Hi all
I'm trying to run TopHat for the first time. I've checked the installation with the complementary test data set and that worked. Now with my own data set I get that message right after it tries to create the rat rn4.fa file since it's lacking in the index_folder. I've downloaded and unpacked the files from the bowtie/tophat webpage and I ran the make script. I've asked our IT people but since they are even more unfamiliar then me (which says a lot) with this program I got no help.
So any help would be greatly appreciated! I 've pasted the entire message from TopHat below.
Sincerely
/Petter
[1] 19633
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:30 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:30 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:30 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /data/archive/bowtie-indexes/chr*.*
tophat -r 100 -p 4 --library-type fr-unstranded chr s_1_1_* s_1_2_* &
[2] 19634
[1] Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded chr* s_1_1_* s_1_2_*
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:40 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:40 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:40 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /data/archive/bowtie-indexes/chr.*
tophat -r 100 -p 4 --library-type fr-unstranded rn4 s_1_1_* s_1_2_* &
[3] 19635
[2] Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded chr s_1_1_* s_1_2_*
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:47 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:47 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:47 2010] Checking for Bowtie index files
[Fri Nov 12 19:28:47 2010] Checking for reference FASTA file
Warning: Could not find FASTA file /data/archive/bowtie-indexes/rn4.fa
[Fri Nov 12 19:28:47 2010] Reconstituting reference FASTA file from Bowtie index
[FAILED]
Error: bowtie-inspect returned an error
[3]+ Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded rn4 s_1_1_* s_1_2_*
I'm trying to run TopHat for the first time. I've checked the installation with the complementary test data set and that worked. Now with my own data set I get that message right after it tries to create the rat rn4.fa file since it's lacking in the index_folder. I've downloaded and unpacked the files from the bowtie/tophat webpage and I ran the make script. I've asked our IT people but since they are even more unfamiliar then me (which says a lot) with this program I got no help.
So any help would be greatly appreciated! I 've pasted the entire message from TopHat below.
Sincerely
/Petter
[1] 19633
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:30 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:30 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:30 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /data/archive/bowtie-indexes/chr*.*
tophat -r 100 -p 4 --library-type fr-unstranded chr s_1_1_* s_1_2_* &
[2] 19634
[1] Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded chr* s_1_1_* s_1_2_*
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:40 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:40 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:40 2010] Checking for Bowtie index files
Error: Could not find Bowtie index files /data/archive/bowtie-indexes/chr.*
tophat -r 100 -p 4 --library-type fr-unstranded rn4 s_1_1_* s_1_2_* &
[3] 19635
[2] Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded chr s_1_1_* s_1_2_*
[petter_v@purple BaseCalls]$
[Fri Nov 12 19:28:47 2010] Beginning TopHat run (v1.1.2)
-----------------------------------------------
[Fri Nov 12 19:28:47 2010] Preparing output location ./tophat_out/
[Fri Nov 12 19:28:47 2010] Checking for Bowtie index files
[Fri Nov 12 19:28:47 2010] Checking for reference FASTA file
Warning: Could not find FASTA file /data/archive/bowtie-indexes/rn4.fa
[Fri Nov 12 19:28:47 2010] Reconstituting reference FASTA file from Bowtie index
[FAILED]
Error: bowtie-inspect returned an error
[3]+ Exit 1 tophat -r 100 -p 4 --library-type fr-unstranded rn4 s_1_1_* s_1_2_*
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