Question: Bowtie indexing error (local Galaxy)
21 months ago by
vebaev • 130
vebaev • 130 wrote:
I'm trying to index human genome 38 (fasta downloaded from GENCODE) but after hours working bowtie indexing gives error:
Traceback (most recent call last): File "/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 611, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/galaxy-central/lib/galaxy/jobs/__init__.py", line 1397, in finish self.tool.exec_after_process( self.queue.app, inp_data, out_data, param_dict, job=job ) File "/galaxy-central/lib/galaxy/tools/__init__.py", line 2201, in exec_after_process assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % ( data_manager_id ) AssertionError: Invalid data manager (bowtie_index_builder_data_manager) requested. It may have been removed before the job completed.
Tool execution generated the following error message:
Unable to finish job
I have indexed tomato genome (which was smaller) but with no problem?
Very strange I tried to index the arabidopsis genome and it gives the same error?!
Was the tomato genome indexed on this same server, same config?
Or have changes been made since then? If so, when you check the status of the installed tool (admin panel), is the tool installed correctly still?
Have other genomes worked with the current config? (If there were changes and item 1 is a no)
Thanks for the extra info. Jen, Galaxy team