SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat - Error: gtf_to_fasta returned an error. papori Bioinformatics 8 09-03-2014 02:16 PM
TopHat - Error: gtf_to_fasta returned an error. jthomas5062 Bioinformatics 20 08-27-2014 02:36 PM
Tophat Error: Error: segment-based junction search failed with err =-6 sjnewhouse RNA Sequencing 8 03-19-2013 04:14 AM
tophat (or tophat-fusion) v2.0.6 error on: Joining segment hits (long_spanning_reads) AndrewUzilov Bioinformatics 6 01-17-2013 11:25 PM
Tophat 2 error: Parse error at line 297359: missing colon in auxiliary data magbju RNA Sequencing 2 01-15-2013 03:57 AM

Reply
 
Thread Tools
Old 02-18-2019, 01:03 PM   #1
fanzhen
Junior Member
 
Location: USA

Join Date: Feb 2019
Posts: 2
Default 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>
sys.exit(main())
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__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: ''

Any ideas how to fix this?
fanzhen is offline   Reply With Quote
Old 02-18-2019, 03:57 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,881
Default

Quote:
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.
GenoMax is offline   Reply With Quote
Old 02-18-2019, 04:53 PM   #3
fanzhen
Junior Member
 
Location: USA

Join Date: Feb 2019
Posts: 2
Default

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: 2.3.4.3
[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
fanzhen is offline   Reply With Quote
Reply

Tags
tophat

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:40 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO