Tophat error 2

[taozuo]

Hi Folks:

I met a problem while aligning RNA-seq data with tophat.

It shows like this:

[Wed Oct 5 17:10:55 2011] Beginning TopHat run (v1.3.2)
-----------------------------------------------
[Wed Oct 5 17:10:55 2011] Preparing output location ./tophat_out/
[Wed Oct 5 17:10:55 2011] Checking for Bowtie index files
[Wed Oct 5 17:10:55 2011] Checking for reference FASTA file
[Wed Oct 5 17:10:55 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Oct 5 17:10:55 2011] Checking for Samtools
Samtools Version: 0.1.18
[Wed Oct 5 17:10:55 2011] Generating SAM header for /mydata/data/personal_data/maize-genome/chr1_seg_index/chr1_seg_index
[Wed Oct 5 17:10:55 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
Left reads: min. length=96, count=18982267
[Wed Oct 5 18:26:16 2011] Mapping left_kept_reads against chr1_seg_index with Bowtie
[Wed Oct 5 18:53:45 2011] Processing bowtie hits
[Wed Oct 5 21:13:26 2011] Mapping left_kept_reads_seg1 against chr1_seg_index with Bowtie (1/4)
[Wed Oct 5 21:46:18 2011] Mapping left_kept_reads_seg2 against chr1_seg_index with Bowtie (2/4)
[Wed Oct 5 22:19:09 2011] Mapping left_kept_reads_seg3 against chr1_seg_index with Bowtie (3/4)
[Wed Oct 5 22:52:10 2011] Mapping left_kept_reads_seg4 against chr1_seg_index with Bowtie (4/4)
[Thu Oct 6 00:06:52 2011] Searching for junctions via segment mapping
[Thu Oct 6 00:14:24 2011] Retrieving sequences for splices
[Thu Oct 6 00:14:28 2011] Indexing splices
[Thu Oct 6 00:14:30 2011] Mapping left_kept_reads_seg1 against segment_juncs with Bowtie (1/4)
[Thu Oct 6 00:25:11 2011] Mapping left_kept_reads_seg2 against segment_juncs with Bowtie (2/4)
[Thu Oct 6 00:35:50 2011] Mapping left_kept_reads_seg3 against segment_juncs with Bowtie (3/4)
[Thu Oct 6 00:46:29 2011] Mapping left_kept_reads_seg4 against segment_juncs with Bowtie (4/4)
[Thu Oct 6 01:02:16 2011] Joining segment hits
[Thu Oct 6 01:06:06 2011] Reporting output tracks
[FAILED]
Error: [Errno 2] No such file or directory
[samopen] SAM header is present: 1 sequences.

Does any one know what happened and how to fix it?

Thanks a lot
Tao

[Artur Jaroszewicz]

Tao,
I am getting the same problem. Have you resolved it yet?
Artur

[taozuo]

Tao,
I am getting the same problem. Have you resolved it yet?
Artur

Hi Artur:

I do not know the exact solution to solve the problem, but when I tried like this, It does work right now.

1. sudo cp .../bowtie bowtie-build bowtie-inspect /usr/bin
2. sudo cp ../samtools /usr/bin
3. test samtools by type:
samtools
sudo samtools
4. chmod your drive like: chmod -R 777 /mydata
5. run tophat on your EBS driver as normal user. You can also try sudo.

Good luck!

[gary]

Hi tao and Artur:
I am having the same problem. Haven't solved it yet.

Could any one give some advise?

Thanks a lot!
gary

[Artur Jaroszewicz]

Hi. I resolved it today. I realized that Tophat was not in my PATH. I'm pretty new to the Unix system, so I thought it was enough to have it in my home directory. Alas, it is not. http://www.go2linux.org/how-to-add-n...the-path-linux
That fixed my problem. Let me know if that works for you. Also, it turns out that the 64-bit Unix version of Tophat does not need to be installed or built; it comes precompiled.

[gary]

Hi. I resolved it today. I realized that Tophat was not in my PATH. I'm pretty new to the Unix system, so I thought it was enough to have it in my home directory. Alas, it is not. http://www.go2linux.org/how-to-add-n...the-path-linux
That fixed my problem. Let me know if that works for you. Also, it turns out that the 64-bit Unix version of Tophat does not need to be installed or built; it comes precompiled.

Thanks Artur! It worked, although I still couldn't understand the error message

[Artur Jaroszewicz]

All it's doing is saying that it can find Samtools but can't use it because it's not in its PATH. Glad it's working!