Error in using repeat mask genome for tophat2

Question

[Whoknows]

Hi

I used Aegilops repeat mask genome for Tophat2 genome option, but it showed this error:

[2015-01-20 16:07:17] Checking for Bowtie
          Bowtie version:     2.1.0.0
[2015-01-20 16:07:17] Checking for Samtools
        Samtools version:     0.1.19.0
[2015-01-20 16:07:17] Checking for Bowtie index files (genome)..
[2015-01-20 16:07:17] Checking for reference FASTA file
[2015-01-20 16:07:17] Generating SAM header for AT_rm
`Traceback (most recent call last):
  File "/usr/local/bin/tophat", line 4072, in <module>
    sys.exit(main())
  File "/usr/local/bin/tophat", line 3926, in main
    params.read_params = check_reads_format(params, reads_list)
  File "/usr/local/bin/tophat", line 1829, in check_reads_format
    zf = ZReader(f_name, params)
  File "/usr/local/bin/tophat", line 1782, in __init__
    self.file=open(filename)

How can I fix this error?

Thanks a lot.

[Devon Ryan]

You'll have to look in the run log for the last command issued and run that manually. You'll then be able to see the entirety of the actual error message (debugging is usually pretty obvious then).

[Manvendra Singh]

May I see your tophat command?

[Whoknows]

tophat2 -r 200 -p 8 -G AT.gtf AT_genome  -- read-mismatches 2 -o Tophat A1.fq A2.fq

[Devon Ryan]

You seem to have an extra space between -- and read-mismatches. Also, the ordering isn't exactly correct (tophat is not that forgiving). Try instead:

tophat2 -r 200 -p 8 -G AT.gtf --read-mismatches 2 -o Tophat AT_genome A1.fq A2.fq

Answer 1

[Whoknows]

I found the problem!! Actually it conflicted with output path -o, after using second output type it worked perfectly.

TNX