Question: Error in building a BWA index
gravatar for jchen015
3.8 years ago by
jchen01580 wrote:

Hi guys

Another problem I am facing from using Data Manager is the building of index for BWA.

So once again, i followed daniel's video tutorial on the usage of DataManager at :

I successfully fetched the reference genome for sacCer2 and when I tried to build the Index for BWA (as shown in "reference_genome_sacCer2_3.png"), after execution, the error displayed (shown in "reference_genome_sacCer2_4.png").


Photo links:


May I know what is the problem over here?? I followed the steps throughout for the video and I did not missed any steps. Will there be any prior activities that I have to perform before coming into this phase?







bwa index data_manager • 1.1k views
ADD COMMENTlink modified 3.8 years ago by Daniel Blankenberg ♦♦ 1.7k • written 3.8 years ago by jchen01580
gravatar for Daniel Blankenberg
3.8 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Julius,


It looks like you are installing from the Test ToolShed (which is probably what happend in the video). Would you mind trying with the Data Managers in the Main ToolShed and see if you get the same error?



Also, if you could click the Bug button which will bring up a page with the whole stderr traceback and provide that, it would be helpful as well.

ADD COMMENTlink written 3.8 years ago by Daniel Blankenberg ♦♦ 1.7k

Hey Daniel !

Great to see you here.

I performed it on the main toolshed with the new tools, but the error still occurs.

Error output:


Traceback (most recent call last):
  File "/home/user/shed_tools/", line 102, in <module>
    if __name__ == "__main__": main()
  File "/home/user/shed_tools/", line 97, in main
    build_bwa_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME, color_space=options.color_space )
  File "/home/user/shed_tools/", line 38, in build_bwa_index
    if os.stat( fasta_filename ).st_size <= ONE_GB: #use 1 GB as cut off for memory vs. max of 2gb database size; this is somewhat arbitrary
OSError: [Errno 2] No such file or directory: '/home/user/galaxy-dist/tool-data/sacCer2/seq/sacCer2.fa,/home/user/galaxy-dist/tool-data/sacCer2/seq/sacCer2.fa,/home/user/galaxy-dist/tool-data/sacCer2/seq/sacCer2.fa'"


Do you know what's the issue?




ADD REPLYlink written 3.8 years ago by jchen01580

Ah, yes. You have Three entries in your all_fasta table for sacCer2. You'll want to remove all except for one of them (easiest to just delete the lines from the .loc files), although we should also prevent this issue from occuring.

ADD REPLYlink written 3.8 years ago by Daniel Blankenberg ♦♦ 1.7k

Hey Daniel

under the directory : /home/user/galaxy-dist/tool-data/

There are 2 files namely all_fasta.loc and bwa_index.loc (screenshot:


But the content of both doesnt seem to have the 3 entries.. am I at the wrong place?

ADD REPLYlink written 3.8 years ago by jchen01580

Hi Daniel

Do you happen to know what's the issue over here?



ADD REPLYlink written 3.7 years ago by jchen01580
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