Re: CAFE software

326 views
Skip to first unread message

Hahn, Matthew

unread,
Apr 15, 2021, 8:40:02 AM4/15/21
to Giuseppe Andolfo, hahnlab-cafe
Hi Giuseppe,

Unfortunately, you will need a species tree to be able to use CAFE. Also, if you have only one family, you won’t be able to make inferences about significance of changes you see. 


sorry,
Matt

On Apr 15, 2021, at 5:01 AM, Giuseppe Andolfo <giusepp...@hotmail.com> wrote:


Dear Matt,

first of all thank you for the speed with which you helped me.
I would like to use CAFE to analyze the expansion/contraction of a specific gene family in four plant species.
CAFE uses a .nwk file releted to the phylogenetic distance of analyzed species. I don't have this information.

I have a .nwk file of genetic distances between the members of my gene family (the orthology/paralogy relationships) of analysed specie.
Can I use this file to estimate the significance of any contractions/expansions?
I assume that I cannot use this .nwk file, is there a way to provide this information to the program?


Thanks.
Cheers,
Giuseppe.



--
Andolfo Giuseppe PhD
Università degli Studi di Napoli Federico II
University of Naples Federico II

Dipartimento di Agraria - Sezione di genetica e biotecnologie vegetali
Department of Agricultural Sciences - Division of plant genetics and biotechnology

Parco Gussone, Edificio 81A
Via Università 133 80055 Portici, Napoli

Editorial Board Member for Bioinformatics and Computational Biology
specialty section of Frontiers in Plant Science, Frontiers in Genetics and Frontiers in Bioengineering and Biotechnology




Da: Hahn, Matthew <m...@indiana.edu>
Inviato: mercoledì 14 aprile 2021 15:54
A: Giuseppe Andolfo <giusepp...@hotmail.com>
Oggetto: Re: CAFE software
 
How about this link: https://hahnlab.sitehost.iu.edu/software.html ? It works for me. 

In any case, a better link for CAFE is here: https://github.com/hahnlab/CAFE5/releases




cheers,
Matt


On Apr 14, 2021, at 9:45 AM, Giuseppe Andolfo <giusepp...@hotmail.com> wrote:

Dear Matthew (CAFE software creator),
I would like to use CAFE for my analyzes.
I can't download the software, can you help me solve this problem?

Thank you very much.

Cheers,

G.


--
Andolfo Giuseppe PhD

Università degli Studi di Napoli Federico II
University of Naples Federico II

Dipartimento di Agraria - Sezione di genetica e biotecnologie vegetali
Department of Agricultural Sciences - Division of plant genetics and biotechnology

Parco Gussone, Edificio 81A
Via Università 133 80055 Portici, Napoli

Editorial Board Member for Bioinformatics and Computational Biology
specialty section of Frontiers in Plant Science, Frontiers in Genetics and Frontiers in Bioengineering and Biotechnology

Phone: +39 081 2535566

Hahn, Matthew

unread,
Apr 19, 2021, 8:46:51 AM4/19/21
to Giuseppe Andolfo, hahnlab-cafe
Hi Giuseppe,

I’m forwarding your email to the CAFE list, as people there may be able to help with all your questions. 


cheers,
Matt

On Apr 19, 2021, at 7:47 AM, Giuseppe Andolfo <giusepp...@hotmail.com> wrote:


Dear Mett,

I would like to run CAFE with a shell script listing CAFE commands and defoult setting:

python caferror.py -i Ortho-group.tab -d output directory-name -o output_filename

I can't enter my .nwk tree as input.

CAFE prints thi error-message:

Traceback (most recent call last):
  File "cafe/caferror.py", line 420, in <module>
    treestring = Tree[Tree.index("("):];
NameError: name 'Tree' is not defined

Can you help me to fix this problem?
Thanks,

Cheers,

--
Giuseppe



Da: Giuseppe Andolfo <giusepp...@hotmail.com>
Inviato: venerdì 16 aprile 2021 10:53
A: Hahn, Matthew <m...@indiana.edu>
Oggetto: R: CAFE software
 
Dear Matt,

I'm sorry if I still take your time.

After numerous attempts, I managed to recover a phylogenetic tree (.nwk) for my species.
Do I necessarlly have to use an outgroup specie for the contractions/expansions analysis of clades identified in my phylogentic tree of analyzed gene family?

Thanks,

G.




