[Errno 2] No such file or directory

Technical Support
1

Hi

qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ez_otus.qza --i-reference-taxonomy ez-taxonomy.qza --o-classifier classifier.qza

I entered the above command, but an error occurred.

Plugin error from feature-classifier:

[Errno 2] No such file or directory: '/ data / sskimvd / tmp / qiime2-archive-fopax8it / e39263e8-c7eb-4257-a172-681d00095a5f / provenance'

Help
Thank you.

2

Hi @shinseung,

That doesn't look good at all :frowning:

We see this error when something else deletes QIIME 2 files while it is operating (or when a disk is unmounted or using unusual file-systems).

I notice that your temporary path is /data/sskimvd/tmp which means we don't have the more typical OS X issue (which deletes files after 3 days).

Could you elaborate more on what this temporary directory is? Running this command should give us a bit more information:

df /data/sskimvd/tmp

Thanks!

2 Likes
3

hi

Filesystem       1K-blocks       Used  Available Use% Mounted on
/dev/sdb1      11717322716 7920509500 3796813216  68% /data

It is the result of execution.
What is the problem? ㅠㅠ

4

Hi @shinseung,

Terribly sorry, I forgot a flag in the last command, could you run again (with the -T flag):

df -T /data/sskimvd/tmp

That will give us the filesystem.

Good news is so far, everything looks ok, which doesn't make this any easier to figure out.

Is this drive a USB drive by chance? Or is it attached to the computer motherboard?

5

Hi
I am using a computer server.

Filesystem     Type   1K-blocks       Used  Available Use% Mounted on
/dev/sdb1      xfs  11717322716 8006675536 3710647180  69% /data

thank you.

7

Hi @shinseung,

Very sorry for the delay, I lost track of this topic :frowning:

XFS is among the most reliable filesystems ever made, so its definitely not that!

The disk is a little bit full, I wonder if it is possible that an out-of-disk error occurred first but was caught and ignored somewhere, eventually resulting in the error you see.

If you repeat this action, do you see the same issue? Is this drive a removable disk? Is there any chance it was accidentally removed (or otherwise disabled/unavailable) during the commands execution?

If you set your TMPDIR to another location, does that help? (I'm assuming you already know how to change this as your current temporary directory isn't the default, but if that isn't the case, let me know! as that is maybe an additional clue).