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Tophat Error: No unambiguous stretches of characters in the input(?).

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  • Tophat Error: No unambiguous stretches of characters in the input(?).

    I suspect this could be due to errors in the GFF file, has any one seen it before? I am aligning 27 bp reads and I know that bowtie-build is in my path. I downloaded GTF file from UCSC and then converted it to GFF using the perl script on this forum. Any help will be REALLY appreciated.


    /data/Mikkelson/SRX001940$ tophat -G /data/mouse2007_GFF_UCSC.txt /progs/tophat/mm9 SRR006806.fastq

    [Fri Mar 5 12:27:37 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Fri Mar 5 12:27:37 2010] Preparing output location ./tophat_out/
    [Fri Mar 5 12:27:37 2010] Checking for Bowtie index files
    [Fri Mar 5 12:27:37 2010] Checking for reference FASTA file
    [Fri Mar 5 12:27:37 2010] Checking for Bowtie
    Bowtie version: 0.12.2.0
    [Fri Mar 5 12:27:37 2010] Checking reads
    seed length: 27bp
    format: fastq
    quality scale: phred33 (default)
    [Fri Mar 5 12:29:37 2010] Reading known junctions from GFF file
    [Fri Mar 5 12:31:25 2010] Mapping reads against mm9 with Bowtie

    [Fri Mar 5 13:49:42 2010] Joining segment hits
    [Fri Mar 5 13:52:08 2010] Searching for junctions via segment mapping
    [Fri Mar 5 13:53:39 2010] Retrieving sequences for splices
    [Fri Mar 5 13:53:40 2010] Indexing splices
    Warning: Empty input file
    Error: No unambiguous stretches of characters in the input. Aborting...
    Command: bowtie-build ./tophat_out/tmp/segment_juncs.fa ./tophat_out/tmp/segment_juncs
    [FAILED]

    Error: Splice sequence indexing failed with err = 1
    Traceback (most recent call last):
    File "/usr/bin/tophat", line 1635, in ?
    sys.exit(main())
    File "/usr/bin/tophat", line 1595, in main
    user_supplied_juncs)
    File "/usr/bin/tophat", line 1456, in spliced_alignment
    ref_fasta)
    File "/usr/bin/tophat", line 981, in build_juncs_index
    external_splices_out_prefix = build_juncs_bwt_index(external_splices_out_prefix)
    File "/usr/bin/tophat", line 939, in build_juncs_bwt_index
    exit(1)
    TypeError: 'str' object is not callable
    Last edited by thinkRNA; 03-05-2010, 04:01 PM.

  • #2
    Error: No unambiguous stretches of characters in the input. Aborting...

    I have this same error. Can anyone please tell me why this is happening.


    [Tue Sep 20 15:26:25 2011] Reading known junctions from GTF file
    [Tue Sep 20 15:27:39 2011] Mapping reads against zv9 with Bowtie
    [Tue Sep 20 16:47:01 2011] Joining segment hits
    [Tue Sep 20 16:53:45 2011] Mapping reads against zv9 with Bowtie(1/4)
    [Tue Sep 20 17:40:17 2011] Mapping reads against zv9 with Bowtie(2/4)
    [Tue Sep 20 18:25:21 2011] Mapping reads against zv9 with Bowtie(3/4)
    [Tue Sep 20 19:12:59 2011] Mapping reads against zv9 with Bowtie(4/4)
    [Tue Sep 20 20:55:40 2011] Searching for junctions via segment mapping
    [Tue Sep 20 20:57:48 2011] Retrieving sequences for splices
    [Tue Sep 20 21:01:18 2011] Indexing splices
    Warning: Empty input file
    Error: No unambiguous stretches of characters in the input. Aborting...
    Command: bowtie-build tophat_BC4_gtf_mix1/tmp/segment_juncs.fa tophat_BC4_gtf_mi
    x1/tmp/segment_juncs
    [FAILED]
    Error: Splice sequence indexing failed with err = 1


    Thanks

    Comment


    • #3
      Me three

      Has anyone figured out what causes this error?

      Thanks,
      Suzi

      Comment

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