Tophat Error Unable to find file in temporary folder that is clearly there

Question

[baunruh]

So I am running an older version of tophat in order to validate some work that was done, unfortunately I am receiving an error that I cannot figure out. Most of the errors similar to this one online were an issue with RAM and running on a cluster. I am running on a cluster but I have determined it is not a RAM problem or a problem with the underlying cluster (I ran it on several different clusters that I have access to and received the same error). It appears that there is a problem calling back to the temporary file, but the file is clearly present in the temporary file!!

Code Ran:

tophat --library-type fr-secondstrand --color --quals -p 4 -G TandemUTR.gtf -o TandemUTR_GTF_out mm9 TandemUTR.csfasta TandemUTR.qual

Using Versions:
SAMtools/0.1.19-foss-2016a
bowtie0.12.7
tophat1.3.3

Error Message Below

[Mon Feb 12 16:49:13 2018] Beginning TopHat run (v1.3.3)
-----------------------------------------------
[Mon Feb 12 16:49:13 2018] Preparing output location /home/baunruh/ALEwork/Vollmer/CT0_Vollmer_gtf/
[Mon Feb 12 16:49:13 2018] Checking for Bowtie index files
[Mon Feb 12 16:49:13 2018] Checking for reference FASTA file
[Mon Feb 12 16:49:13 2018] Checking for Bowtie
    Bowtie version:          0.12.7.0
[Mon Feb 12 16:49:13 2018] Checking for Samtools
    Samtools Version: 0.1.19
[Mon Feb 12 16:49:13 2018] Generating SAM header for /home/baunruh/ALEwork/ZhangKerry/mm9/mm9
[Mon Feb 12 16:49:13 2018] Preparing reads
    format:      fasta
[Mon Feb 12 16:49:13 2018] Reading known junctions from GTF file
    Left  reads: min. length=50, count=32461692
[Mon Feb 12 16:56:37 2018] Mapping left_kept_reads against mm9 with Bowtie 

gzip: stdout: Broken pipe
[Mon Feb 12 16:56:37 2018] Processing bowtie hits
Traceback (most recent call last):
  File "/home/baunruh/tophat1.3.3/tophat", line 2604, in <module>
    sys.exit(main())
  File "/home/baunruh/tophat1.3.3/tophat", line 2563, in main
    user_supplied_deletions)
  File "/home/baunruh/tophat1.3.3/tophat", line 2218, in spliced_alignment
    segment_len)
  File "/home/baunruh/tophat1.3.3/tophat", line 1820, in split_reads
    zreads = ZReader(reads_filename, params.system_params, False)
  File "/home/baunruh/tophat1.3.3/tophat", line 1190, in __init__
    self.file=open(filename)
IOError: [Errno 2] No such file or directory: '/home/baunruh/ALEwork/Vollmer/CT0_Vollmer_gtf/tmp/left_kept_reads_missing.fq'

[Devon Ryan]

There's no reason to use tophat anymore. Please switch to a more recent and supported aligner, such as STAR, hisat2, or BBMap.

[baunruh]

I know, its I am trying to repeat some steps to make sure we don't have errors.