Plugin error from diversity: [Errno 2] no such file or directory

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:

  1. Missing data in the metadata file should be left empty, not filled with NA or somesuch, correct?
  2. Is there some error in the metadata file? Is there some column that I think is numeric that isn’t?
  3. Is this a cluster or qiime error?

Thanks,
Steve

Hi @skimble!

Yep, its the column labeled H/L - there was an old bug that I think was fixed a while ago that caused that / in the label to be interpreted as a directory. Two suggestions: 1) upgrade to a newer version of QIIME 2 (2019.10 is pretty old), 2) change the name of the MD column to something without a / character.

Hope that helps!

:qiime2:

1 Like

Thanks, thermokarst, that fixed it!

Steve

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