Problem using FastML for ancestral sequence reconstruction
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Entering edit mode
7 weeks ago
CM • 0

Dear forumers, I've been trying to generate an ancestral sequence using the ancestral sequence reconstruction software FAstML. I am using the command line and have made sure the input files (both the aligned sequences and the phylogenetic tree) are in correct format, but every time I start the program it terminates, showing the following message:

sh: 1: cannot create outdir/fastml.std: Directory nonexistent

FASTML EXIT ON ERROR: FASTML failed to run, one of the files seq.marginal.txt or prob.marginal.txt were not created...

I've tried different methods, and made sure the files and software were in the right directory but I still keep getting this message.

Any help or insight is appreciated ! Thank you so much.

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Entering edit mode
7 weeks ago
Mensur Dlakic ★ 20k

It does not seem that you understand the meaning of this error message:

sh: 1: cannot create outdir/fastml.std: Directory nonexistent

The program is trying to create a file fastml.std in directory outdir, but it can't do so because that directory doesn't exist. That means one of two things: 1) you don't have write permissions in the directory in which you are trying to run the program; 2) the program can't create the directory on its own, so you have to do it manually before running FastML by typing:

mkdir outdir

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Entering edit mode

Hi Mensur, thank you so much for the reply! I manually created the output directory before running FastML but I still get the same message:

sh: 1: cannot create outdir/fastml.std: Directory nonexistent

FASTML EXIT ON ERROR:


FASTML failed to run, one of the files seq.marginal.txt or prob.marginal.txt were not created...

It's almost like the output folder cannot be detected... Is there perhaps a file that I need to create beforehand as well ?