Tophat errors

[alig]

Hi,

I have just run Tophat for the first time and get the following errors.

It still gives me some output files, but I would like to be sure that it did run properly before continuing with the analysis.

[Mon Aug 10 17:43:05 2009] Indexing splices
Warning: Encountered reference sequence with only gaps

Warning: Encountered reference sequence with only gaps
[Mon Aug 10 17:43:27 2009] Mapping reads against segment_juncs with Bowtie
[Mon Aug 10 17:56:42 2009] Mapping reads against segment_juncs with Bowtie
[Mon Aug 10 18:10:02 2009] Joining segment hits
[Mon Aug 10 18:14:24 2009] Mapping reads against HumanRefSeq with Bowtie
[Mon Aug 10 18:31:04 2009] Joining segment hits
*** buffer overflow detected ***: /home/neuro/Documents/Ali/tophat-1.0.10/bin/long_spanning_reads terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x37)[0x7f15666d8887]
/lib/libc.so.6[0x7f15666d6750]

These are the 2 error messages I am concerned with.

Thanks for any help

alig

[Cole Trapnell]

This is a failed run, and I'll need to look at what happened more closely. Can you send me your logs?

Are you able to reproduce this with a relatively small data set that you can put somewhere for me to download?

[lindylou]

Hi,
I've been trying to use tophat 1.0.10. However when I try to use the accepted_hits.sam output to view the pileups with samtools I get the following error:-

samtools pileup -f ebwt_human.fa -S accepted_hits.sam
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

Looking at the output file there appears to be no header lines at the beginning of the file and therefore I can't use it for any downstream analysis as samtools doesn't see it as valid sam output, is anyone else having similar problems? any solutions would be welcome!

[Cole Trapnell]

TopHat doesn't currently use the SAM header, but I'm planning on adding headers in the next version of the program. In the very short term, it's relatively straightforward to prepend the sequence dictionary portion of the header to TopHat's output after the fact.