bunzip2: I/O or other error, bailing out.  Possible reason follows.
bunzip2: Stale NFS file handle
	Input file = /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_1_concat_qseq.txt.bz2, output file = /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_1_concat_qseq.txt
bunzip2: Deleting output file /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_1_concat_qseq.txt, if it exists.

bunzip2: I/O or other error, bailing out.  Possible reason follows.
bunzip2: Stale NFS file handle
	Input file = /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_2_concat_qseq.txt.bz2, output file = /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_2_concat_qseq.txt
bunzip2: Deleting output file /projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_2_concat_qseq.txt, if it exists.
Traceback (most recent call last):
  File "/home/rcorbett/slx_service_rc/trunk/run_tophat.py", line 464, in ?
    main()
  File "/home/rcorbett/slx_service_rc/trunk/run_tophat.py", line 97, in main
    fq1, fq2, s1, s2 = make_fastq_qseq(lane, outDir, f)
  File "/home/rcorbett/slx_service_rc/trunk/run_tophat.py", line 156, in make_fastq_qseq
    createFastq(False, 0, 1, s1, outDir)
  File "/home/rcorbett/slx_service_rc/trunk/qseq2fastq.py", line 154, in createFastq
    fh_in = open(qseqpath, 'r')
IOError: [Errno 2] No such file or directory: '/projects/NBL/HS1803/616GYAAXX_6/tophat_wj/616GYAAXX_6_1_concat_qseq.txt'