Question: Bowtie2 index builder error
0
gravatar for catic.andre
3.3 years ago by
United States
catic.andre0 wrote:

Hello,

I am running Galaxy on Ubuntu 14.04. I recently downloaded hg19.fa from UCSC using the data manager with fetch_genome_all_fasta (see https://vimeo.com/74265510).

I also installed data_manager_bowtie2_index_builder, bowtie2, package_bowtie_2_2_4, and package_samtools_0_1_18. All show green installation status. I updated the all_fasta.loc file in [/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b] to reference hg19.fa.

When I run the bowtie2 index builder, I am getting the following error:

 Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/home/catic/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder.py", line 76, in <module>
    if __name__ == "__main__": main()
  File "/home/catic/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder.py", line 71, in main
    build_bowtie2_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 )
  File "/home/catic/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/9458af1ab90b/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder.py", line 33, in build_bowtie2_index
    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

 

What am I missing?
Many thanks!

Andre

 

 

 

software error galaxy • 1.2k views
ADD COMMENTlink written 3.3 years ago by catic.andre0

Our team is reviewing and will get back to you shortly. Thanks, Jen, Galaxy team

ADD REPLYlink written 3.3 years ago by Jennifer Hillman Jackson25k
0
gravatar for catic.andre
3.3 years ago by
United States
catic.andre0 wrote:

I figured it out: I had changed the all_fasta.loc file of the index builder to reflect the location of the hg19.fa file. Instead, just leave the file unchanged (with no location specified) and pick the right .fa file in the galaxy menu.

Thanks!

ADD COMMENTlink written 3.3 years ago by catic.andre0

Glad all is sorted out! Thanks for letting us know. Jen

ADD REPLYlink written 3.3 years ago by Jennifer Hillman Jackson25k
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