Unable to finish job

Traceback (most recent call last): File "/home/azureuser/galaxy/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/azureuser/galaxy/lib/galaxy/jobs/__init__.py", line 1199, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/azureuser/galaxy/lib/galaxy/datatypes/binary.py", line 281, in set_meta proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) ) 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

3.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 http://usegalaxy.org to see if the issue can be replicated, to rule out issues with input content.

Hopefully this helps! Jen, Galaxy team

ADD COMMENT • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

Hi,

I've upgrade the database, and it still doesn't work. I tested the dataset on usegalaxy.org 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 REPLY • link written 3.5 years ago by Marc • 30

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

ADD REPLY • link written 3.5 years ago by Marc • 30

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

ADD REPLY • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 3.5 years ago by Marc • 30

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 REPLY • link written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

Hi again, I dont think data manager is gonna solve my problem. Another guy had the same problem and i dont see that fixed(https://biostar.usegalaxy.org/p/10697/).

ADD REPLY • link written 3.5 years ago by Marc • 30

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 REPLY • link modified 3.5 years ago • written 3.5 years ago by Jennifer Hillman Jackson ♦ 25k

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.

Regards,

Marc

ADD REPLY • link written 3.5 years ago by Marc • 30

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