merlyescalona/indelible-ngsphy

This is a fork of the original INDELible (Fletcher and Yang, 2009), a simulator of biological evolution. Now allowing the use of a sequence as ancestral.

indelible-ngsphy's Issues

fix binaries

Remove original binaries and find how to download the indelible-ngsphy binary properly

Reference sequence read with 0 bp when specifying tree

Hi,

I am trying to use indelible-ngsphy to seed an ancestral sequence. My machine is a MacOS 10.13.6 (4.2 GHz Intel Core i7). I compiled indelible-ngsphy after cloning it using

git clone https://github.com/merlyescalona/indelible-ngsphy.git indelible-ngsphy

First I'd like to suggest including in the help that the partition name should match the fasta sequence name. :)

I ran the example control file without the 'ancestral.fasta' in the directory and indelible-ngsphy prints an error but apparently works anyway.

+----------------------------------------------------+
| ERROR in [TREE] block treename                     |
| Something is wrong in the getnextdepthcommand.     |
|  Please report this and it will be promptly fixed! |
+----------------------------------------------------+


 * Block 1 completed.   Time taken: 0.252472 seconds.


*** SIMULATION COMPLETED - PLEASE CONSULT OUTPUT FILES ***                                                                     


INDELible V1.03 Simulations completed at: Thu Jul 19 18:28:10 2018

Same when I add the 'ancestral.fasta' in the directory OR when I use my own tree in the control file:

 +----------------------------------------------------+
 | ERROR in [TREE] block treename                     |
 | Something is wrong in the getnextdepthcommand.     |
 |  Please report this and it will be promptly fixed! |
 +----------------------------------------------------+


[NGSPhy I/O] Validation ended.
[NGSPhy I/O] Reference sequence read with 1197 bp
  * Block 1 completed.   Time taken: 0.000574 seconds.


 *** SIMULATION COMPLETED - PLEASE CONSULT OUTPUT FILES ***                                                                     


 INDELible V1.03 Simulations completed at: Thu Jul 19 18:26:17 2018

However adding the 'ancestral.fasta' in the directory AND using my own tree does not work:
(it seems something goes wrong when reading the fasta)

 +----------------------------------------------------+
 | ERROR in [TREE] block treename                     |
 | Something is wrong in the getnextdepthcommand.     |
 |  Please report this and it will be promptly fixed! |
 +----------------------------------------------------+


[NGSPhy I/O] Validation ended.
[NGSPhy I/O] Reference sequence read with 0 bp
libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: vector
Abort trap: 6

I tried with two different trees that worked OK with the original indelible.
Any feedback is welcome (:

Cheers,
Julian