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HyPhy help for a newbie
Jan 27^th, 2012 at 12:29pm

I received the error message below when attempting to run Slatkin Maddison on a file I had exported from FigTree v1.3.1 as a Newick file. Can anyone help me understand what I did wrong? Thank you!

DEAD END
An error occured:
Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:TemplateBatchFiles:MacintoshHD[etcetc]
could not be opened for reading by fscanf. Path stack: {MacintoshHD:Applications:,Macintos
Current Operation/job has been terminated.

Quit / Skip Further / Oh well

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: HyPhy help for a newbie Reply #1 - Jan 28^th, 2012 at 1:32pm Hi there, This is odd - seems like a path error. Can you look into messages.log (Analyeses->View messages.log menu option) and paste the entire error message here? Sergei
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Re: HyPhy help for a newbie
Reply #2 - Jan 30^th, 2012 at 11:38am

Thank you, Sergei. Full message from log below. Eli

Variable 'PROMPT_FOR_FILE' was not initialized prior to being used
Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:TemplateBatchFiles:NIH:boritze:
Desktop:SGA analysis:VRC200_004:004 tree files:004.nwk could not be opened for reading by fscanf. Path stack: {Macintosh HD:Applications:,Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:,Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:TemplateBatchFiles:}
Variable 'A_DISTANCE_METHOD' was not initialized prior to being used
Variable 'categoriesUsed' was not initialized prior to being used
Variable 'IS_BOOTSTRAP_AVAILABLE' was not initialized prior to being used
Variable 'IS_NPBOOTSTRAP_AVAILABLE' was not initialized prior to being used
Variable 'IS_DNDS_AVAILABLE' was not initialized prior to being used
Variable '_Genetic_Code' was not initialized prior to being used
Variable 'GeneticCodeExclusions' was not initialized prior to being used

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Re: HyPhy help for a newbie
Reply #3 - Jan 30^th, 2012 at 3:44pm

Hi Eli,

Looks like HyPhy is having issues opening files from an external drive (looks like you are opening the file from a drive other than "Macintosh HD").

This is a bit surprising to me, because I thought I had fixed that issue a long time ago. Could you try copying the .nwk file to the desktop prior to opening it in HyPhy and seeing if this fixes the issue?

Sergei

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Re: HyPhy help for a newbie
Reply #4 - Jan 31^st, 2012 at 11:12am

Hi Sergei, the file was already saved in a desktop folder, but I re-exported from FigTree in Newick format directly to the desktop anyway. That yielded the error message below.

I don't know if this matters, but when I was trying to open the file in HyPhy, it was not showing up as a readable file. Several files in .nex and .fas format did show up as readable, but I understand these cannot be used because there is no tree, just an alignment, right?

Variable 'PROMPT_FOR_FILE' was not initialized prior to being used
Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:TemplateBatchFiles:NIH:boritze:
Desktop:200_004.nwk could not be opened for reading by fscanf. Path stack: {Macintosh HD:Applications:,Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:,Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:TemplateBatchFiles:}
Variable 'A_DISTANCE_METHOD' was not initialized prior to being used
Variable 'categoriesUsed' was not initialized prior to being used
Variable 'IS_BOOTSTRAP_AVAILABLE' was not initialized prior to being used
Variable 'IS_NPBOOTSTRAP_AVAILABLE' was not initialized prior to being used
Variable 'IS_DNDS_AVAILABLE' was not initialized prior to being used
Variable '_Genetic_Code' was not initialized prior to being used
Variable 'GeneticCodeExclusions' was not initialized prior to being used

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Re: HyPhy help for a newbie
Reply #5 - Jan 31^st, 2012 at 1:29pm

I was able to open the file by opening HyPhy, then using File>open to choose the original/unexported file from FigTree. A tree window opened and looked like the tree I had viewed in FigTree. I then saved the tree to my desktop as a Newick string. Then I repeated the original procedure, opening HyPhy, choosing Slatkin/Maddison from compartmentalization analyses, and selecting the Newick string file (which again showed up as non-readable). Seems like the same problem happened again. Error message from log below. Getting closer - actually viewed a tree in HyPhy - but still no analysis!

