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HYPHY Package >> HyPhy bugs >> error during NielsenYang.bf
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1287493565
Message started by Paasei on Oct 19th, 2010 at 6:06am

Title: error during NielsenYang.bf
Post by Paasei on Oct 19th, 2010 at 6:06am
I just started using HyPhy for dN/dS calculations. I did a number of runs using the quickselectiondetection.bf (SLAC) without a problem. However, if I run NielsenYang or the dNdSrateanalysis, I always get the same kind of error messages (see attach). Any idea would could be the problem ?
error.JPG (22 KB | )

Title: Re: error during NielsenYang.bf
Post by Sergei on Oct 19th, 2010 at 5:57pm
Hi there,

I can't see to recreate the problem. Could you provide more information to help me identify the cause:

1). Which version of HyPhy are you using?
2). Which analysis options did you select before the error popped up?

Sergei


Paasei wrote on Oct 19th, 2010 at 6:06am:
I just started using HyPhy for dN/dS calculations. I did a number of runs using the quickselectiondetection.bf (SLAC) without a problem. However, if I run NielsenYang or the dNdSrateanalysis, I always get the same kind of error messages (see attach). Any idea would could be the problem ?


Title: Re: error during NielsenYang.bf
Post by Paasei on Oct 21st, 2010 at 12:45am
Hi,
I use the win32 GUI version 2.0.

I specified these options :
- run all distributions
- MG94 3x4 custom, specifying 012230
- cutoff 0.95
- 3 categories in distribution

Thanks !

Title: Re: error during NielsenYang.bf
Post by Sergei on Oct 21st, 2010 at 6:29pm
Hi there,

Sorry, I can't replicate the issue. Can you possibly attach your alignment file to see if I can find the issue using it?

