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Question: RNA STAR index builder error : unable to open file
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gravatar for chaoyuan
2.6 years ago by
chaoyuan • 80
chaoyuan • 80 wrote:

I just installed data_manager_rnastar_index_builder ( owner sanbi-uwc, revision 70316134a316 ) from the test tool shed. While I was trying to build index for the galGal4 genome, I encountered this error :

EXITING because of INPUT ERROR: could not open genomeFastaFile: /home/chuonglab/galaxy-dev/tool-data/galGal4/seq/galGal4.fa,/home/chuonglab/galaxy-dev/tool-data/galGal4/seq/galGal4.fa

This is the job command line :

python /home/chuonglab/shed_tools/testtoolshed.g2.bx.psu.edu/repos/sanbi-uwc/data_manager_rnastar_index_builder/70316134a316/data_manager_rnastar_index_builder/data_manager/rnastar_index_builder.py "/home/chuonglab/galaxy-dev/database/files/000/dataset_13.dat" --fasta_filename "/home/chuonglab/galaxy-dev/tool-data/galGal4/seq/galGal4.fa,/home/chuonglab/galaxy-dev/tool-data/galGal4/seq/galGal4.fa" --fasta_dbkey "galGal4,galGal4" --fasta_description "galGal4,Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) (galGal4)" --data_table_name "rnastar_index"

It would appear that the wrapper is duplicating commands ?

This is what I have in my Data Manager : all_fasta

Value dbkey name path
galGal4 galGal4 galGal4 /home/chuonglab/galaxy-dev/tool-data/galGal4/seq/galGal4.fa
galGal4 galGal4 Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) (galGal4) /home/chuonglab/galaxy-dev/tool-data/galGal4/seq/galGal4.fa

How can I get around this problem?

rna-seq software error rnastar • 1.0k views
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modified 2.6 years ago • written 2.6 years ago by chaoyuan • 80
1
gravatar for chaoyuan
2.6 years ago by
chaoyuan • 80
chaoyuan • 80 wrote:

So this problem apparently comes from duplicate entries in data table.

I located all_fasta.loc ( at ~/galaxy-dev/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/fb744a070bee/all_fasta.loc ) and saw that there were actually three entries in there. Two are exactly the same. I only kept one and this solve the problem.

ADD COMMENT • link written 2.6 years ago by chaoyuan • 80
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