Question: Galaxy commits subprocess errors !!!
0
gravatar for kaji331
3.1 years ago by
kaji3310
China
kaji3310 wrote:

Hello everyone:

Sorry to my English. I am installing Galaxy into my server with 12 cores and 128GB RAM. I manage it using SSH, use Apache and MySQL for a website that I can use Galaxy in my laptop. Recently, I am constructing a workflow for WES variants. When I use Markduplicates of Picards and BAM filter of Bamtools, they gave me errors below:

Traceback (most recent call last):
  File "/home/galaxy/galaxy-master/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-master/lib/galaxy/jobs/__init__.py", line 1199, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/home/galaxy/galaxy-master/lib/galaxy/datatypes/binary.py", line 281, in set_meta
    proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
    raise child_exception
OSError: [Errno 13] Permission denied

When I run Galaxy with root user, I still get similar errors below Traceback (most recent call last):

Traceback (most recent call last):
  File "/home/galaxy/galaxy-master/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/galaxy/galaxy-master/lib/galaxy/jobs/__init__.py", line 1199, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/home/galaxy/galaxy-master/lib/galaxy/datatypes/binary.py", line 281, in set_meta
    proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

I need your help, emergently. Thanks very very much !

path galaxy samtools • 1.3k views
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by kaji3310
1
gravatar for Bjoern Gruening
3.1 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

you need to install samtools on your $PATH from which you start your Galaxy server. samtools is used to index BAM files so it is a Galaxy dependency.

Ciao,

Bjoern

ADD COMMENTlink written 3.1 years ago by Bjoern Gruening5.1k
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Has Samtools been installed on your instance? If not, please install from the Tool Shed, double check the installation status of all of your repositories and dependencies (including these tools), then re-run. It is best to use tools sourced from the Main Tool Shed only (specifically, not sourcing from the Test Tool Shed).

This was the solution for another user reporting a similar error. 

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k
0
gravatar for kaji331
3.1 years ago by
kaji3310
China
kaji3310 wrote:

Thanks very much! I did install the Samtools and Picards on my instance from Main Tool Shed, and all dependencies were installed correctly (green signs). So I don't know how to fix it!

ADD COMMENTlink written 3.1 years ago by kaji3310
0
gravatar for kaji331
3.1 years ago by
kaji3310
China
kaji3310 wrote:

@Bjoern Gruening I did add the $PATH of samtools and picard to my galaxy server. It still showed same errors.

ADD COMMENTlink written 3.1 years ago by kaji3310

I'm pretty sure this is your setup. Running as user gives you a strange permission error, try to solve this as first step. Because if you are running as root, and this seems to work ... you don't have samtools in your $PATH (as root).

ADD REPLYlink written 3.1 years ago by Bjoern Gruening5.1k

I have tried to run galaxy as root. It showed similar error subprocess.py "no such file or directory". I'm sure there exists a subprocess.py

发自我的 Windows Phone


发件人: Bjoern Gruening on Galaxy Biostar<mailto:notifications@biostars.org> 发送时间: ‎2015/‎8/‎3 18:05 收件人: kaji331@hotmail.com<mailto:kaji331@hotmail.com> 主题: [galaxy-biostar] C: Galaxy commits subprocess errors !!!

Bjoern Gruening posted the Comment: "Galaxy commits subprocess errors !!!":

I'm pretty sure this is your setup. Running as user gives you a strange permission error, try to solve this as first step. Because if you are running as root, and this seems to work ... you don't have samtools in your $PATH (as root).

ADD REPLYlink written 3.1 years ago by kaji3310

Thanks for your help~I tried to run Galaxy by root or reinstall it, but it couldn't help. Now I tried to run Picard MarkDuplicates in command line out of Galaxy by myself, then uploaded bam file to Galaxy. I found when I uploaded bam file after MarkDuplicates, the uploading process showed the same errors : subprocess.py no permission, like running MarkDuplicates in Galaxy. I could upload fastq files without any problem (err...fastq.gz was always decompressed automatically, I don't know how to disable it).

Subject: [galaxy-biostar] C: Galaxy commits subprocess errors !!! From: notifications@biostars.org To: kaji331@hotmail.com Date: Mon, 3 Aug 2015 10:05:11 +0000

Activity on a post you are following on Galaxy Biostar

User Bjoern Gruening wrote Comment: Galaxy commits subprocess errors !!!:

I'm pretty sure this is your setup. Running as user gives you a strange permission error, try to solve this as first step. Because if you are running as root, and this seems to work ... you don't have samtools in your $PATH (as root).

You may reply via email or visit C: Galaxy commits subprocess errors !!!">C: Galaxy commits subprocess errors !!!
ADD REPLYlink written 3.1 years ago by kaji3310
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