Shiv198922
commented
6 years ago Bowtie2 mapping showing this error..how to solve this issue.
Fatal error: Exit code 1 () Error, fewer reads in file specified with -2 Error, fewer reads in file specified with -2 than in file specified with -1than in file specified with -1Error, fewer reads in file specified with -2 than in file specified with -1
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"