galaxyproject / galaxyproject/tools-devteam

bowtie2 index data manager fails if index already exists

Open
#127 1 comment 0 reactions 1 assignee Claimed by @blankenberg View on GitHub
bug
Dominant language
Python
Stars
37
Forks
94
PR merge metrics
No merged PRs in 30d

Description

I believe the issue is caused if the genome index is already built or it handles multiple fasta files during index building.

During multiple fasta file index building, if the _basename of the index files_ is the same it fails. ( i'm guessing this should fail). But if the index already exists on the galaxy instance, it should just tell us that it exists and not build the index again..

_The error below is because of same index being built again, or simultaneously_
#### Error Message:

`Fatal error: Exit code 1 ()
Error: could not open /mnt/transient_nfs/tmp/job_working_directory/000/58/dataset_58_files/ce10.fa
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 /mnt/transient_nfs/tmp/job_working_directory/000/58/dataset_58_files/ce10.fa ce10,ce10,ce10,ce10
Error building index.`
#### Job Command line:

`python /mnt/galaxy/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 "/mnt/galaxy/files/000/dataset_58.dat" --fasta_filename "/mnt/galaxyIndices/ce10/seq/ce10.fa,/mnt/galaxyIndices/ce10/seq/ce10.fa,/mnt/galaxyIndices/ce10/seq/ce10.fa,/mnt/galaxyIndices/ce10/seq/ce10.fa" --fasta_dbkey "ce10,ce10,ce10,ce10" --fasta_description "C. elegans Oct. 2010 (WS220/ce10) (ce10),C. elegans Oct. 2010 (WS220/ce10) (ce10),C. elegans Oct. 2010 (WS220/ce10) (ce10),C. elegans Oct. 2010 (WS220/ce10) (ce10)" --data_table_name "bowtie2_indexes"`

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.