Tophat2 running test_data Errno 8 failed to Index splices

[MadGenome]

Hello,
I am running into problems when trying to get Tophat2 set up following this tutorial: https://ccb.jhu.edu/software/tophat/tutorial.shtml
I have Bowtie2, Bowtie2-build, and bowtie2-insect in my path as well as the directory to my tophat2 file.
When I run the command [tophat2 -r 20 test_ref reads_1.fq reads_2.fq]
I get the following message:
[2019-06-04 09:43:21] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-06-04 09:43:21] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 1.1.2.0
[2019-06-04 09:43:21] Checking for Bowtie index files (genome)..
Found both Bowtie1 and Bowtie2 indexes.
[2019-06-04 09:43:21] Checking for reference FASTA file
[2019-06-04 09:43:21] Generating SAM header for test_ref
[2019-06-04 09:43:21] Preparing reads
left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
[2019-06-04 09:43:21] Mapping left_kept_reads to genome test_ref with Bowtie
[2019-06-04 09:43:21] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2019-06-04 09:43:21] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2019-06-04 09:43:21] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2019-06-04 09:43:21] Mapping right_kept_reads to genome test_ref with Bowtie
[2019-06-04 09:43:21] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2019-06-04 09:43:22] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2019-06-04 09:43:22] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2019-06-04 09:43:22] Searching for junctions via segment mapping
[2019-06-04 09:43:22] Retrieving sequences for splices
[2019-06-04 09:43:22] Indexing splices
[FAILED]
[Errno 8] Exec format error

I have seen that others have discovered they have installed the wrong type however I have check and I have installed bowtie2-2.3.3.1-linux-x86_64 and tophat-2.1.1.Linux_x86_64 on my windows system working on a 64 bit PuTTY system.
Sorry for the drawn out question, I'm fairly new to this and wanted to provide as much info as I could.
Thanks in advance for anyone who could help