Getting an error when trying to align sequence data with bowtie2

Question: Getting an error when trying to align sequence data with bowtie2

18 months ago by

On a local instance of galaxy, I created a reference gnome and tried to use 'bowtie2' to align some sequence data with the reference gnome. After waiting for hours, I got the following error:

Traceback (most recent call last):

 File "/Users/tleis/GitHub/galaxy/galaxy/lib/galaxy/jobs/runners/local.py", line 130, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/Users/tleis/GitHub/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1354, in finish
dataset.datatype.set_meta( dataset, overwrite=False )
File "/Users/tleis/GitHub/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 391, in set_meta
exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

I couldn't happen to see what file or directory it is referring to. I inspected the code in 'subprocess.py' where the exception is arose, but couldn't happen to get an idea on what is going on:

1328             if data != "":
1329                 try:
1330                     _eintr_retry_call(os.waitpid, self.pid, 0) 
1331                 except OSError as e:
1332                     if e.errno != errno.ECHILD:
1333                         raise
1334                 child_exception = pickle.loads(data)
1335                 raise child_exception

Any ideas on the cause of the error?

alignment galaxy chip-seq • 479 views

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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by mohammedtleis • 0

18 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The genome was installed but the genome indexes need to be created. How-to is covered in a prior Q&A that includes links to tutorials and other advice. Please see: https://biostar.usegalaxy.org/p/12409/#12468

If you have done something different to create the index (this will result in a simliar error to indexes not being created at all, (eg) different order of indexing, start over with a new database "dbkey". Do not reuse the prior, as this will cause conflicts. Or, you can start over in a new instance.

Cleaning up indexes is a non-trivial process. Possible, but complicated. Even experienced admins often start over when doing this for the majority of cases where duplicates or other content problems are introduced accidentally as the correction methods differ for each case and are time intensive to do on the command-line.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

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