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fanzhen 02-18-2019 01:03 PM

Tophat error
I am new to RNAseq, I am trying to map my reads to my reference genome. It generates this error
Generating SAM header for /path/ref
Traceback (most recent call last):
File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 4107, in <module>
File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 3961, in main
params.read_params = check_reads_format(params, reads_list)
File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 1856, in check_reads_format
zf = ZReader(f_name, params)
File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 1809, in __init__
IOError: [Errno 2] No such file or directory: ''

Any ideas how to fix this?

GenoMax 02-18-2019 03:57 PM


IOError: [Errno 2] No such file or directory: ''
This is the critical piece. TopHat is not finding some file/directory that you specified in your command. Since you have not included your full command you will need to investigate which it may be.

fanzhen 02-18-2019 04:53 PM

The following is my command.
tophat2 -p 8 -r 300 -N 1 -o tophat_out /path/ref read1 read2
And I have ref.fa and Bowtie built reference in this folder.
The last line in log file is 'Generating SAM header for /path/ref'
[2019-02-18 20:27:51] Beginning TopHat run (v2.1.2)
[2019-02-18 20:27:51] Checking for Bowtie
Bowtie version:
[2019-02-18 20:27:51] Checking for Bowtie index files (genome)..
[2019-02-18 20:27:51] Checking for reference FASTA file
[2019-02-18 20:27:51] Generating SAM header for /path/ref

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