No space left on device

Question: No space left on device

2.9 years ago by

Malaysia

I keep on getting this message and I have been unable to upload files using filezila:

STOR PandaMetagenomeF1.fastq
Response:   150 Opening BINARY mode data connection for PandaMetagenomeF1.fastq
Response:   452 Transfer aborted. No space left on device
Error:   File transfer failed after transferring 29,360,128 bytes in 34 seconds
Status:   Starting upload of C:\Users\Owner-PC\Desktop\PandaMetagenomeF1.fastq
Status:   Retrieving directory listing of "/"...

Is there a solution to this issue?

software error ftp galaxy • 3.0k views

ADD COMMENT • link •

modified 2.9 years ago by Nate Coraor ♦ 3.2k • written 2.9 years ago by jayarajvijayakumaran • 30

What server are you trying to upload to?

ADD REPLY • link written 2.9 years ago by Martin Čech ♦♦ 4.9k

This one: https://usegalaxy.org/

ADD REPLY • link modified 2.9 years ago by Martin Čech ♦♦ 4.9k • written 2.9 years ago by jayarajvijayakumaran • 30

I have just uploaded 200MB and did not find a problem. How much space are you using there?

ADD REPLY • link written 2.9 years ago by Martin Čech ♦♦ 4.9k

I have used up 31% of 250G available, and the file is around 3.8G....did you use filezilla? I managed to upload a 2G file earlier but it was gunzipped so I had to delete it.......

ADD REPLY • link written 2.9 years ago by jayarajvijayakumaran • 30

2.9 years ago by

skasowitz • 70

skasowitz • 70 wrote:

Some Tophat mapping jobs I had started about 4 hours ago all began failing over the past hour with various errors. They had all finished mapping left and right sequences. Some other jobs in the queue then failed to begin returning "No space left on device" errors. I encountered a similar problem as jayarajvijayakumaran when trying to upload a fastq file, although I was using the web interface.

ADD COMMENT • link written 2.9 years ago by skasowitz • 70

Thank for chiming in, we will investigate.

ADD REPLY • link written 2.9 years ago by Martin Čech ♦♦ 4.9k

I have tried using WinSCP, the same thing happens....

the error box

Copying files to remote side failed.
Transfer aborted. No space left on device

ADD REPLY • link written 2.9 years ago by jayarajvijayakumaran • 30

I was able to upload several files by through the web interface yesterday at around 18:30 UTC. [edit: All files were compressed fastq files in the range of 1.5-2.0GB compressed.] No jobs seem able to start up beyond this, regardless of data quota. I have no retried the mapping that originally generated errors yesterday, however fastq QC tools such as sequence grooming have been invariably failing to start since yesterday. Typical error is:

Traceback (most recent call last):
  File "/galaxy-repl/instances/main/server/lib/galaxy/jobs/runners/drmaa.py", line 150, in queue_job
    self.write_executable_script( ajs.job_file, script )
  File "/galaxy-repl/instances/main/server/lib/galaxy/jobs/runners/__init__.py", line 316, in write_executable_script
    f.write( contents )
IOError: [Errno 28] No space left on device

ADD REPLY • link modified 2.9 years ago • written 2.9 years ago by skasowitz • 70

2.9 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

Hi all,

Our storage system was reporting intermittent "No space left on device" errors until about 2 hours ago. However, these have stopped. If you continue to encounter the error, please respond to let us know and I'll pass it on to the storage support group.

--nate

ADD COMMENT • link written 2.9 years ago by Nate Coraor ♦ 3.2k

Thanks for the update! I have started some QC jobs and will try mapping again tonight. Everything looks good so far (no immediate errors).

ADD REPLY • link written 2.9 years ago by skasowitz • 70

2.9 years ago by

olivier.buhard • 10

France

olivier.buhard • 10 wrote:

Hi,

I have the same problems wathever the analysis or operation I try to submit to the server I'm on usegalaxy.org).

I first thought I was doing something wrong with tophat on my datasets but I could not complete any work on some samples datasets provided in the tutos or even have a FastQC working correctly.

View details give the same kind of output as reported by skasowitz:

Traceback (most recent call last):
  File "/galaxy-repl/instances/main/server/lib/galaxy/jobs/runners/drmaa.py", line 150, in queue_job
    self.write_executable_script( ajs.job_file, script )
  File "/galaxy-repl/instances/main/server/lib/galaxy/jobs/runners/__init__.py", line 316, in write_executable_script
    f.write( contents )
IOError: [Errno 28] No space left on device

I use 84 GB on the 250GB available.

ADD COMMENT • link written 2.9 years ago by olivier.buhard • 10