tophat-fusion error

[ptong7]

Hi guys,

is anybody use tophat-fusion?
I use 'tophatfusion-0.1.0-OSX_x86_64' ran my RNA-seq data get some error like:

Traceback (most recent call last):
File "/Users/ptong/Downloads/tophatfusion-0.1.0-OSX_x86_64/tophat-fusion", line 2611, in <module>
sys.exit(main())
File "/Users/ptong/Downloads/tophatfusion-0.1.0-OSX_x86_64/tophat-fusion", line 2567, in main
user_supplied_deletions)
File "/Users/ptong/Downloads/tophatfusion-0.1.0-OSX_x86_64/tophat-fusion", line 2252, in spliced_alignment
left_reads_map = maps[left_reads].unspliced_bwt
AttributeError: 'list' object has no attribute 'unspliced_bwt'

The command I used is :

'tophat-fusion -o output --segment-length 20 --solexa1.3-quals Myco s_2_sequence.fastq'

is anybody know how to fix it?

Thanks a million.

[Jon_Keats]

I've tried it with both the Mac and Linux binaries. Tophat-fusion worked with both, tophat-fusion-post was another issue (see related thread). Couple of things are you dealing with single end reads? I'm not perfectly sure that is supported. How many reads are you aligning? The only time I saw this error was in a test data set with a limited number of reads. Test the install with the test data you can download

[SCPHSD]

I also use tophatfusion, but when I run tophat-fusion-post, sometimes it will have the following problem, is there anybody know how to fix it?

Traceback (most recent call last):
File "/usr/local/bin/tophat-fusion-post", line 1904, in <module>
sys.exit(main())
File "/usr/local/bin/tophat-fusion-post", line 1884, in main
generate_html(params)
File "/usr/local/bin/tophat-fusion-post", line 1785, in generate_html
cluster_fusion(fusion_list, cluster_list)
File "/usr/local/bin/tophat-fusion-post", line 1585, in cluster_fusion
cluster_temp_list[i]["index"] = sorted(cluster_temp_list[i]["index"], cmp=cmp)
File "/usr/local/bin/tophat-fusion-post", line 1583, in cmp
return int(fusion_list[b]["score"] - fusion_list[a]["score"])
KeyError: 'score'

[tyxer]

I got the same error as SCPHSD too.
Anyone has any ideas about this?

Thank you so much

[NKAkers]

I just encountered the same problem as tyxer and SCPHSD. Changing the options of my run fixed it. Try running the command given in the getting started guide, and adjusting from there.

tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /path/to/h_sapiens/bowtie_index

[Emilie]

Hi,
I also had the same problem with one of sample I was analyzing, using TopHat v2.0.3 and 2.0.4. I realized, by looking at the tophat-fusion-post code, that the problem seems to happen specifically when only one fusion cluster is detected (in my case, one cluster with 4 putative fusions). It seems that the sorted() cmp function, which includes a calculation of score, needs more than one cluster in the list to work correctly.
I modified the line 1708, in tophat-fusion-post v2.0.3:

cluster_temp_list[i]["index"] = sorted(cluster_temp_list[i]["index"], cmp=cmp)

by:

if len(cluster_temp_list) > 1:
cluster_temp_list[i]["index"] = sorted(cluster_temp_list[i]["index"], cmp=cmp)
# cluster_temp_list[i]["index"] = sorted(cluster_temp_list[i]["index"], cmp=cmp)

Now it's skipping the score calculation when only one cluster of fusions is determined in a sample, but at least it gives a result! However, the code of tophat-fusion-post v2.0.4 is slightly different, and this modification isn't sufficient (a new error appears).
Tyxer, SCPHSD, does this modification work for you?
I sent an email to the developers, I hope the future version of tophat-fusion-post will be corrected !
Regards,

Emilie

[tyxer]

Hi, Emilie:

It is good to know this bug. However, it is not the reason of my problem.
For my problem, the reason is stupid that I did not name the folders correctly.

Bests

Yuxiang

[bharati]

TopHat-fusion-post error

I am not getting any error while running tophat-fusion-post after running TopHat-fusion with tophat2.0.0 and bowtei1 index, but it generates Tophatfusion_out folder which reports 0 filtered fusions and contains 0kb file.

I am unable to figure it out, can anybody pls help, its urgent.

[NKAkers]

Hi Bharati,

Your tophatfusion_out folder has just one empty file? no logs? If there is a sample_list.txt file, check that to make sure tophat-fusion-post is recognizing your samples. Otherwise try to give us a little more info to go from. What standard output do you get when you run tophat-fusion-post? How long does it take to finish?

[bharati]

Hi NKAkers,
sorry for my late reply.
I only gave a single sample to filter false positives and it took less then a minute to complete and showed 0 filtered fusions.