BWA-MEM Index Error - fail to open file

Hello,

I am pretty new here, and I sincerely apologize if this is a duplicate question. I tried to search for this for two days but did not find a similar topic here.

I recently set up a local Galaxy Serve on my office Mac. I am trying to run a metadata analysis, so I needed to run a large dataset. I installed it on my external hard-drive.

Everything worked fine until I tried to run BWA-MEM index. I got data_manager_fetch_genome_dbkeys_all_fasta and got hg38. After downloading hg38 and checked to see whether hg38 is in my drive, I got data_manager_bwa_mem_index_builder.
When I execute BWA_MEM index, it immediately shows the error message saying

[bwa_idx_build] fail to open file ‘/Volumes/Backup/galaxy/database/jobs_directory/000/32/dataset_116_files/hg38.fa’ : No such file or directory
Error building index.

{“param_dict”: {“index_algorithm”: “bwtsw”, “datatypes_config”: “/Volumes/Backup/galaxy/database/jobs_directory/000/32/registry.xml”, “GALAXY_DATA_INDEX_DIR”: “/Volumes/Backup/galaxy/tool-data”, “userId”: “1”, “userEmail”: “”, “dbkey”: “?”, “get_data_table_entry”: “<function get_data_table_entry at 0x1291cfe60>”, “admin_users”: “”, “all_fasta_source”: “hg38”, “user”: “galaxy.model:SafeStringWrapper(galaxy.model.User:<class ‘galaxy.tools.wrappers.ToolParameterValueWrapper’>,<class ‘galaxy.util.object_wrapper.SafeStringWrapper’>,<class ‘numbers.Number’>,<type ‘NoneType’>,<type ‘NotImplementedType’>,<type ‘bool’>,<type ‘bytearray’>,<type ‘ellipsis’>)”, “input”: “lt__function input at 0x12a86e758__gt”, “app”: “galaxy.app:UniverseApplication”, “user_email”: “”, “sequence_name”: “”, “local_working_directory”: “/Volumes/Backup/galaxy/database/jobs_directory/000/32”, “GALAXY_DATATYPES_CONF_FILE”: “/Volumes/Backup/galaxy/database/jobs_directory/000/32/registry.xml”, “user_name”: “”, “sequence_id”: “”, “tool_directory”: “/Volumes/Backup/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/46066df8813d/data_manager_bwa_mem_index_builder/data_manager”, “new_file_path”: “/Volumes/Backup/galaxy/database/tmp”, “user_id”: “1”, “out_file”: “/Volumes/Backup/galaxy/database/files/000/dataset_116.dat”, “GALAXY_ROOT_DIR”: “/Volumes/Backup/galaxy”, “tool_data_path”: “/Volumes/Backup/galaxy/tool-data”, “root_dir”: “/Volumes/Backup/galaxy”, “chromInfo”: “/Volumes/Backup/galaxy/tool-data/shared/ucsc/chrom/?.len”}, “output_data”: [{“extra_files_path”: “/Volumes/Backup/galaxy/database/jobs_directory/000/32/dataset_116_files”, “ext”: “data_manager_json”, “out_data_name”: “out_file”, “hda_id”: 116, “file_name”: “/Volumes/Backup/galaxy/database/files/000/dataset_116.dat”, “dataset_id”: 116}], “job_config”: {“GALAXY_ROOT_DIR”: “/Volumes/Backup/galaxy”, “TOOL_PROVIDED_JOB_METADATA_FILE”: “galaxy.json”, “GALAXY_DATATYPES_CONF_FILE”: “/Volumes/Backup/galaxy/database/jobs_directory/000/32/registry.xml”}}

I tried to run the older genome fetcher and older BWA-MEM, but I had no luck. I even tried to get hg19, but it did not run also.

What am I doing wrong? Is there a way to fix it?

Thanks,
In