search

rambaut / Seq-Gen

Sequence simulator
51 stars 17 forks source link

Cannot give tree with "<<<" #23

Closed carlosj-rr closed 1 year ago

carlosj-rr commented 1 year ago

Hello,

I'm following a pipeline which used Seq-Gen as a subprocess within a python script, and it gives the tree in text with <<< instead of as a file name. I've seen in other issues that this is not a problem, but for some reason, it is for me. I'm running Seq-Gen 1.3.4 installed from conda, but I also had the same problem with the latest version, compiled from source:

seq-gen -mGTR -q -a1000 -z1686042325.0655584 -l 1000 -f0.277,0.228,0.246,0.249 -r1,1.68369,1,1,1.91645,1 <<< "(B:0.3598052239,D:0.3425989485,(A:0.4731590178,C:0.46432
18278):0.0822832145);"
Error reading tree number 1: .

Not sure whether I'm doing something wrong. I tried with a simpler command, used by @SamStudio8 on Issue #4, but I get the same error:

seq-gen -mGTR <<< "(A:0.1,B0.1,C:0.1);"
Sequence Generator - seq-gen
Version 1.3.4
(c) Copyright, 1996-2017 Andrew Rambaut and Nick Grassly
Institute of Evolutionary Biology, University of Edinburgh

Originally developed at:
Department of Zoology, University of Oxford

Error reading tree number 1: .

However, saving the tree and passing it as a filename works perfectly:

echo "(B:0.3598052239,D:0.3425989485,(A:0.4731590178,C:0.4643218278):0.0822832145);" > tree.nwk
seq-gen -mGTR -q -a1000 -z1686042325.0655584 -l 1000 -f0.277,0.228,0.246,0.249 -r1,1.68369,1,1,1.91645,1 < tree.nwk
# Sequences produced...

Thus, it seems to not be a problem of the tree format (also, the pipeline I'm following uses the exact line I pasted in the first code block), but I'm at loss as to what else could I test.

Many thanks.

-carlos

carlosj-rr commented 1 year ago

Update - I compiled from source at my group's servers (where I ultimately have to run these anayses), and it runs well! I really have no idea why it doesn't work on my laptop, still, though...but FTM I'll close this issue.