Sergei

Title: Re: error during NielsenYang.bf
Post by Paasei on Oct 25th, 2010 at 5:10am
I have narrowed down the error, I do not get it while running the single rate model, only when doing the others (neutral and selection).
The input are 635 nucleotide sequences (but I also get the error with less sequences):
>K03455
CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT
>A04321
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT
>A07867
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT
>AB078005
CCTCAAATCACTCTTTGGCAACGACCCCTCGTTACAATAAAGGTAGGGGGGCAACTAAAG
GAAGCTCTGTTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCGAAAATGATAGGGGGAATTGGAGGTTTTATTAAAGTAAGACAGTATGAT
CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTGGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT
>AB097870
CCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAATTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGACATGGATTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACCCATAGAAATCTGTGGACACAAAGCTATAGGTACAGTATTAGTAGGACCAACA
CCTGTCAACATAATTGGAAGAAATCTGCTGACTCAGGTTGGTTGCACTTTAAATTTT
>AB221005
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT
>AB221125
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAGTAAAAATAGGGGGACAGCTAAAG
GAAGCTCTGTTAGATACAGGGGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGGTACCCATAGAAATCTGTGAACATAAAGTTATAGGTACAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTT
>AB221126
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAGTAAAAATAGGGGGACAGCTAAAG
GAAGCTCTGTTAGATACAGGGGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGGTACCCATAGAAATCTGTGAACATAAAGTTATAGGTACAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTT
>AB253432
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTT
>AB286955
CCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGGTAGGGGGACAGCTAAAA
GAGGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTCGTAGAAATCTGTGGACATAAAGCTATAGGTACAGTCTTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAACCTGTTGACTCAGATTGGCTGCACTTTAAATTTT
>AB286956
CCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGGTAGGGGGACAGCTAAAA
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTCGTAGAAATCTGTGGACATAAAGCTATAGGTACAGTCTTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAACCTGTTGACTCAGATTGGCTGCACTTTAAATTTT
>AB287363
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACCCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAATAGGACCTACA
CCCGTCAACATAATTGGAAGAAATTTGTTGACGCAGCTTGGGTGTACTTTAAATTTT
>AB287364
CCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGGTAGGGGGACAGCTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATAGATTTACCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTAGTAGAAATTTGTGGACATAGAGCTATAGGTACAGTATTAGTAGGACCTACA
CCTGTTAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTT
>AB287365
CCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGGTAGGGGGACAGCTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATAGATTTACCAGGA
AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACTAGTAGAAATTTGTGGACATAGAGCTATAGGTACAGTATTAGTAGGACCTACA
CCTGTTAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTT
>AB287366
CCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAGGATAGGAGGGCAGCTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCGGGA
AGATGGAAACCGAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACCCATAGAAATCTGTGGAAAGAAAACTATAGGTACAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGATGCACTTTAAATTTT
>AB287367
CCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAGGATAGGAGGGCAGCTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCGGGA
AGATGGAAACCGAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGATACCCATAGAAATCTGTGGAAAGAAAACTATAGGTACAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGATGCACTTTAAATTTT
>AB287368
CCTCAGATCACTCTTTGGCAACGACCCCTTGTCACAGTAAAGGTAGGGGGGCAACTAAGG
GAAGCCCTATTAGATACAGGAGCAGATGATACAGTGTTAGAAGAAATGAATTTGCCAGGA
AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAAATACCTGTAGACATCTGTGGTCATAAAGCTGTAGGTACAGTGTTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGGTGCACTTTAAATTTT
>AB287369
CCTCAAATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAACTAAAA
GAGGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCAAAAATGATAGTGGGAATTGGAGGTTTTGTCAAAGTAAGACAGTATGAT
CAGGTACCCATAGAAATCTGTGGGCATAAAATTGAAGGTACAGTGTTAATAGGACCTACC
CCTGCCAACATAATTGGAAGAAATCTGATGACTCAGCTTGGTTGCACTTTAAATTTT
>AB287370
CCTCAAATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAACTAAAA
GAGGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCAAAAATGATAGTGGGAATTGGAGGTTTTGTCAAAGTAAGACAGTATGAT
CAGGTACCCATAGAAATCTGTGGGCATAAAATTGAAGGTACAGTGTTAATAGGACCTACC
CCTGCCAACATAATTGGAAGAAATCTGATGACTCAGCTTGGTTGCACTTTAAATTTT
>AB287371
CCTCAAATCACTCTTTGGCAACGACCCATCGTCACAGTAAAGATAGGGGGGCAACTAAAA
GAGGCTATATTAGATACAGGAGCAGATAATACAGTATTAGAAGACATGAATTTGCCAGGA
AGATGGACACCAAAAATAATAGGAGGAATTGGAGGTTTTGTCAAAGTAAGACAGTATGAT
CAGGTACCCATAGAAATCTGTGGGCACAAAACTGAAGGTACAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAGATCTGATGACTCAGCTTGGTTTCACTTTAAATTTT
>AB287372
CCTCAAATCACTCTTTGGCAACGACCCATCGTCACAGTAAAGATAGGGGGGCAACTAAAA
GAGGCTATATTAGATACAGGAGCAGATAATACAGTATTAGAAGACATGAATTTGCCAGGA
AGATGGACACCAAAAATAATAGGAGGAATTGGAGGTTTTGTCAAAGTAAGACAGTATGAT
CAGGTACCCATAGAAATCTGTGGGCACAAAACTGAAGGTACAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAGATCTGATGACTCAGCTTGGTTTCACTTTAAATTTT
>AB289587
CCTCAGATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAACTGAGG
GAAGCTCTATTGGATACAGGAGCAGATGATACAGTGTTAGAAGAAATAAATTTGCCAGGA
AAATGGAAACCAAAAATAATAGGGGGAATTGGAGGTCTTATCAAAGTAAGACAGTATGAT
AATATACCCATAGAAATCTGTGGACATAAAGTTATAGGTTCAGTATTAGTAGGACCTACA
CCTACCAACATAATTGGAAGAAGTCTGATGACTCAACTTGGTTGCACTTTAAATTTT
>AB289588
CCTCAGATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAACTGAGG
GAAGCTCTATTGGATACAGGAGCAGATGATACAGTGTTAGAAGAAATAAATTTGCCAGGA
AAATGGAAACCAAAAATAATAGGGGGAATTGGAGGTCTTATCAAAGTAAGACAGTATGAT
AATATACCCATAGAAATCTGTGGACATAAAGTTATAGGTTCAGTATTAGTAGGACCTACA
CCTACCAACATAATTGGAAGAAGTCTGATGACTCAACTTGGTTGCACTTTAAATTTT
>AB289589
CCTCAGATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAGCTAAAG
GAAGCACTATTAGATACAGGAGCAGATAATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCAAAAATAATAGGGGGAATTGGAGGTTTTCTCAAAGTAAGACAGTATGAT
CAGATACCCATAGAAATCTGTGGACATAAAACTATAGGTACAGTATTAGTAGGACCTACA
CCTGTCAACGTAGTTGGAAGGGATCTGATGACTCAGCTTGGTTGCACTTTAAATTTT
>AB289590
CCTCAGATCACTCTTTGGCAACGACCCATCGTCACAATAAAGATAGGGGGGCAGCTAAAG
GAAGCACTATTAGATACAGGAGCAGATAATACAGTATTAGAAGAAATGAATTTGCCAGGA
AGATGGAAACCAAAAATAATAGGGGGAATTGGAGGTTTTCTCAAAGTAAGACAGTATGAT
CAGATACCCATAGAAATCTGTGGACATAAAACTATAGGTACAGTATTAGTAGGACCTACA
CCTGTCAACGTAGTTGGAAGGGATCTGATGACTCAGCTTGGTTGCACTTTAAATTTT
>AB428551
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCCCAATAAAGATAGGGGGGCAACTAAAG
GAAGCCCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AAATGGAAACCAAAAATAATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGGTACCCGTAGAAATCTGCGGACATAAAGCTATAGGTGCAGTATTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGTTGCACTTTAAATTTT
>AB428552
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAA
CAGGTACCCATAGAAATCTGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGATGACTCAGCTTGGGTGCACTTTAAATTTT
>AB428553
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AAATGGAAACCAAAAATAATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGGTAACCGTAGAAATCTGCGGACATAAAGCTATAGGTGCAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGTTGCACTTTAAATTTT
>AB428554
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAA
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AAATGGAAACCAAAAATAATAGGGGGAATTGGAGGCTTTATCAAAGTAAGACAGTATGAT
CAGGTAACCGTAGAAATCTGCGGACATAAAGCTATAGGTGCAGTATTAATAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGTTGCACTTTAAATTTT
>AB428555
CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG
GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGA
AAATGGAAACCAAAAATAATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT
CAGGTACCCATAGAAATCTGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA
CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGTTGCACTTTAAATTTT

Title: Re: error during NielsenYang.bf
Post by Sergei on Oct 25th, 2010 at 12:11pm
Dear Paasei,

Could you attach the alignment file (and the tree that comes with it), instead of pasting the sequences in as text.

Sergei

Title: Re: error during NielsenYang.bf
Post by Paasei on Oct 25th, 2010 at 12:15pm

Sergei wrote on Oct 25th, 2010 at 12:11pm:
Dear Paasei,

Could you attach the alignment file (and the tree that comes with it), instead of pasting the sequences in as text.

Sergei

I'll try the zip-file.

Another thing, I get the error on my laptop and on my desktop at work, however, it works fine on my desktop at home, so there seems to be a computerspecific error ? (Windows version ? )
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=protease.zip (18 KB | )

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