Question: Bowtie indexing error (local Galaxy)
gravatar for vebaev
12 months ago by
vebaev130 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/", line 611, in finish_job
    job_state.job_wrapper.finish( stdout, stderr, exit_code )
  File "/galaxy-central/lib/galaxy/jobs/", line 1397, in finish
    self.tool.exec_after_process(, inp_data, out_data, param_dict, job=job )
  File "/galaxy-central/lib/galaxy/tools/", 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?

bowtie index • 334 views
ADD COMMENTlink written 12 months ago by vebaev130

Very strange I tried to index the arabidopsis genome and it gives the same error?!

ADD REPLYlink written 12 months ago by vebaev130
  1. Was the tomato genome indexed on this same server, same config?

  2. 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?

  3. 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

ADD REPLYlink modified 12 months ago • written 12 months ago by Jennifer Hillman Jackson24k
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