bunzip2: I/O or other error, bailing out.  Possible reason follows.
bunzip2: No such file or directory
	Input file = /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/616GYAAXX_5_1_concat_qseq.txt.bz2, output file = /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/616GYAAXX_5_1_concat_qseq.txt

[Wed Jun 16 10:34:20 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Wed Jun 16 10:34:20 2010] Preparing output location /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/
[Wed Jun 16 10:34:20 2010] Checking for Bowtie index files
[Wed Jun 16 10:34:20 2010] Checking for reference FASTA file
[Wed Jun 16 10:34:20 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:34:20 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 10:41:50 2010] Reading known junctions from GFF file
[Wed Jun 16 10:53:49 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 11:02:28 2010] Joining segment hits
	[FAILED]
Error: Segment join failed with err = 1
Traceback (most recent call last):
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1636, in ?
    sys.exit(main())
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1596, in main
    user_supplied_juncs)
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1371, in spliced_alignment
    unspliced_sam)
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1300, in join_mapped_segments
    exit(1)
TypeError: 'str' object is not callable