merlyescalona / indelible-ngsphy Goto Github PK
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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.
Remove original binaries and find how to download the indelible-ngsphy binary properly
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
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