Question: HISAT Error on local Galaxy
1
gravatar for ChickenRNA
14 months ago by
ChickenRNA50
ChickenRNA50 wrote:

Hi, I am trying to do RNA analysis on local instance of Galaxy running in Linux mint. I have tried assembling the sequences using TopHat and got the error (see post: https://biostar.usegalaxy.org/p/19570/). I tried running HISAT, as I thought it may be a TopHat problem with the resources available. However when I run HISAT I am getting the same error (see below). I am not sure what the problem is, but I would really appreciate it if you can help me sort this out. I have been struggling with this error for over two weeks now. Any help and guidance will be greatly appreciated. Thanks in advance for your time.

Error:

Traceback (most recent call last):

File "/home/vythegi/galaxy1111/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code )

File "/home/vythegi/galaxy1111/lib/galaxy/jobs/__init__.py", line 1265, in finish dataset.datatype.set_meta( dataset, overwrite=False )

File "/home/vythegi/galaxy1111/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

rna-seq hisat local • 376 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by ChickenRNA50
1

The server is set up to run jobs on a cluster? This looks like a problem with that configuration.

Do other tools work that are deployed to the cluster? I am guessing not, but please confirm. (not just local jobs that run on the server)

The galaxy log would be a good place to find out where jobs are going and what the problems are a the root.

ADD REPLYlink modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson23k
1

Hello,

I should have asked this first: Is Samtools and Picard installed? Running any of those tools is successful?

This type of error can come up when a dependency is missing as explained in this other recent post: https://biostar.usegalaxy.org/p/19938/

Consider creating SAM and Picard indexes with Data Managers for any genome that you use to assign "database" to datasets for and use in routine analysis to avoid problems. The indexes are not always needed, but you won't be able to tell that from the tool form in most cases. Any genome that you indexed for mapping tools would need this anyway.

Hopefully one of these helps, Jen, Galaxy team

ADD REPLYlink modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson23k
2
gravatar for ChickenRNA
14 months ago by
ChickenRNA50
ChickenRNA50 wrote:

Hi Jennifer Thanks for your prompt response. I did have both of those installed and they were working without any trouble from what I can tell. From reading previous posts on Biostar, I found this post, and it was very similar to what I was dealing with, so I tried to follow their instructions and install samtools system wide, and that seems to have solved the problem. I am posting what worked for me here, in case it someone else runs into the same problem in the future. I hope that is okay. Thanks for all your help though..

ADD COMMENTlink written 14 months ago by ChickenRNA50

Perfect! Glad all worked out and thanks for posting back the prior Q&A that helped! Jen

ADD REPLYlink written 14 months ago by Jennifer Hillman Jackson23k
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: 114 users visited in the last hour