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Old 08-10-2011, 12:48 PM   #1
M&M
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Location: Michigan

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Default Tophat Fusion error with mRNAseq data

I tried to run TopHat Fusion on canine mRNA-seq data (Illumina paired-end), but received the error below.

Perhaps it is an inappropriate use of the software (giving it RNA data instead of DNA data)?

Any other ideas? Anyone else gotten this error or tried using Tophat Fusion in this way?

[Wed Aug 10 04:40:50 2011] Joining segment hits
Traceback (most recent call last):
File "./tophatfusion-0.1.0-bin/tophat-fusion", line 2610, in ?
sys.exit(main())
File "./tophatfusion-0.1.0-bin/tophat-fusion", line 2566, in main
user_supplied_deletions)
File "./tophatfusion-0.1.0-bin/tophat-fusion", line 2255, in spliced_alignment
right_reads_map = maps[right_reads].unspliced_bwt
AttributeError: 'list' object has no attribute 'unspliced_bwt'
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Old 08-11-2011, 01:16 PM   #2
Jon_Keats
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What version are you using? I've encountered some weird differences between the version I compiled on linux, versus the pre-compiled linux or mac binaries. Basically the only version that works for me top to bottom is the pre-compiled Mac binary. The self compiled linux version failed during the tophat-fusion process, the linux binary works for tophat-fusion but failed for tophat-fusion-post. The mac version seems to work all the way through less a blast error that looks like a memory error that could be due to the small footprint I have on my laptop.
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Old 08-11-2011, 02:02 PM   #3
M&M
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I was using the pre-compiled linux binary. Another member of our group had no problems generating fusion files with human RNA data from the same install. I run the standard flavor of Tophat just fine with my canine files though...
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Old 10-05-2011, 09:27 AM   #4
Carlos Borroto
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Were you able to find a work around for this error? I'm having this error too, even when trying to reproduce the tutorial with the test data. I builded Tophat-Fusion from source on Mac OS X 10.6. This is my whole run:
Code:
$ /usr/local/Cellar/tophatfusion/0.1.0/bin/tophat-fusion -o tophat_MCF7 -p 8 --allow-indels --no-coverage-search -r 0 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 /Volumes/Data/db/ucsc/hg19/bowtie_path/base/hg19 SRR064286_1.fastq SRR064286_2.fastq

[Wed Oct  5 13:12:33 2011] Beginning TopHat run (v0.1.0 (Beta))
-----------------------------------------------
[Wed Oct  5 13:12:33 2011] Preparing output location tophat_MCF7/
[Wed Oct  5 13:12:33 2011] Checking for Bowtie index files
[Wed Oct  5 13:12:33 2011] Checking for reference FASTA file
[Wed Oct  5 13:12:33 2011] Checking for Bowtie
	Bowtie version:			 0.12.7.0
[Wed Oct  5 13:12:33 2011] Checking for Samtools
	Samtools Version: 0.1.17
[Wed Oct  5 13:12:36 2011] Checking reads
	min read length: 50bp, max read length: 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
Traceback (most recent call last):
  File "/usr/local/Cellar/tophatfusion/0.1.0/bin/tophat-fusion", line 2611, in <module>
    sys.exit(main())
  File "/usr/local/Cellar/tophatfusion/0.1.0/bin/tophat-fusion", line 2567, in main
    user_supplied_deletions)
  File "/usr/local/Cellar/tophatfusion/0.1.0/bin/tophat-fusion", line 2252, in spliced_alignment
    left_reads_map = maps[left_reads].unspliced_bwt
AttributeError: 'list' object has no attribute 'unspliced_bwt'

Last edited by Carlos Borroto; 10-05-2011 at 10:28 AM.
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Old 10-05-2011, 10:27 AM   #5
Jon_Keats
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On a mac use the pre-compiled binary, it seems to work well, building from source did not work in my hands either. I'm guessing there are some dependancies that are on the developers box which are required and unique to tophat fusion. In my hand tophat-fusion works on the mac both tophat-fusion and tophat-fusion-post, except I can't get the Blast part of fusion-post to work.
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Old 10-05-2011, 11:09 AM   #6
Carlos Borroto
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Thanks, seems to be working now using the provided binaries.
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Old 01-03-2012, 12:29 PM   #7
tgenahmet
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I'm also running into this issue - but it seems like a different stage:

Quote:
[Fri Dec 30 10:34:32 2011] Reading known junctions from GTF file
Left reads: min. length=101, count=116510405
Right reads: min. length=101, count=116485011
[Fri Dec 30 12:55:51 2011] Mapping right_kept_reads against genome with Bowtie
[Fri Dec 30 14:55:30 2011] Processing bowtie hits
[Fri Dec 30 16:51:16 2011] Mapping right_kept_reads_seg1 against genome with Bowtie (1/4)
[Fri Dec 30 18:28:02 2011] Mapping right_kept_reads_seg2 against genome with Bowtie (2/4)
[Fri Dec 30 20:02:27 2011] Mapping right_kept_reads_seg3 against genome with Bowtie (3/4)
[Fri Dec 30 21:39:32 2011] Mapping right_kept_reads_seg4 against genome with Bowtie (4/4)
Traceback (most recent call last):
File "/home/akurdogl/bin/tophat/tophat", line 2604, in ?
sys.exit(main())
File "/home/akurdogl/bin/tophat/tophat", line 2563, in main
user_supplied_deletions)
File "/home/akurdogl/bin/tophat/tophat", line 2253, in spliced_alignment
left_reads_map = maps[left_reads].unspliced_bwt
AttributeError: 'list' object has no attribute 'unspliced_bwt'
Any ideas?
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Old 05-26-2012, 02:06 AM   #8
dadada4ever
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I have similar errors like this...Anyone can help?
Quote:
[Sat May 26 17:17:07 2012] Beginning TopHat run (v0.1.0 (Beta))
-----------------------------------------------
[Sat May 26 17:17:07 2012] Preparing output location /share/disk2-4/zengchq/gongkn/Glioma/tissue/tophat_fusion/
[Sat May 26 17:17:07 2012] Checking for Bowtie index files
[Sat May 26 17:17:07 2012] Checking for reference FASTA file
Warning: Could not find FASTA file /share/disk2-4/zengchq/gongkn/Glioma/solid_hg19_index/hg19_c.fa
[Sat May 26 17:17:07 2012] Reconstituting reference FASTA file from Bowtie index
Executing: /share/biosoft/bin/bowtie-inspect /share/disk2-4/zengchq/gongkn/Glioma/solid_hg19_index/hg19_c > /share/disk2-4/zengchq/gongkn/Glioma/tissue/tophat_fusion/tmp/hg19_c.fa
[Sat May 26 17:19:38 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Sat May 26 17:19:38 2012] Checking for Samtools
Samtools Version: 0.1.7
[Sat May 26 17:21:01 2012] Checking reads
min read length: 35bp, max read length: 50bp
format: fasta
Traceback (most recent call last):
File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion.py", line 2610, in ?
sys.exit(main())
File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion.py", line 2566, in main
user_supplied_deletions)
File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion.py", line 2251, in spliced_alignment
left_reads_map = maps[left_reads].unspliced_bwt
AttributeError: 'list' object has no attribute 'unspliced_bwt'
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