Question: Tool error "IOError: [Errno 2] No such file or directory"
gravatar for tran_tim
2.2 years ago by
tran_tim10 wrote:

I receive the following error while running tophat: Traceback (most recent call last): File "/galaxy-repl/main/jobdir/013/902/13902630/", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/cvmfs/", line 85, in set_metadata datatypes_registry.load_datatypes( root_dir=galaxy_root, config=datatypes_config ) File "/cvmfs/", line 97, in load_datatypes tree = galaxy.util.parse_xml( config ) File "/cvmfs/", line 209, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/cvmfs/", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/galaxy/main/scratch/tmp1ilzMo'

Please help. I already try to rerun it now. I use tophat and my input file is a large fastq files >12 G, and a reference genome hg19

error tool tophat job • 1.5k views
ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson25k • written 2.2 years ago by tran_tim10

Hello, This is a cluster error that a few users have reported. Our administrator is looking into the reason why. Re-running is the best solution I can offer right now, but we'll have more feedback once this is fully resolved. Thanks for posting the question in a new thread! Jen, Galaxy team

ADD REPLYlink written 2.2 years ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The confirmed solution is to re-run jobs that report an error ending with "IOError: [Errno 2] No such file or directory". This was related to some cluster issues from yesterday that were resolved a few hours ago this morning at

Thanks for reporting the problem and our apologies for the confusion, Jen, Galaxy team

ADD COMMENTlink written 2.2 years ago by Jennifer Hillman Jackson25k
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