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Old 04-02-2013, 07:32 AM   #1
angerusso
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Location: US

Join Date: Oct 2011
Posts: 47
Default tophat-fusion-post: KeyError: 'score'

Hello, I am tophat-fusion-post. My job ran fine until the very end where I get the error ("Score") as below.

I get 6898 fusions in potential_fusion.txt with the command:

> tophat-fusion-post -p $np --num-fusion-reads 1 --num-fusion-pairs 1 --num-fusion-both 2 $index

can anyone help me resolve this error?

[Mon Apr 1 23:34:39 2013] Reporting final fusion candidates in html format
Traceback (most recent call last):
File "/tophat/v2.0.8/tophat-fusion-post", line 2627, in <module>
sys.exit(main())
File "/tophat/v2.0.8/tophat-fusion-post", line 2607, in main
generate_html(params)
File /tophat/v2.0.8/tophat-fusion-post", line 2506, in generate_html
cluster_fusion(fusion_list, fusion_gene_list, cluster_list)
File "/tophat/v2.0.8/tophat-fusion-post", line 1875, in cluster_fusion
cluster_temp_list = sorted(cluster_temp_list2, cmp=cmp)
File "/tophat/v2.0.8/tophat-fusion-post", line 1870, in cmp
a_score = pair_count(a_indices)
File "/tophat/v2.0.8/tophat-fusion-post", line 1836, in pair_count
score = fusion_list[index]["score"]
KeyError: 'score'
Tue Apr 2 01:13:57 EDT 2013

Thanks,
Angel

Last edited by angerusso; 04-02-2013 at 09:43 AM.
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Old 04-24-2013, 10:37 PM   #2
tgenahmet
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same problem here. Any fixes, anyone?
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Old 05-07-2013, 06:36 AM   #3
tankman
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Location: usa

Join Date: Sep 2012
Posts: 22
Default KeyError:score

Yeah, I also have the same problem. Emailed the cufflinks/tophat people so far to no avail. I tried on tophat/2.0.8b as well...note that suspending the html creation via --skip-html doesn't produce results.txt either, which kind of makes it useless although it avoids the error.
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Old 06-22-2013, 11:26 AM   #4
nbahlis
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Location: Canada

Join Date: May 2013
Posts: 25
Default KeyError: 'score'

same error here, anyone figured out the problem? It was running fine a week ago? so nothing to do with the way I compiled these files.
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Old 06-24-2013, 01:11 AM   #5
ymc
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Location: Hong Kong

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Posts: 498
Default

same here with 2.0.8b

Tried Emilie's hack but also fail for 2.0.8b
http://seqanswers.com/forums/showthread.php?t=13940

I will give v2.0.3 a try later
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Old 06-24-2013, 10:48 AM   #6
ymc
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Oh well. I tried v2.0.3 without Emilie hack and it completed.

I suppose you just have to try different versions of tophat until it works....
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