BWA-MEM corrupted indexes

[jennaj]

These seem to be CVMFS

Identified so far

• dm3
• testing history using the hic workflow in this tutorial. This is the Ghelp topic

  Traceback (most recent call last):
  File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/ebb02ba5987c/bwa_mem/bwa_mem.py", line 234, in __main__
  raise Exception( 'Error generating alignments. ' + str( e ) )
  Exception: Error generating alignments. can only concatenate str (not "bytes") to str

Human

• hg38female
• hg19canon
• testing history and ghelp topic

          [E::bwa_idx_load_from_disk] fail to locate the index files
  [W::hts_set_opt] Cannot change block size for this format
  samtools sort: failed to read header from "-"

Related to this? https://help.galaxyproject.org/t/genomes-are-missing-from-the-dbdey-table-while-present-in-bowtie2/11972/4?u=jennaj

[nsoranzo]

@jennaj For the dm3 one, you've used an ancient and deprecated version of the bwa_mem wrapper (owner crs4), so that first Python exception should go away if you use a newer version from devteam.

[jennaj]

Oh, that was from a user. I'll figure it out, thanks for the clue @nsoranzo I totally missed the version part! Opps

Turns out this was a GTN tutorial issue! We'll get this fixed at the source.