[2017-06-27 16:03:45] Beginning TopHat run (v2.1.1)
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[2017-06-27 16:03:45] Checking for Bowtie
		  Bowtie version:	 2.2.8.0
[2017-06-27 16:03:45] Checking for Bowtie index files (genome)..
[2017-06-27 16:03:45] Checking for reference FASTA file
	Warning: Could not find FASTA file /data/images/proton2/run342/inserts/inserted-sequences-run342.fa
[2017-06-27 16:03:45] Reconstituting reference FASTA file from Bowtie index
  Executing: /data/results/tools/align/bowtie2-2.2.8/bowtie2-inspect /data/images/proton2/run342/inserts/inserted-sequences-run342 > tophatCheckIns_034/tmp/inserted-sequences-run342.fa
[2017-06-27 16:03:45] Generating SAM header for /data/images/proton2/run342/inserts/inserted-sequences-run342
[2017-06-27 16:03:45] Preparing reads
	 left reads: min. length=25, max. length=349, 1995498 kept reads (3 discarded)
[2017-06-27 16:04:28] Mapping left_kept_reads to genome inserted-sequences-run342 with Bowtie2 
Traceback (most recent call last):
  File "/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat", line 4107, in <module>
    sys.exit(main())
  File "/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat", line 4073, in main
    user_supplied_deletions)
  File "/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat", line 3564, in spliced_alignment
    segment_len)
  File "/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat", line 3000, in split_reads
    split_record(read_name, read_seq, read_quals, out_segfiles, offsets, params.read_params.color)
  File "/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat", line 2955, in split_record
    print >> f, "+"
KeyboardInterrupt