partition file error

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DC

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Aug 2, 2021, 5:05:40 AMAug 2
to raxml
Hello all,
I have run  
>>> raxmlHPC -m ASC_GTRCAT -V --K80 --asc-corr=felsenstein -n out_ -s varsite.phy -p 12345 -b 54321 -q part
I used ascbias.py and deleteAlignColumn.pl for removing invariable sites considering that asc requres just varsites, both work perfectly. But when it comes to runing raxml (raxml-8.2.8)  with -q part  I have problem. Considering I am running ascertainment bias correction I need part file, but I  am getting error  >>  "The file part you want to open for reading does not exist, exiting ..."
 this is my part file>>   
ASC_GTRCAT, p1=1-2177

What is wrong with it? Why it does not recognise part file? Anyone with same problem and possible solution?  Any advice will be greatly appreciated!

Cheers,

Di

Alexandros Stamatakis

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Aug 2, 2021, 5:15:57 AMAug 2
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That's weird, is it located in the same directory as the alignment file?

Alexis

On 02.08.21 12:03, Dijana Cortan wrote:
>
> Hello all,
> I have run
> >>> raxmlHPC -m ASC_GTRCAT -V --K80 --asc-corr=felsenstein -n out_ -s
> varsite.phy -p 12345 -b 54321 -q part
> I used/ascbias.py/ and /deleteAlignColumn.pl /for removing invariable
> sites considering that asc requres just varsites, both work perfectly.
> But when it comes to runing raxml (raxml-8.2.8)  with -q part  I have
> problem. Considering I am running ascertainment bias correction I need
> part file, but I  am getting error  >>  "/The file part you want to open
> for reading does not exist, exiting .../"
>  this is my part file>>
> ASC_GTRCAT, p1=1-2177
>
> What is wrong with it? Why it does not recognise part file? Anyone with
> same problem and possible solution?  Any advice will be greatly appreciated!
>
> Cheers,
>
> Di
>
> --
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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org

DC

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Aug 2, 2021, 5:25:18 AMAug 2
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yes it is in same directory  :(
Should I go with full path, but it recognised already input file without full path. So that should not be issue

Alexandros Stamatakis

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Aug 2, 2021, 5:31:16 AMAug 2
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weird, can you send me the input files please?

alexis

On 02.08.21 12:25, DC wrote:
> yes it is in same directory  :(
> Should I go with full path, but it recognised already input file without
> full path. So that should not be issue
>
> понедељак, 02. август 2021. у 11:15:57 UTC+2 Alexis је написао/ла:
>
> That's weird, is it located in the same directory as the alignment
> file?
>
> Alexis
>
> On 02.08.21 12:03, Dijana Cortan wrote:
> >
> > Hello all,
> > I have run
> > >>> raxmlHPC -m ASC_GTRCAT -V --K80 --asc-corr=felsenstein -n
> out_ -s
> > varsite.phy -p 12345 -b 54321 -q part
> > I used/ascbias.py/ <http://ascbias.py/> and /deleteAlignColumn.pl
> <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer
> <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP)
> lab,
> Institute of Molecular Biology and Biotechnology, Foundation for
> Research and Technology Hellas
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
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> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com?utm_medium=email&utm_source=footer>.

Alexandros Stamatakis

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Aug 3, 2021, 12:19:58 AMAug 3
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Hi Dijana,

There are a couple of things:

Which RAxML version are you using? It seems to be rather old.

The first error I get is this one:

stamatak@psiloritis:~/Desktop/Playground$ ./raxmlHPC-AVX -m ASC_GTRCAT
-V --K80 --asc-corr=felsenstein -n out_ -s varsite.phy -p 12345 -b 54321
-q part
Error, you have specified a random number seed via -x or -b for some
sort of bootstrapping,
but you have not specified a number of replicates via -N or -#, exiting ....

So you need to add the number of BS reps via -N to the command line.

Then, you want to use felsenstein correction, for this you will need to
provide an additional file containing the number of invariant sites,
please see the example on page 44 of the manual at:

https://cme.h-its.org/exelixis/resource/download/NewManual.pdf

Also, you should consider upgrading to RAxML-NG as standard RAxML is no
longer supported:

https://github.com/amkozlov/raxml-ng

Alexis

>
> On Mon, Aug 2, 2021 at 11:51 AM Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> yes, just to my personal email,
>
> alexis
>
> On 02.08.21 12:47, DC wrote:
> > it is reporting error while posting it here.
> > Can I send you on your mail?
> >
> >
> > понедељак, 02. август 2021. у 11:31:16 UTC+2 Alexis је написао/ла:
> >
> >     weird, can you send me the input files please?
> >
> >     alexis
> >
> >     On 02.08.21 12:25, DC wrote:
> >      > yes it is in same directory  :(
> >      > Should I go with full path, but it recognised already
> input file
> >     without
> >      > full path. So that should not be issue
> >      >
> >      > понедељак, 02. август 2021. у 11:15:57 UTC+2 Alexis је
> написао/ла:
> >      >
> >      > That's weird, is it located in the same directory as the
> alignment
> >      > file?
> >      >
> >      > Alexis
> >      >
> >      > On 02.08.21 12:03, Dijana Cortan wrote:
> >      > >
> >      > > Hello all,
> >      > > I have run
> >      > > >>> raxmlHPC -m ASC_GTRCAT -V --K80
> --asc-corr=felsenstein -n
> >      > out_ -s
> >      > > varsite.phy -p 12345 -b 54321 -q part
> >      > > I used/ascbias.py/ <http://ascbias.py/>
> <http://ascbias.py/ <http://ascbias.py/>> <http://ascbias.py/
> <http://ascbias.py/>
> >     <http://ascbias.py/ <http://ascbias.py/>>> and
> <mailto:raxml%2Bun...@googlegroups.com>
> >      > > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bun...@googlegroups.com>>.
>  <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com>>
>  <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer>>
> >
> >      >
> >
>  <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer>
> >
>  <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer>>>>.
> >
> >      >
> >      >
> >      > --
> >      > Alexandros (Alexis) Stamatakis
> >      >
> >      > Research Group Leader, Heidelberg Institute for
> Theoretical Studies
> >      > Full Professor, Dept. of Informatics, Karlsruhe Institute of
> >     Technology
> >      > Affiliated Scientist, Evolutionary Genetics and
> Paleogenomics (EGP)
> >      > lab,
> >      > Institute of Molecular Biology and Biotechnology,
> Foundation for
> >      > Research and Technology Hellas
> >      >
> >      > www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>
> >     <http://www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>>
> >      >
> >      > --
> >      > You received this message because you are subscribed to
> the Google
> >      > Groups "raxml" group.
> >      > To unsubscribe from this group and stop receiving emails
> from it,
> >     send
> >      > an email to raxml+un...@googlegroups.com
> <mailto:raxml%2Bun...@googlegroups.com>
> >      > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bun...@googlegroups.com>>.
>  <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com>>
> >
> >      >
> >
>  <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com?utm_medium=email&utm_source=footer>
> >
>  <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com?utm_medium=email&utm_source=footer>>>.
> >
> >
> >     --
> >     Alexandros (Alexis) Stamatakis
> >
> >     Research Group Leader, Heidelberg Institute for Theoretical
> Studies
> >     Full Professor, Dept. of Informatics, Karlsruhe Institute of
> Technology
> >     Affiliated Scientist, Evolutionary Genetics and Paleogenomics
> (EGP)
> >     lab,
> >     Institute of Molecular Biology and Biotechnology, Foundation for
> >     Research and Technology Hellas
> >
> > www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>

Alexandros Stamatakis

unread,
Aug 3, 2021, 12:20:13 AMAug 3
to ra...@googlegroups.com
Hi Dijana,

There are a couple of things:

Which RAxML version are you using? It seems to be rather old.

The first error I get is this one:

stamatak@psiloritis:~/Desktop/Playground$ ./raxmlHPC-AVX -m ASC_GTRCAT
-V --K80 --asc-corr=felsenstein -n out_ -s varsite.phy -p 12345 -b 54321
-q part
Error, you have specified a random number seed via -x or -b for some
sort of bootstrapping,
but you have not specified a number of replicates via -N or -#, exiting ....

So you need to add the number of BS reps via -N to the command line.

Then, you want to use felsenstein correction, for this you will need to
provide an additional file containing the number of invariant sites,
please see the example on page 44 of the manual at:

https://cme.h-its.org/exelixis/resource/download/NewManual.pdf

Also, you should consider upgrading to RAxML-NG as standard RAxML is no
longer supported:

