Importing data [error no 28]No space left on device

import
(Dixi Modi) #1

Hi,
This is my first time using qiime2 and I am using QIIME2-2019.1 on HPC cluster using conda env. I am having questions about importing. I have my Fastq files in a directory on the cluster and I am trying to execute the following command:
(qiime2-2019.1) [[email protected] ~]$ qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path dixi-paired-end-sequences --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza

Getting the following error:

Traceback (most recent call last):
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/tools.py”, line 146, in import_data
view_type=input_format)
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 240, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 265, in _from_view
result = transformation(view)
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/transform.py”, line 70, in transformation
new_view = transformer(view)
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 76, in _4
dirfmt, SingleLanePerSamplePairedEndFastqDirFmt)
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 52, in _single_lane_per_sample_fastq_helper
read_number=read_number)
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/plugin/model/directory_format.py”, line 87, in write_data
result.path._move_or_copy(self.path_maker(**kwargs))
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/path.py”, line 35, in _move_or_copy
return shutil.copy(str(self), str(other))
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/shutil.py”, line 241, in copy
copyfile(src, dst, follow_symlinks=follow_symlinks)
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/shutil.py”, line 122, in copyfile
copyfileobj(fsrc, fdst)
File “/home/dixi06/.local/easybuild/software/2017/Core/miniconda3/4.3.27/envs/qiime2-2019.1/lib/python3.6/shutil.py”, line 82, in copyfileobj
fdst.write(buf)
OSError: [Errno 28] No space left on device

An unexpected error has occurred:

[Errno 28] No space left on device

See above for debug info.

I tried all the things but I think I do not understand where to make dir tmp or export it or where to see if there is enough space. I am still posting the following.

(qiime2-2019.1) [[email protected] ~] /data df -h
-bash: /data$: No such file or directory
(qiime2-2019.1) [[email protected] ~] cd /data (qiime2-2019.1) [[email protected] data] df -h
Filesystem Size Used Avail Use% Mounted on
devtmpfs 126G 0 126G 0% /dev
tmpfs 126G 624M 126G 1% /dev/shm
tmpfs 126G 4.0G 122G 4% /run
tmpfs 126G 0 126G 0% /sys/fs/cgroup
/dev/mapper/ROOTDISK-root 50G 11G 40G 21% /
/dev/mapper/ROOTDISK-scratch 320G 33M 320G 1% /localscratch
/dev/mapper/ROOTDISK-cvmfs 50G 23G 28G 46% /var/lib/cvmfs
/dev/md126p2 494M 206M 289M 42% /boot
tmpfs 126G 126G 727M 100% /tmp
/dev/md126p1 200M 12M 189M 6% /boot/efi
cvmfs-nfs:/export/nfs/local-cedar 15T 4.4T 11T 30% /opt/software
172.16.121.42:/pnfs/sfu.ca/data/atlas/atlasscratchdisk 1.0E 2.5P 1022P 1% /wlcg/storage/cedar/atlas/atlasscratchdisk
172.16.121.42:/pnfs/sfu.ca/data/atlas/atlasdatadisk 1.0E 2.5P 1022P 1% /wlcg/storage/cedar/atlas/atlasdatadisk
172.16.121.42:/pnfs/sfu.ca/data/atlas/atlaslocalgroupdisk 1.0E 2.5P 1022P 1% /wlcg/storage/cedar/atlas/atlaslocalgroupdisk
[email protected]:[email protected]:/cedar_ho 231T 31T 189T 15% /home
[email protected]:[email protected]:/lustrefs 13P 8.0P 4.3P 66% /project
[email protected]:[email protected]:/cedar_sc 4.6P 2.3P 2.1P 52% /scratch
cvmfs2 44G 23G 21G 53% /cvmfs/cvmfs-config.computecanada.ca
cvmfs2 44G 23G 21G 53% /cvmfs/grid.cern.ch
cvmfs2 44G 23G 21G 53% /cvmfs/soft.computecanada.ca
cvmfs2 44G 23G 21G 53% /cvmfs/soft.mugqic
tmpfs 26G 0 26G 0% /run/user/3000123
tmpfs 26G 0 26G 0% /run/user/3052846
tmpfs 26G 0 26G 0% /run/user/3079059
tmpfs 26G 0 26G 0% /run/user/13200023
cvmfs2 44G 23G 21G 53% /cvmfs/restricted.computecanada.ca
cvmfs2 44G 23G 21G 53% /cvmfs/snoplus.egi.eu
cvmfs2 44G 23G 21G 53% /cvmfs/ganga.cern.ch
tmpfs 26G 0 26G 0% /run/user/3050042
tmpfs 26G 0 26G 0% /run/user/3078933
cvmfs2 44G 23G 21G 53% /cvmfs/ref.mugqic
cvmfs2 44G 23G 21G 53% /cvmfs/soft-dev.computecanada.ca
tmpfs 26G 0 26G 0% /run/user/3023114
tmpfs 26G 0 26G 0% /run/user/3010296
tmpfs 26G 0 26G 0% /run/user/3061173

Please help me with this. I am using HPC cluster also for the first time so I may be not understanding its use too. But I am confused whether this error is regarding the cluster or QIIME2 space.

Many thanks.

(Dixi Modi) #2

Hi I solved it.

It was tmp dir that was full.

Use the following command from one of the topics on the same error.

export TMPDIR=/home/dir/

Just change the TMPdir place to my home directory which has quite a lot of space.

Thanks.

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