Question: Top Hat Error
0
gravatar for ChickenRNA
21 months ago by
ChickenRNA50
ChickenRNA50 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 • 577 views
ADD COMMENTlink modified 20 months ago by deane30 • written 21 months ago by ChickenRNA50
1

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 REPLYlink written 20 months ago by deane30

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 REPLYlink written 20 months ago by ChickenRNA50
1
gravatar for ChickenRNA
20 months ago by
ChickenRNA50
ChickenRNA50 wrote:

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

ADD COMMENTlink written 20 months ago by ChickenRNA50
1
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k

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 REPLYlink modified 21 months ago • written 21 months ago by ChickenRNA50
1

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 REPLYlink written 21 months ago by Jennifer Hillman Jackson25k

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 REPLYlink written 21 months ago by ChickenRNA50

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 REPLYlink written 21 months ago by ChickenRNA50
1

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 REPLYlink modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson25k

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 REPLYlink written 21 months ago by ChickenRNA50

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 REPLYlink modified 21 months ago • written 21 months ago by ChickenRNA50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 109 users visited in the last hour