alpha_correlation.qzv
--verbose
which gives:
Traceback (most recent call last):
File "/share/apps/compute/anaconda/envs/qiime2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</share/apps/compute/anaconda/envs/qiime2/lib/python3.6/site-packages/decorator.py:decorator-gen-420>", line 2, in alpha_correlation
File "/share/apps/compute/anaconda/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/share/apps/compute/anaconda/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 445, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/share/apps/compute/anaconda/envs/qiime2/lib/python3.6/site-packages/q2_diversity/_alpha/visualizer.py", line 216, in alpha_correlation
with open(os.path.join(output_dir, filename), 'w') as fh:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/qiime2-temp-08dq9w4/column-H/L.jsonp'
Plugin error from diversity:
[Errno 2] No such file or directory: '/tmp/qiime2-temp-08dq9w4_/column-H/L.jsonp'
See above for debug info.
But I don't know how to interpret this. Based on other plugin errors I see on the forum, it may be some error in my metadata file (attached) but I can't find it.
Questions:
- Missing data in the metadata file should be left empty, not filled with NA or somesuch, correct?
- Is there some error in the metadata file? Is there some column that I think is numeric that isn't?
- Is this a cluster or qiime error?
Thanks,
Steve
