Hi,
I have a number of questions about how to transform my set of predicted trees into a valid submission file; but I think the easiest way to answer them and other peoples' would be for you to create even a one-line dummy example of what the lines in the file should look like. So would you please create and publish a small dummy tree, and the line needed to successfully submit it? Thanks.
And this would probably be useful for the other subchallenges too.
Created by Phil Rennert philrennert You are right phil, I think we found a solution.
Thanks for your patience Seriously? In some trees there are sets of 7 or 8 cells with identical strings for the 10 markers! So you want us to randomly decide which of these identical siblings are more closely related than others, and reduce this to a binary tree? If your scoring system is assigning weight to which way these decisions come out compared to ground truth, it's adding noise to the score. If it isn't assigning weight this way, can't you make it less finicky? Dear @philrennert there is a problem with your submission to subchallenge 1:
you mostly submitted non-binary trees and hence there are a lot of NANs in the score, these are trees where a cell has more than 2 daughters.
Could you please review your submission so that you submit binary trees only?
thanks
pablo Hi @philrennert (and others),
Because SC1 involves more than one tree, the "must use correct identifier names and contain x cell lines" error message is actually in regards to another tree, not the tree of dreamID 1. You are correct - your tree for dreamID 1 is valid! Apologies for the confusion. I have updated the validation script for SC1 so that the error messages are more elaborate and helpful.
As for the "column x" error messages: these are generated by the [dendropy](https://dendropy.org/) library and I believe the column number actually refers to the character number (or general vicinity) of where the incorrect Newick format is located.
Best,
Verena Okay, it got past that filter...here's the error message:
Your submission (parsimony with split pairs) is invalid, below are the invalid reasons:
Prediction tree(s) not a valid Newick tree format: Error parsing data source on line 1 at column 44: Malformed tree statement
Prediction tree(s) not a valid Newick tree format: Error parsing data source on line 1 at column 142: Malformed tree statement
Prediction tree must use the correct identifier names, and contain 20 cell lines.
1) sub_test_1 has only four cell lines, not 20, And my first content line doesn't have 142 columns. What do these messages mean?
2) Does your Newick format require distances on each branch, as in your example from TeamNamesub1_submission.txt :
(((1_2012210001:0.2845811716,3_2012210001:0.2845811716):0.06745990453,2_2112210001:0.3520410761):0.05180365419,4_2212210001:0.4038447303)root;
or can they be omitted? I didn't include them, is that what the problem is? Because otherwise my Newick format is correct as far as commas and parentheses go,
and I'm using the right four identifier names.
3) Do you require a tab after the Newick tree? I'm wondering how your system got 142 columns...here's my first content line:
1 (((1_2012210001,3_2012210001),4_2212210001),2_2112210001)root;
Does anything strike you as wrong format?
As you can see it is still invalid:
" INVALID
Two tab-delimited columns are expected" Once more, maybe I got it this time... Thanks. I think I submitted the file this time
Phil @philrennert,
Happy new year! I see that you submitted your actual project and not the actual file. You will want to upload your respective file and go to the file.
Once you on on the file, you can click **File Tools** and click **Submit File to Challenge**. The way you submitted to subchallenge 1 is how you would submit a project submission. You want to actually submit a File.
Best,
Tom Great, I see the other two. Thanks! Hello all,
Happy Holidays! The queues are now open for submission. You may now submit to subchallenge 1 and 2.
Best,
Tom Hi Phil,
we were planning on making them live early january, but let me see if we can do it now!
thanks!
Okay, I'm ready to submit my subchallenge1 predictions.
But when I follow your procedure under Submit to challenge. where it says
"For subchallenges 1 and 2, you are allowed one submission each.
For subchallenge 3, you are allowed five total submissions, for the leaderboard dataset. The leaderboard dataset will be available up through November and a different test set will be available afterward starting in January."
it automatically assumes I'm submitting to subchallenge 3, here's the popup:
Select the Entity that you would like to submit:
Submitting to the following challenge
Allen Institute Cell Lineage Reconstruction Subchallenge 3
Submission name (optional)
I can't edit it. How do I submit to subchallenge 1? I see them; thanks! They should be in there now, thanks! Thanks; but in that folder I only see one of those - TeamNamesub3_submission.nw .
And in the Subchallenge1 subfolder, there are only ground truth and test_sub files.
Hi Phil,
on the [data file folder](https://www.synapse.org/#!Synapse:syn20821809) you can find 3 dummy submissions, one for each challenge.
Their names are:
TeamNamesub1_submission.txt
TeamNamesub2_submission.nw
TeamNamesub3_submission.nw
thanks for your interest
Pablo
Drop files to upload
subchallenge 1: exact format for submission file? page is loading…