TopHat error when attempting to execute bowtie2-align: Could not locate a Bowtie index corresponding to basename

[Eric Jaehnig]

When I try to run TopHat (v2.0.10), I receive an error message stating that the Bowtie index specified by the basename I used to build the Bowtie2 library with could not be located (the text below shows my input in the command line in bold and the text outputted to my terminal after executing the command; see first example).  However, I did use bowtie2-build to construct this library, and the bowtie2 command itself recognizes the basename properly (see the third example below) while the bowtie2-align command has the same issue that TopHat did (see the second example below).  It looks like there may be an issue with Bowtie2 since I have this problem when I try to execute bowtie2-align.  However, I just noticed the message on the TopHat website stating that the latest version of Bowtie2 is not compatible with the latest version of TopHat 2.  Is this the problem, or is there something else awry with my Bowtie2 installation that is specifically causing problems with bowtie2-align?
 
tophat ~ejaehnig/bowtie_libraries/yeastORFs/orf_genomic_all/orf_genomic_all ~ejaehnig/RNAseq/wt_test/lane1/parsed/lane1_Undetermined_L001_R1_001_D701.fastq

[2014-02-26 14:45:06] Beginning TopHat run (v2.0.10)
-----------------------------------------------
[2014-02-26 14:45:06] Checking for Bowtie
                  Bowtie version:        2.2.0.0
[2014-02-26 14:45:06] Checking for Samtools
                Samtools version:        0.1.19.0
[2014-02-26 14:45:06] Checking for Bowtie index files (genome)..
[2014-02-26 14:45:06] Checking for reference FASTA file
[2014-02-26 14:45:06] Generating SAM header for /Volumes/dataraid/users/Eric/bowtie_libraries/yeastORFs/orf_genomic_all/orf_genomic_all
[2014-02-26 14:45:06] Preparing reads
         left reads: min. length=36, max. length=36, 9388864 kept reads (21326 discarded)
Warning: you have only one segment per read.
        If the read length is greater than or equal to 45bp,
        we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2014-02-26 14:46:47] Mapping left_kept_reads to genome orf_genomic_all with Bowtie2
        [FAILED]
Error running bowtie:
Could not locate a Bowtie index corresponding to basename "/Volumes/dataraid/users/Eric/bowtie_libraries/yeastORFs/orf_genomic_all/orf_genomic_all"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/local/bin/bowtie2-align -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 1 --sam-no-hd -x /Volumes/dataraid/users/Eric/bowtie_libraries/yeastORFs/orf_genomic_all/orf_genomic_all -

bowtie2-align -x ~ejaehnig/bowtie_libraries/yeastORFs/orf_genomic_all/orf_genomic_all -U lane1_Undetermined_L001_R1_001_D701.fastq -S output.txt

Warning: Could not open read file "lane1_Undetermined_L001_R1_001_D701.fastq" for reading; skipping...
Error: No input read files were valid

bowtie2 -x ~ejaehnig/bowtie_libraries/yeastORFs/orf_genomic_all/orf_genomic_all -U lane1_Undetermined_L001_R1_001_D701.fastq -S bowtie_out.txt

9410190 reads; of these:
  9410190 (100.00%) were unpaired; of these:
    4641168 (49.32%) aligned 0 times
    3544648 (37.67%) aligned exactly 1 time
    1224374 (13.01%) aligned >1 times
50.68% overall alignment rate

[Rick Westerman]

Hard to say but the simple test is to, of course, go back to the older version of bowtie2.  I'd be willing to bet (a little bit) that is the problem.  At the very least since the tophat site says "problems with 2.2.0 then not using it is a good idea.

[Eric Jaehnig]

Yes, we're planning to install an earlier version of Bowtie2 next week, but we had already installed the latest version before the message was posted on the TopHat website, so I thought I might try to see if anyone had a better idea of what's going on in the meantime.