# Issue tmp space \[Errno 28\] tools import **URL:** \ **Category:** Technical Support\ **Tags:** tmp\ **Created:** [November 28, 2024, 4:37pm UTC](https://forum.qiime2.org/t/issue-tmp-space-errno-28-tools-import/32005 "2024-11-28T16:37:08Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![msalamon2](https://forum.qiime2.org/user_avatar/forum.qiime2.org/msalamon2/32/19776_2.png) [@msalamon2](https://forum.qiime2.org/u/msalamon2)\ **Post date:** [November 28, 2024, 4:37pm UTC](https://forum.qiime2.org/t/issue-tmp-space-errno-28-tools-import/32005/1 "2024-11-28T16:37:08Z")
Hello, I am trying to convert a midori2 database downloaded specifically in the qiime2 format (MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME.fasta) to the qiime2 archive format, but I am having issues with space in the tmp folder. I saw that there was many discussions on this topic on the forum and I went through them but couldn't find a solution that worked. I am running Qiime2 on a computing cluster from the digital reasearch alliance of Canada. Here are the commands I used and the error message I got: #SBATCH --mem=150G #SBATCH --cpus-per-task=31 #SBATCH --time=2:00:00 #SBATCH --account=def-mcristes #SBATCH --mail-type=ALL module load StdEnv/2023 qiime2/2024.5 cd /home/msalamon/projects/def-mcristes/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/ export TMPDIR='/home/msalamon/AMPtk/TEMP/' qiime tools import --input-path /lustre03/project/6006581/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME.fasta --output-path /lustre03/project/6006581/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME.fasta.qza --type 'FeatureData[Sequence]' Matplotlib created a temporary cache directory at /tmp/matplotlib-qra2psto because the default path (/home/qiime2/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDI\> Traceback (most recent call last): File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/builtin/tools.py", line 852, in \_import artifact = qiime2.sdk.Artifact.import\_data( File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 332, in import\_data return cls._from\_view(type_, view, view\_type, provenance\_capture, File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 360, in \_from\_view result = transformation(view, validate\_level) File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 70, in transformation new\_view = transformer(view) File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 224, in wrapped new\_view.file.write\_data(file\_view, self.\_wrapped\_view\_type) File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/plugin/model/directory\_format.py", line 93, in write\_data result.path.\_move\_or\_copy(self.path\_maker(\*\*kwargs)) File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/path.py", line 45, in \_move\_or\_copy return self.\_copy\_dir\_or\_file(other) File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/core/path.py", line 35, in \_copy\_dir\_or\_file return shutil.copy(str(self), str(other)) File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/shutil.py", line 427, in copy copyfile(src, dst, follow\_symlinks=follow\_symlinks) File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/shutil.py", line 277, in copyfile \_fastcopy\_sendfile(fsrc, fdst) File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/shutil.py", line 166, in \_fastcopy\_sendfile raise err from None File "/opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/shutil.py", line 152, in \_fastcopy\_sendfile sent = os.sendfile(outfd, infd, offset, blocksize) OSError: [Errno 28] No space left on device: '/lustre03/project/6006581/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME.fasta' -\> '/tmp/q2-DNASequencesDirectoryFormat-qzk\> An unexpected error has occurred: [Errno 28] No space left on device: '/lustre03/project/6006581/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME.fasta' -\> '/tmp/q2-DNASequencesDirectoryFormat-qzkf0v3f/d\> See above for debug info. Matplotlib created a temporary cache directory at /tmp/matplotlib-z8hrb7fq because the default path (/home/qiime2/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDI\> Usage: qiime feature-classifier classify-consensus-vsearch (1/1) Invalid value for '--i-reference-reads': /lustre03/project/6006581/msal amon/scripts/QIIME2\_taxonomy/12SMimammal/MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME. fasta.qza does not exist. I tried changing the TMPDIR in different ways to other directories including in the home directory which should have sufficient space: export TMPDIR=$SLURM\_TMPDIR or cd /home/msalamon/projects/def-mcristes/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/ mkdir -p TEMP export TMPDIR='/home/msalamon/projects/def-mcristes/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/TEMP' However I still got the same error message, so it doesn't seem like I was able to change the tmp directory. I also tried increasing the memory to 150G (the fasta file itself is ~110MB) but this didn't change the issue. Thank you for your help, Mathilde Salamon ---
**Author:** ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)\ **Post date:** [December 2, 2024, 5:46pm UTC](https://forum.qiime2.org/t/issue-tmp-space-errno-28-tools-import/32005/2 "2024-12-02T17:46:44Z")
Hello @msalamon2, Welcome to the forums! :qiime2: Thank you for your detailed post. It looks like you are setting `TMPDIR` correctly: ```plaintext export TMPDIR=$SLURM_TMPDIR or cd /home/msalamon/projects/def-mcristes/msalamon/scripts/QIIME2_taxonomy/12SMimammal/ mkdir -p TEMP export TMPDIR='/home/msalamon/projects/def-mcristes/msalamon/scripts/QIIME2_taxonomy/12SMimammal/TEMP' ``` and yet... > Matplotlib created a temporary cache directory at /tmp/matplotlib-qra2psto because the default path (/home/qiime2/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDI\> > [Errno 28] No space left on device: '/lustre03/project/6006581/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME.fasta' -\> '/tmp/q2-DNASequencesDirectoryFormat-qzkf0v3f/d\> Maybe you could try reading and files from the TMPDIR? ```sh echo $TMPDIR touch $TMPDIR/test1.txt ls $TMPDIR ``` If that all works, I think it's time to bring this to your cluster admins. They will know if there is a special way you pass environment variables or something when you run this on the queue. If you figure this out, let us know! That will help future users! ---
**Author:** ![msalamon2](https://forum.qiime2.org/user_avatar/forum.qiime2.org/msalamon2/32/19776_2.png) [@msalamon2](https://forum.qiime2.org/u/msalamon2)\ **Post date:** [December 6, 2024, 4:47pm UTC](https://forum.qiime2.org/t/issue-tmp-space-errno-28-tools-import/32005/3 "2024-12-06T16:47:12Z")
Hello @colinbrislawn, thank you for your reply. The tech support from the computing cluster were able to solve the issue with apptainer. The solution was: salloc --mem=50G cd /home/msalamon/projects/def-mcristes/msalamon/scripts/QIIME2\_taxonomy/12SMimammal/ # [Appendix — Apptainer User Guide main documentation](https://apptainer.org/docs/user/main/appendix.html) # Bind source:destination, bind current directory to /data export APPTAINER\_BIND=$PWD:/data # Set the working directory to be used for /tmp, /var/tmp and $HOME export APPTAINER\_WORKDIR=$SLURM\_TMPDIR module load StdEnv/2023 qiime2/2024.5 # run with /data mounted qiime tools import --input-path /data/MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME.fasta --output-path /data/MIDORI2\_UNIQ\_NUC\_GB261\_srRNA\_QIIME.fasta.qza --type 'FeatureData[Sequence]' I hope this can help other users ! ---
**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\ **Post date:** [January 6, 2025, 10:47pm UTC](https://forum.qiime2.org/t/issue-tmp-space-errno-28-tools-import/32005/4 "2025-01-06T22:47:48Z")
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