Top Hat Error

Question: Top Hat Error

2.2 years ago by

ChickenRNA • 50 wrote:

Hi all,

I'm going through the RNAseq tutorial posted here:

https://vimeo.com/channels/884356/128265983

Data upload and setting up collection goes well; however, I run into a problem with the tophat step. I keep getting a "Tool Error: An error with this dataset" I am using the dataset that I downloaded from the tutorial, so not sure what the issue will be.

Here is the detailed error I received: "Traceback (most recent call last): File "/home/vythegi/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/vythegi/galaxy/lib/galaxy/jobs/__init__.py", line 1265, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/vythegi/galaxy/lib/galaxy/datatypes/binary.py", line 347, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib/python2.7/subprocess.py", line 523, in call return Popen(popenargs, *kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1340, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory"

Any help you can provide is greatly appreciated.

error tophat rna-seq local • 865 views

ADD COMMENT • link •

modified 2.1 years ago by deane • 30 • written 2.2 years ago by ChickenRNA • 50

Hi, did you ever solve this error? I have the same error running Tophat on a local server. My failure seems to be related to setting metadata for the Accepted Hits file. See below. This propagates to the "finish method" Job wrapper which gives the error you stated in your post.

galaxy.jobs.output_checker INFO 2016-10-18 21:58:11,363 Job 7: Log: tool progress galaxy.jobs.output_checker INFO 2016-10-18 21:58:11,363 Job 7: Log: tool progress galaxy.model.metadata DEBUG 2016-10-18 21:58:11,455 loading metadata from file for: HistoryDatasetAssociation 15 galaxy.model.metadata DEBUG 2016-10-18 21:58:11,662 loading metadata from file for: HistoryDatasetAssociation 16 galaxy.model.metadata DEBUG 2016-10-18 21:58:11,732 loading metadata from file for: HistoryDatasetAssociation 17 galaxy.model.metadata DEBUG 2016-10-18 21:58:11,805 loading metadata from file for: HistoryDatasetAssociation 18 galaxy.model.metadata DEBUG 2016-10-18 21:58:11,838 setting metadata externally failed for HistoryDatasetAssociation 19: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-10-18 21:58:11,894 Job wrapper finish method failed

ADD REPLY • link written 2.1 years ago by deane • 30

Hi, I have tried resetting the meta-data like suggested, but it keeps running for greater than a week, and it doesn't seem to finish on my local instance of Galaxy. I tried uninstalling and reinstalling a new instance of local galaxy, and I am getting the same error. I am running the local instance of Galaxy on Linux Mint, and have 16 GB of RAM. not sure what the problem might be, but would greatley appreciate any help or guidance on this.

Also is there an alternate tool I can try instead of Tophat2, such as HISAT?

Traceback (most recent call last): File "/home/vythegi/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/vythegi/galaxy/lib/galaxy/jobs/__init__.py", line 1265, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/vythegi/galaxy/lib/galaxy/datatypes/binary.py", line 347, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib/python2.7/subprocess.py", line 523, in call return Popen(popenargs, *kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1340, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

ADD REPLY • link written 2.2 years ago by ChickenRNA • 50

2.1 years ago by

ChickenRNA • 50

ChickenRNA • 50 wrote:

Please check this post, This is how I got it to work https://biostar.usegalaxy.org/p/19953/#20011

ADD COMMENT • link written 2.1 years ago by ChickenRNA • 50

2.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This looks like an input dataset metadata problem or a cluster failure. Please see the troubleshooting help here: https://wiki.galaxyproject.org/Support#Example:_Dataset_metadata_missing_or_incomplete

Best, Jen, Galaxy team

ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer, Once again thank you for your prompt response. Are there any issues with Tophat? I tried running same on just a subset of my data using the web based platform and I received a similar error. When I try to auto-detect the metadata, the process just runs for hours without any results (both on local instance and web based). Thanks again

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by ChickenRNA • 50

The error is the same? Seems odd, but we can check. My guess is that if the same inputs/jobs are failing in both places, in the same way, there is an input problem that is untrapped by the wrapper, resulting in this error message.

If you want to send in a bug report, I can take a look. Please make sure the inputs and outputs are undeleted and include a link to this Biostars post.

Tophat jobs are not failing in general right now at http://usegalaxy.org, however there might be a few cluster errors occasionally. They do not end like this from what I have seen the last few days.

There is a known issue with metadata not setting for the accepted hits files from one of the clusters, but those are not failed jobs, they are green with a warning, resolved by using "auto-detect".

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

HI Jennifer, I tried using "auto-detect" to resolve the issue with the tophat as you suggested, but I am still getting the exact same error. I am not sure what I can do to resolve it.

"Traceback (most recent call last): File "/home/vythegi/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/vythegi/galaxy/lib/galaxy/jobs/__init__.py", line 1265, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/vythegi/galaxy/lib/galaxy/datatypes/binary.py", line 347, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib/python2.7/subprocess.py", line 523, in call return Popen(popenargs, *kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1340, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory"

ADD REPLY • link written 2.2 years ago by ChickenRNA • 50

Also the auto-detect for the metadata, does that take a long time? I had selected "auto-detect" for only one sample, and it is at the "meta-data being detected" status for hours. Is this normal?

ADD REPLY • link written 2.2 years ago by ChickenRNA • 50

First, click on the history refresh icon to make sure the job really is not complete. "Refresh" is the double circle icon at the top of the history panel.

If still going, it is not that unusual for this to take a while to run. How long depends on the size of the dataset, what else the database is doing, and the available resources (RAM, etc). I suggest allowing it to complete - it is the only way forward. Jen

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you Jennifer. I will keep you updated on the process. Is performing "auto-detect" for just sample set sufficient, or do I need to do it individually for every sample set I have? Thanks again for your prompt answers

ADD REPLY • link written 2.2 years ago by ChickenRNA • 50

Hi Jennifer, The auto-detect for the metadata, has been running for 3 days and the status is"meta-data being detected". I had only selected this option for one dataset, so I am not sure why its taking this long. I am not sure I should proceed, and any guidance you can provide will be greatly appreciated.

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by ChickenRNA • 50

Please log in to add an answer.

Similar posts • Search »