BWA-MEM Index Error - fail to open file

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Hi @incho

In the application, log into your admin account then click on the tab “Admin”.

Under section “Server” are links to the installed data managers and index tables. Start by examining “Local Data”. The data managers will be listed with their associated tables.

Examine those tables – problems you may find are:

  1. Missing content in tables – that can indicate a path problem in your config based on your error. Is the data actually on disk and is the “galaxy user” granted read/write permissions for the exact path reported? /Volumes/Backup/galaxy/database/jobs_directory/000/32/dataset_116_files/hg38.fa
  2. A “dbkey” assigned to more than one row per tool – if you ran a DM twice on the same exact genome (dbkey/database) any duplications can cause problems. Removing duplications is non-trivial but certainly possible. There is no automatic “undo” for data managers.

More help, example usage, and tutorials are in this prior post and may also help to resolve the problem: Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting

Let’s start there :slight_smile: