Tophat Error IOError: [Errno 13] Permission denied

Question

[punjabdhaputar]

Hello, I am trying to align a fastq file with a reference hg19 genome and obtain a BAM file output. To do this I am running topat. When I run tophat however I get an error that I cannot figure out what it represents.

My original command:

tophat \
  /Storage/Ubuntu/Bowtie2/Indexes/hg19 \
  /Storage/Ubuntu/Sample_bigRNA_04_HOK_E6_E7/genome.fastq

Output:

[2014-08-07 00:50:41] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2014-08-07 00:50:41] Checking for Bowtie
          Bowtie version:     2.1.0.0
[2014-08-07 00:50:41] Checking for Samtools
        Samtools version:     0.1.19.0
[2014-08-07 00:50:41] Checking for Bowtie index files (genome)..
[2014-08-07 00:50:41] Checking for reference FASTA file
[2014-08-07 00:50:41] Generating SAM header for /media/pranavubuntu/Storage/Ubuntu/Bowtie2/Indexes/hg19
Traceback (most recent call last):
  File "/usr/bin/tophat", line 4072, in <module>
    sys.exit(main())
  File "/usr/bin/tophat", line 3926, in main
    params.read_params = check_reads_format(params, reads_list)
  File "/usr/bin/tophat", line 1832, in check_reads_format
    freader=FastxReader(zf.file, params.read_params.color, zf.fname)
  File "/usr/bin/tophat", line 1578, in __init__
    self.lastline=self.ifile.readline()
IOError: [Errno 13] Permission denied

I cannot figure out why it gave this error. I would really appreciate any help with this. I have attempted altering the permissions of the tophat file in usr/bin/tophat so that it can be rewritten but that did not change this output.

Thanks!

[Devon Ryan]

If you look in the run log, the last line will be the command that tophat was attempting to execute. If you post that command, it'll probably be apparent what the issue was (I'm guessing that something lacked an executable bit or there was a file lacking write permissions).

[punjabdhaputar]

Here is the run log.

[2014-08-07 00:50:41] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2014-08-07 00:50:41] Checking for Bowtie
          Bowtie version:     2.1.0.0
[2014-08-07 00:50:41] Checking for Samtools
        Samtools version:     0.1.19.0
[2014-08-07 00:50:41] Checking for Bowtie index files (genome)..
[2014-08-07 00:50:41] Checking for reference FASTA file
[2014-08-07 00:50:41] Generating SAM header for /media/pranavubuntu/Storage/Ubuntu/Bowtie2/Indexes/hg19

It doesn't say anything new.

[Devon Ryan]

Wrong log file :)

[punjabdhaputar]

Hi I looked at all the Log files. They were three of them. One was the one I already posted and the another one was empty and the last one had the command I originally inputted. The lines which the code was stuck on are in the original post which stated lines 4072, 3926, 1832, and 1578.

[5heikki]

Does it work if you run it as su?

Answer 1

[Sebastian Kurscheid]

"tophat" is the executable file. Altering its permission will not change the behaviour which caused this error. I would suggest inspecting the permissions of the directory "/media/pranavubuntu/Storage/Ubuntu/Bowtie2/Indexes/" where you store the "hg19" genome reference file, as it seems that the I/O error is caused when trying to write the SAM header.