https://github.com/amkozlov/raxml-ng

Alexis


> > понедељак, 02. август 2021. у 11:31:16 UTC+2 Alexis је написао/ла:
> >
> >     weird, can you send me the input files please?
> >
> >     alexis
> >
> >     On 02.08.21 12:25, DC wrote:
> >      > yes it is in same directory  :(
> >      > Should I go with full path, but it recognised already
> input file
> >     without
> >      > full path. So that should not be issue
> >      >
> >      > понедељак, 02. август 2021. у 11:15:57 UTC+2 Alexis је
> написао/ла:
> >      >
> >      > That's weird, is it located in the same directory as the
> alignment
> >      > file?
> >      >
> >      > Alexis
> >      >
> >      > On 02.08.21 12:03, Dijana Cortan wrote:
> >      > >
> >      > > Hello all,
> >      > > I have run
> >      > > >>> raxmlHPC -m ASC_GTRCAT -V --K80
> --asc-corr=felsenstein -n
> >      > out_ -s
> >      > > varsite.phy -p 12345 -b 54321 -q part
> >      > > I used/ascbias.py/ <http://ascbias.py/>
> >     <http://ascbias.py/ <http://ascbias.py/>>> and
> <mailto:raxml%2Bun...@googlegroups.com>
> >      > > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bun...@googlegroups.com>>.
>  <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com>>
>  <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/d99c756f-9930-4f56-881f-fa2d5ed382d8n%40googlegroups.com?utm_medium=email&utm_source=footer>>>>.
> >
> >      >
> >      >
> >      > --
> >      > Alexandros (Alexis) Stamatakis
> >      >
> >      > Research Group Leader, Heidelberg Institute for
> Theoretical Studies
> >      > Full Professor, Dept. of Informatics, Karlsruhe Institute of
> >     Technology
> >      > Affiliated Scientist, Evolutionary Genetics and
> Paleogenomics (EGP)
> >      > lab,
> >      > Institute of Molecular Biology and Biotechnology,
> Foundation for
> >      > Research and Technology Hellas
> >      >
> >      > www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>>
> >      >
> >      > --
> >      > You received this message because you are subscribed to
> the Google
> >      > Groups "raxml" group.
> >      > To unsubscribe from this group and stop receiving emails
> from it,
> >     send
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> <mailto:raxml%2Bun...@googlegroups.com>>.
> >      > To view this discussion on the web visit
> >      >
> >
> https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com
>  <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/4d5b448f-e48a-4526-af98-95d944cf1bcfn%40googlegroups.com?utm_medium=email&utm_source=footer>>>.
> >
> >
> >     --
> >     Alexandros (Alexis) Stamatakis
> >
> >     Research Group Leader, Heidelberg Institute for Theoretical
> Studies
> >     Full Professor, Dept. of Informatics, Karlsruhe Institute of
> Technology
> >     Affiliated Scientist, Evolutionary Genetics and Paleogenomics
> (EGP)
> >     lab,
> >     Institute of Molecular Biology and Biotechnology, Foundation for
> >     Research and Technology Hellas
> >

DC

unread,
Aug 3, 2021, 6:36:55 AMAug 3
to raxml
Hi  Alexis ,
Thank you for your fast inputs. Yes, it is definitly older version, raxml-8.2.8. I have added -# autoFC and waiting for update to last version. 

There is thing that I still do not understand and that is if I am running alingment with just variant sites (because  asc requires to remove all invariant sites) why it is asking to state how many invariant sites is there. I just need to put 0?
I am trying to transfer to RAxML-NG and it is same thing  (ASC_FELS{0}). I have feeling I am missing something? Or I am just puting 0?

Thank you!

Di

Alexandros Stamatakis

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Aug 3, 2021, 7:01:10 AMAug 3
to ra...@googlegroups.com
Well, you are stating in your command line that you want to use the
Felsenstein correction, and this correction needs to know how many
invariant sites you have to compute the respective ascertainment bias
correction.

Alexis
> <http://ascbias.py/>>> <http://ascbias.py/ <http://ascbias.py/>
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/raxml/d2fc44aa-7957-4d95-9ca1-011f552b4911n%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/d2fc44aa-7957-4d95-9ca1-011f552b4911n%40googlegroups.com?utm_medium=email&utm_source=footer>.
Message has been deleted

Alexandros Stamatakis

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Aug 3, 2021, 2:25:27 PMAug 3
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But then it makes absolutely no sense to use any ascertainment bias
correction.

Maybe you should read the paper again in which we describe it:

https://academic.oup.com/sysbio/article/64/6/1032/1669226?login=true

Alexis

On 03.08.21 15:49, DC wrote:
> OK! Then is zero! :)
> Thank youuuu!
> All the best!
>
> Di
> > <http://ascbias.py/ <http://ascbias.py/>>>> <http://ascbias.py/
> > You received this message because you are subscribed to the Google
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> > an email to raxml+un...@googlegroups.com
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> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/raxml/d2fc44aa-7957-4d95-9ca1-011f552b4911n%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/d2fc44aa-7957-4d95-9ca1-011f552b4911n%40googlegroups.com>
>
> >
> <https://groups.google.com/d/msgid/raxml/d2fc44aa-7957-4d95-9ca1-011f552b4911n%40googlegroups.com?utm_medium=email&utm_source=footer
> <https://groups.google.com/d/msgid/raxml/d2fc44aa-7957-4d95-9ca1-011f552b4911n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP)
> lab,
> Institute of Molecular Biology and Biotechnology, Foundation for
> Research and Technology Hellas
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
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DC

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Aug 4, 2021, 2:20:19 AMAug 4
to raxml
OK.  I think I see a point now and how to get there.
Thank you so much for you time!
All the best,

Di

DC

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Aug 6, 2021, 2:43:50 AMAug 6
to raxml
Hi,
Just small update. It is finaly working. 
It worked at the end when I put whole directorium path to partition file. And it was also looking to put whole path in partition file for p1.txt. But input phy file was ok without whole path. Anyway thank you for your time.
All the best,
Di
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