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  • Problems with TopHat v1.4.0

    Dear all I'm trying to use the last version of tophat (v1.4.0) by using the -GTF flag (the reads are mapped before on transcripts). What exactly I'm running is:

    tophat --output-dir=<$Output_dir> --mate-inner-dist=30 --mate-std-dev=20 --min-anchor-length=5 --num-threads=8 --closure-search --keep-tmp --GTF=<$transcriptome_file> --transcriptome-index=<$Out_index> <$Index_File> <$R1_Fast> <$R2_Fast>

    Obviously the $ items are replaced by the real names

    The programs seems to work for more than nine hours but after the point "Searching for junctions via segment mapping" it stopped with the following error:

    Traceback (most recent call last):
    File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 3063, in ?
    sys.exit(main())
    File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 3029, in main
    user_supplied_deletions)
    File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 2681, in spliced_alignment
    [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]],
    TypeError: list indices must be integers


    am I doing something wrong or alternatively it is a program problem?

    Thanks in advance
    luigi
    Luigi Grassi
    Università degli Studi di Roma La Sapienza
    Dipartimento di Fisica
    Piazzale Aldo Moro 5, 00185 Roma

  • #2
    I also met this problem

    I also met this problem. Waiting for senior guys give some suggestion.

    Comment


    • #3
      Originally posted by luigra View Post
      Dear all I'm trying to use the last version of tophat (v1.4.0) by using the -GTF flag (the reads are mapped before on transcripts). What exactly I'm running is:

      tophat --output-dir=<$Output_dir> --mate-inner-dist=30 --mate-std-dev=20 --min-anchor-length=5 --num-threads=8 --closure-search --keep-tmp --GTF=<$transcriptome_file> --transcriptome-index=<$Out_index> <$Index_File> <$R1_Fast> <$R2_Fast>

      Obviously the $ items are replaced by the real names

      The programs seems to work for more than nine hours but after the point "Searching for junctions via segment mapping" it stopped with the following error:

      Traceback (most recent call last):
      File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 3063, in ?
      sys.exit(main())
      File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 3029, in main
      user_supplied_deletions)
      File "/work/ahc/grassi/Shared_Programs/tophat-1.4.0/src/tophat", line 2681, in spliced_alignment
      [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]],
      TypeError: list indices must be integers


      am I doing something wrong or alternatively it is a program problem?

      Thanks in advance
      luigi

      if you do not use "--closure-search", The result is OK!

      Comment

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