Question: Bowtie2 index builder error
0
catic.andre • 0 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
Our team is reviewing and will get back to you shortly. Thanks, Jen, Galaxy team