Question: RNA STAR unable to finish job
1
gravatar for chaoyuan
20 months ago by
chaoyuan80
chaoyuan80 wrote:

I encountered this error message while I was trying to run RNA STAR 2.4.0 (owner:iuc, revision: ace9f5a2b40f ) on my data:

Traceback (most recent call last):
File "/home/chuonglab/galaxy-dev/lib/galaxy/jobs/runners/local.py", line 128, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
File "/home/chuonglab/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1248, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
File "/home/chuonglab/galaxy-dev/lib/galaxy/datatypes/binary.py", line 339, in set_meta
    exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
File "/usr/lib/python2.7/subprocess.py", line 522, in call
    return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

This error looks exactly the same as the one I posted several weeks earlier. This of course led me to believe that it could come from the same cause, that samtools can not be found by RNA Star.

I checked the tool dependency directory ( ~/galaxy-dev/tool_dependency/samtools/0.1.19/devteam/package_samtools_0_1_19/95d2c4aefb5f ) and see that there is an env.sh file. So this should be fine?

Now, adding samtools to the system PATH might not be a good idea because different tools might actually use different version of samtools.

Since I ran into the same problem with Bowtie2 and RNA Star, I tend to believe that there is a common mistake I make. Could anyone advice me on how to solve ( or troubleshoot ) this issue?

Thanks

ADD COMMENTlink modified 19 months ago • written 20 months ago by chaoyuan80
2
gravatar for chaoyuan
19 months ago by
chaoyuan80
chaoyuan80 wrote:

I did two things and I think the problem is gone

  1. Instead of downloading source codes as zip file from the galaxy github repository, I used git clone.

  2. I installed virtualenv.

I guess these are just what should be done if one wishes to install a local Galaxy instance. It's really difficult to find a good step-by-step tutorial for this matter, though...

Update: It turned out that these procedures did not solve the problem. I believe they're necessary when setting up Galaxy ,though. Please see a newer post

ADD COMMENTlink modified 19 months ago • written 19 months ago by chaoyuan80
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Different tools often require different versions of dependencies. Did you install the tools with managed dependencies?

If you are not sure, and even if you believe you did, uninstalling and reinstalling this way might resolve the issue. It is the best first pass troubleshooting step. Please let us know if this does not work.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson23k

Thanks for the reply. I installed the tools with managed dependencies. That is, when I select the tool and click 'Install to Galaxy', I leave the 'Handle repository dependencies' and 'Handle tool dependencies' checked. In the tool dependency directory, I see that binaries for all the tool dependencies are there, including the bin folder and an env.sh file. Re-installation doesn't help me because it's really just repeating the process. From what I tell on the folder/file content, nothing's changed.

For example, in the tool_dependency folder ~/galaxy-dev/tool_dependency/, I have these folders, bowtie2, ncurses, samtools, tophat, zlib. And in the samtools folder, I have 0.1.19, 1.2. In 1.2, I then have devteam and iuc, then within iuc, I have package_samtools_1_2, then folder bearing the name of revision, which then contains bin folder and an env.sh. The folder structure looks convoluted and I'm not sure if there's any problem with it?

What's odd is I ran into the same problem with Bowtie2 and RNA-Star, which both require samtools. That led me to believe I may have made a common mistake while installing those tools but I just couldn't figure it out.

What would be the next step for troubleshooting?

ADD REPLYlink written 19 months ago by chaoyuan80
0
gravatar for y.hoogstrate
19 months ago by
y.hoogstrate450
Netherlands
y.hoogstrate450 wrote:

Could you run the commands within the env.sh in terminal (not ./env.sh or sh env.sh but copy all the commands and drop them into the terminal right away because export commands are contained within their subshell) and then run which STAR and maybe also samtools etc.?

ADD COMMENTlink modified 19 months ago • written 19 months ago by y.hoogstrate450

If I do that, I'll find the samtools found by the system to be the version where the env.sh is located. I checked the env.sh, it's recording correctly the path to the samtools. That's whey I suspect it's not sourced by Galaxy before a job runs. Otherwise, samtools would have been found correctly.

ADD REPLYlink written 19 months ago by chaoyuan80
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