Variable 'PROMPT_FOR_FILE' was not initialized prior to being used
Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:TemplateBatchFiles:NIH:boritze:
Desktop:Tree_1 could not be opened for reading by fscanf. Path stack: {Macintosh HD:Applications:,Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:,Macintosh HD:Applications:HyPhy.app:Contents:Resources:HBL:TemplateBatchFiles:}
Variable 'A_DISTANCE_METHOD' was not initialized prior to being used
Variable 'categoriesUsed' was not initialized prior to being used
Variable 'IS_BOOTSTRAP_AVAILABLE' was not initialized prior to being used
Variable 'IS_NPBOOTSTRAP_AVAILABLE' was not initialized prior to being used
Variable 'IS_DNDS_AVAILABLE' was not initialized prior to being used
Variable '_Genetic_Code' was not initialized prior to being used
Variable 'GeneticCodeExclusions' was not initialized prior to being used

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Re: HyPhy help for a newbie
Reply #6 - Feb 1^st, 2012 at 12:06pm

Hi Eli,

This path problem is very odd: it still looks like HyPhy thinks that your file is in NIH/boritze/Desktop/Tree_1, not on the standard Desktop. I have never seen anything quite like this before. Could you do me a favor: open the Terminal application, drag the tree file into it, and then copy and paste the path that is inserted.

In terms of not being able to see Newick tree files in the open dialog, please see Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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eab YaBB Newbies Offline Curious HyPhy user Posts: 9	Re: HyPhy help for a newbie Reply #7 - Feb 2^nd, 2012 at 11:54am Hi Sergei, here is the path that I got. NIH\boritze$ /Users/NIH\\boritze/Desktop/Tree_1 Our computer guy says he's sure the double-backslash is the problem, but not being a computer guy myself, I have no idea why. Do you know how I can fix this? Thank you! Eagerly awaiting my first tree stats! Eli
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Re: HyPhy help for a newbie
Reply #8 - Feb 2^nd, 2012 at 12:58pm

Hi Eli,

Your computer guy is correct: your user name is NIH\boritze and HyPhy interprets the backslash as a part of the Windows pathname. This is not an error that I have encountered before; I will fix it in the next minor version release (this will require a source code update), but in the meantime in order to fix the issue I would suggest moving your tree file path that does not include the backslash -- e.g. a USB stick or the /Users/Shared folder

Sorry it is an ugly solution, but it is also the fastest. A more permanent solution will be forthcoming in a few weeks.

Thanks,
Sergei

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Re: HyPhy help for a newbie
Reply #9 - Feb 3^rd, 2012 at 2:50pm

It works now! Thank you.

I now have one additional question for you, though. I am running Slatkin Maddison on trees of sequences from multiple subsets (6-14 per tree). The subsets are not mutually exclusive, but instead were derived by splitting the total population of sequences up into "Hi" vs "Lo" for several markers whose expression levels overlap. What I want to do I determine whether the "Hi" and "Lo" for each marker are compartmentalized. Do I need to make a separate tree for the sequences for each marker, and then run Slatkin Maddison on each tree, or can I use the single tree with all markers to analyze each individually?

Thanks so much for your help.

Eli

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Re: HyPhy help for a newbie
Reply #10 - Feb 3^rd, 2012 at 2:53pm

Hi Eli,

As implemented in HyPhy, SM will permit more than 2 subsets, BUT it cannot test compartmentalization of 2 out of N subsets. What it will do, is test for joint compartmentalization. I can modify the script to handle your case, since you were so patient with HyPhy's buggy behavior. Can you attach an example tree and annotation?

Sergei

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eab YaBB Newbies Offline Curious HyPhy user Posts: 9	Re: HyPhy help for a newbie Reply #11 - Feb 7^th, 2012 at 7:12am Hi Sergei, how very kind of you! Attached is a zip of one tree file and associated group file. Thank you so much for your help. Eli
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: HyPhy help for a newbie Reply #12 - Feb 7^th, 2012 at 9:52am Hi Eli, The tree file did not come through (it was an alias to the tree file). Can you please reattach? Sergei
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eab YaBB Newbies Offline Curious HyPhy user Posts: 9	Re: HyPhy help for a newbie Reply #13 - Feb 8^th, 2012 at 6:09pm Sorry about that, Sergei. Here's the tree in a txt. The group file is ok? Thanks again for this. Eli
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