Question: Unable to finish job
gravatar for Marc
3.5 years ago by
United Kingdom
Marc30 wrote:

Hi there, 

I've been running the local galaxy on a vm, when I try to run markduplicates and AddOrReplaceReadGroups, I get this error, anyone knows how to fix it?


Traceback (most recent call last):
  File "/home/azureuser/galaxy/lib/galaxy/jobs/runners/", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/azureuser/galaxy/lib/galaxy/jobs/", line 1199, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/home/azureuser/galaxy/lib/galaxy/datatypes/", line 281, in set_meta
    proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib/python2.7/", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
galaxy picard • 1.8k views
ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson25k • written 3.5 years ago by Marc30
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This error is a standard python error generally related to expected input/temp files being missing (never produced), unreadable, or not found where expected. Memory can be a factor (the job requires more memory than available on your VM). But on a local, the database used can also sometimes be involved.

Did you upgrade to a production instance database? If not, do that first. Odd errors can pop out if you don't and work with larger datasets or run several jobs concurrently.

Another quick test to upload the BAM dataset to to see if the issue can be replicated, to rule out issues with input content. 

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson25k


I've upgrade the database, and it still doesn't work. I tested the dataset on and it works fine. My vm has 4 cores and 14 GB of memory. Can you think of anything else that might cause this?

Many thanks

ADD REPLYlink written 3.5 years ago by Marc30

By the way, all the tools that cant run are from picard.

ADD REPLYlink written 3.5 years ago by Marc30

Are the reference genomes indexed for SAM-tools and Picard? (I know this seem obvious, but is a place to start). Jen


ADD REPLYlink written 3.5 years ago by Jennifer Hillman Jackson25k

Do you mind explaining a bit more? I'm new to all these. Thanks

ADD REPLYlink written 3.5 years ago by Marc30

Of course! To use many tools, a reference genome is required. This must be installed into your instance. The basic install is the fasta sequence of the genome. From there, indexes are created that are used by tools. I was asking about two important indexes that are required for most Picard tools. 

A question earlier today is probably a good place to start, since it is related and I put in extra detail for anyone who hasn't done this before, or is a bit stuck in the processing. Please see: Reference genome download - a step-by-step please?

ADD REPLYlink written 3.5 years ago by Jennifer Hillman Jackson25k

Hi again, I dont think data manager is gonna solve my problem. Another guy had the same problem and i dont see that fixed(


ADD REPLYlink written 3.5 years ago by Marc30

Yes, that was a similiar problem. But based on a different Galaxy release and Picard tool repository. I believe this was resolved for them, but I don't know the final solution, as it wasn't linked back in (if in another post or the development mailing list). Now, that is something I generally do if posts are timely and the connection between Q&A on oall ur other support channels is clear. And not all questions are wrapped up with feedback from the original question asker. I'll ask for more information in that post.

Reference genomes and associated indexes are required by most of these tools. Even if it is not on the tool form (the input's metadata "database" is interpreted). Has that been done for the genomes ("databases") assigned to the inputs in your failed runs?

Also, if picard was installed before the database updates (release is current? it may need to be installed again or upgraded to the latest version, as the repository has undergone a major upgrade in the last few months as well.

Let's start there (if anything is changed, re-run), Additional information will help if this does not resolve the problem, it will be easier to help diagnose the root cause for your issue.

1. galaxy version 
2. picard version (a link to the repository that you are using along with the version)

Best, Jen



ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Jennifer Hillman Jackson25k

Hi, just so you know, i fixed the problem. It turns out that I need to install samtools on vm. I assumed that when I installed package samtools in galaxy, that wouldn't be a problem, but I'm wrong. Anyway, hope this information helps you as well.



ADD REPLYlink written 3.5 years ago by Marc30
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