Error while building reference genome index

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Error while building reference genome index

laurent.fournier
Hi,

As the topic says, i am trying to populate the "built in" list.
Fetching with the tool "Create DBKey and Reference Genome" in the Local datas works just fine but when i try to complete the procedure with "BWA-MEM index" (as well as "SAM FASTA index"), the job stops quickly.

There are some shell outputs :


export PATH=$PATH:'/home/mass/ifilesets/GAL/APP/galaxy/database/dependencies/_conda/envs/__samtools@1.3.1/bin' ; python "/home/mass/ifilesets/GAL/APP/galaxy/database/jobs_directory/000/80/set_metadata_WKziP5.py" "/home/mass/GAL/DATATMP/tmpsX8JCw" "/home/mass/ifilesets/GAL/APP/galaxy/database/jobs_directory/000/80/working/galaxy.json" "/home/mass/ifilesets/GAL/APP/galaxy/database/jobs_directory/000/80/metadata_in_HistoryDatasetAssociation_81_RSHoLb,/home/mass/ifilesets/GAL/APP/galaxy/database/jobs_directory/000/80/metadata_kwds_HistoryDatasetAssociation_81_cGTIQh,/home/mass/ifilesets/GAL/APP/galaxy/database/jobs_directory/000/80/metadata_out_HistoryDatasetAssociation_81_6hf9L8,/home/mass/ifilesets/GAL/APP/galaxy/database/jobs_directory/000/80/metadata_results_HistoryDatasetAssociation_81_0CUrCX,/home/mass/GAL/DATA/032/dataset_32404.dat,/home/mass/ifilesets/GAL/APP/galaxy/database/jobs_directory/000/80/metadata_override_HistoryDatasetAssociation_81_XBr_WZ" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.drmaa DEBUG 2017-08-29 12:06:50,938 (80) submitting file /home/mass/ifilesets/GAL/APP/galaxy/database/jobs_directory/000/80/galaxy_80.sh
galaxy.jobs.runners.drmaa DEBUG 2017-08-29 12:06:50,938 (80) native specification is: -p all_5hrs
galaxy.jobs.runners.drmaa INFO 2017-08-29 12:06:51,045 (80) queued as 2333510
galaxy.jobs DEBUG 2017-08-29 12:06:51,045 (80) Persisting job destination (destination id: slurm_default)
galaxy.jobs.runners.drmaa DEBUG 2017-08-29 12:06:51,238 (80/2333510) state change: job is queued and active
galaxy.jobs.runners.drmaa DEBUG 2017-08-29 12:06:52,247 (80/2333510) state change: job is running
galaxy.jobs.runners.drmaa DEBUG 2017-08-29 12:06:57,373 (80/2333510) state change: job finished normally
galaxy.jobs.output_checker INFO 2017-08-29 12:06:57,416 Job 80: Fatal error: Exit code 1 ()
galaxy.jobs.output_checker DEBUG 2017-08-29 12:06:57,417 Tool exit code indicates an error, failing job.
galaxy.jobs DEBUG 2017-08-29 12:06:57,482 (80) setting dataset 32404 state to ERROR
galaxy.jobs INFO 2017-08-29 12:06:57,578 Collecting metrics for Job 80
galaxy.jobs DEBUG 2017-08-29 12:06:57,584 job 80 ended (finish() executed in (170.899 ms))
galaxy.model.metadata DEBUG 2017-08-29 12:06:57,586 Cleaning up external metadata files


and then, in galaxy's frontend :


Traceback (most recent call last):
  File "/home/mass/ifilesets/GAL/APP/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py", line 87, in <module>
    if __name__ == "__main__": main()
  File "/home/mass/ifilesets/GAL/APP/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py", line 82, in main
    build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
  File "/home/mass/ifilesets/GAL/APP/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py", line 30, in build_sam_index
    assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename
AssertionError: FASTA file "/home/mass/ifilesets/GAL/APP/galaxy/tool-data/mm10/seq/mm10.fa,/home/mass/ifilesets/GAL/APP/galaxy/tool-data/mm10/seq/mm10.fa" is missing, cannot build samtools index.


BUT if i check, the unexisting file is right where it is supposed to :


[f043030@big-cloud19 tmp]$ ls -l /home/mass/ifilesets/GAL/APP/galaxy/tool-data/mm10/seq/
total 2720208
-rw-r--r--. 1 4294967294 4294967294 2785490220 Aug 28 09:47 mm10.fa


Any ideas on what i do wrong ?

Regards,
Laurent Fournier.


---
Laurent FOURNIER
IT Specialist
University of Li├Ęge, GIGA +1
[hidden email]
+32 497 87 96 46
www.giga.ulg.ac.be
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/