我想在Docker容器上使用QIIME2分析数据。请注意,这是我第一次使用Docker。 我先创建图像,然后创建容器,然后开始成功地分析数据的一小部分子样本。 但是,流水线的一个步骤系统性地失败,并显示以下错误消息,提示剩余空间:
Plugin error from feature-classifier:
[Errno 28] No space left on device
Debug info has been saved to /tmp_mount/qiime2-q2cli-err-8hbv6l2e.log
该日志文件对我说的不多:
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "<decorator-gen-326>", line 2, in classify_sklearn
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in _callable_executor_
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 215, in classify_sklearn
confidence=confidence)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/_skl.py", line 45, in predict
for chunk in _chunks(reads, chunk_size)) for m in c)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py", line 789, in __call__
self.retrieve()
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py", line 699, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/multiprocessing/pool.py", line 644, in get
raise self._value
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/multiprocessing/pool.py", line 424, in _handle_tasks
put(task)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/pool.py", line 371, in send
CustomizablePickler(buffer, self._reducers).dump(obj)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/pool.py", line 240, in __call__
for dumped_filename in dump(a, filename):
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle.py", line 484, in dump
NumpyPickler(f, protocol=protocol).dump(value)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/pickle.py", line 408, in dump
self.save(obj)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle.py", line 278, in save
wrapper.write_array(obj, self)
File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle.py", line 93, in write_array
pickler.file_handle.write(chunk.tostring('C'))
OSError: [Errno 28] No space left on device
但是还有足够的空间...
我的图像不大(6G),inode也可以。我要分析的输入文件很小,只是一个测试。
我发现了其他一些具有相同问题的主题,但是我尝试的所有尝试都失败了。
我尝试过:
-删除所有退出的容器并悬挂图像
-升级Docker
-将TMPDIR环境变量设置为/ custom_tmp /我已经在容器中创建了自己。我尝试了几种方法:在QIIME2环境中,在容器中但不在QIIME2环境中,在Dockerfile中添加ENV TMPDIR =“ / cutom_tmp” /然后重建映像。
-将TMPDIR环境变量设置为在主机服务器上创建的/ tmp_mount /,然后将容器作为卷安装
在每种情况下都会出现相同的问题。我的猜测是,也许Docker想要写入自己的tmp目录,也许只剩下64M的“ tmpfs”之一(请参阅下面的命令结果),也许我无法用TMPDIR变量解决这个问题,但是我陷入了困境那里...
许多感谢您的关注和建议。
OS:Ubuntu 14.04。
df -h
Filesystem Size Used Avail Use% Mounted on
none 197G 57G 131G 31% /
tmpfs 64M 0 64M 0% /dev
tmpfs 32G 0 32G 0% /sys/fs/cgroup
/dev/sda1 939G 772G 120G 87% /tmp_mount
/dev/dm-0 197G 57G 131G 31% /data
shm 64M 0 64M 0% /dev/shm
tmpfs 32G 0 32G 0% /proc/acpi
tmpfs 32G 0 32G 0% /proc/scsi
tmpfs 32G 0 32G 0% /sys/firmware
docker版本
Client:
Version: 18.06.1-ce
API version: 1.38
Go version: go1.10.3
Git commit: e68fc7a
Built: Tue Aug 21 17:24:58 2018
OS/Arch: linux/amd64
Experimental: false
Server:
Engine:
Version: 18.06.1-ce
API version: 1.38 (minimum version 1.12)
Go version: go1.10.3
Git commit: e68fc7a
Built: Tue Aug 21 17:23:24 2018
OS/Arch: linux/amd64
Experimental: false
env
CONDA_SHLVL=1
LC_ALL=C.UTF-8
CONDA_EXE=/opt/conda/bin/conda
XDG_CONFIG_HOME=/home/qiime2
LANG=C.UTF-8
CONDA_PREFIX=/opt/conda/envs/qiime2-2018.8
R_LIBS_USER=/opt/conda/envs/qiime2-2018.8/lib/R/library/
TINI_VERSION=v0.16.1
PYTHONNOUSERSITE=/opt/conda/envs/qiime2-2018.8/lib/python*/site-packages/
PWD=/
HOME=/home/qiime2
CONDA_PYTHON_EXE=/opt/conda/bin/python
DEBIAN_FRONTEND=noninteractive
TMPDIR=/tmp_mount/
CONDA_PROMPT_MODIFIER=(qiime2-2018.8)
TERM=xterm
MPLBACKEND=Agg
SHLVL=1
PATH=/opt/conda/envs/qiime2-2018.8/bin:~/miniconda3/bin:/opt/conda/envs/qiime2-2018.8/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
CONDA_DEFAULT_ENV=qiime2-2018.8
_=/usr/bin/env
OLDPWD=/data
答案 0 :(得分:0)
我在那里找到了解释:forum.qiime2.org/t/error-no-28-out-of-memory/5758/16。多线程处理此任务是大声地占用内存的方法,因此我尝试了1个线程,此方法确实有效... 希望有一天能对某人有所帮助。