Error while building reference genome index

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Error while building reference genome index

Laurent Fournier
This post was updated on .
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
www.giga.ulg.ac.be