Da: Hahn, Matthew <m...@indiana.edu>
Inviato: giovedì 15 aprile 2021 14:39
A: Giuseppe Andolfo <giusepp...@hotmail.com>
Cc: hahnlab-cafe <hahnl...@googlegroups.com>
Oggetto: Re: CAFE software
 

Gregg Thomas

unread,
Apr 19, 2021, 1:53:27 PM4/19/21
to Hahn, Matthew, Giuseppe Andolfo, hahnlab-cafe
Hi Giuseppe,

Right now it looks like you're trying to provide caferror.py with your gene count data file directly. However, for caferror.py, your input file (-i) should be a shell script that contains the commands for CAFE to run as if you were running it directly. Specifically, it is required that you provide in this file the path to the CAFE executable on the first line (in the form of #!/path/to/cafe), the load command where you provide your gene count data file, the tree command where you provide your Newick formatted tree, and the lambda command (usually just lambda -s). caferror.py reads this info from the file to try different error models on the provided data. However, this file should also be able to be run by itself with CAFE, though this will not estimate error.

An example of such a CAFE input file can be found here: https://iu.app.box.com/v/cafetutorial-files/file/150464938905. So I could give this file as input to caferror.py and it should run (provided I have the data file): caferror.py -i cafetutorial_run1.sh -d caferror-output-dir

You can find more info about the commands (load, tree, lambda, etc.) here: https://github.com/hahnlab/CAFE/blob/master/docs/cafe_manual.pdf .

Please let us know if you need anything else!
-Gregg

--
You received this message because you are subscribed to the Google Groups "hahnlab-cafe" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hahnlabcafe...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/hahnlabcafe/36492EF9-8A41-4453-81BC-2CF982AD91C1%40indiana.edu.

Fulton, Ben

unread,
Apr 26, 2021, 8:25:13 AM4/26/21
to Gregg Thomas, Giuseppe Andolfo, hahnlab-cafe

I’m forwarding your email to the CAFE list, as people there may be able to help with all your questions. 

 

Try running the following:

 

$ make clean

$ ./configure

$ make

 

If that doesn’t work, send the output of those commands.

 

--

Ben Fulton

Research Applications and Deep Learning

Research Technologies

Indiana University

E-Mail: befu...@iu.edu

 

From: Gregg Thomas <greg...@gmail.com>
Sent: Saturday, April 24, 2021 10:37 AM
To: Giuseppe Andolfo <giusepp...@hotmail.com>
Cc: Fulton, Ben <befu...@iu.edu>
Subject: Re: CAFE software

 

Hey Giuseppe,

Since we've hit what appears to be an installation issue I'm forwarding this to Ben Fulton, the lead programmer on CAFE now. He'll be able to help you with this issue more than I can!

 

Ben, the error we're encountering is:

 

:~/Scaricati/CAFE$ make

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/birthdeath.o libtree/birthdeath.c

libtree/birthdeath.c:17:10: fatal error: mkl.h: No such file or directory

 #include "mkl.h"

          ^~~~~~~

compilation terminated.

make: *** [Makefile:107: release/birthdeath.o] Error 1

 

Keep me updated!

-Gregg

 

On Sat, Apr 24, 2021 at 1:03 AM Giuseppe Andolfo <giusepp...@hotmail.com> wrote:

Hi Gregg,

 

unfortunately I am not familiar with anaconda.

 

--

Giuseppe

 

 

 

 

Da: Gregg Thomas <greg...@gmail.com>
Inviato: sabato 24 aprile 2021 01:43


A: Giuseppe Andolfo <giusepp...@hotmail.com>
Oggetto: Re: CAFE software

 

No worries, we can figure this out!

Are you familiar with Anaconda? If so, CAFE is available as a package there (https://anaconda.org/bioconda/cafe). That should make installing pretty easy. If you don't know Anaconda that's ok, just let me know and we'll go from there.

-Gregg

 

On Fri, Apr 23, 2021 at 8:04 AM Giuseppe Andolfo <giusepp...@hotmail.com> wrote:

Caro Gregg,

 

 

I have downloading the version from the following link https://github.com/hahnlab/CAFE/releases/latest.

In this version there is the configuration file, but CAFE installation found a error...

 

 

:~/Scaricati/CAFE$ make

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/birthdeath.o libtree/birthdeath.c

libtree/birthdeath.c:17:10: fatal error: mkl.h: No such file or directory

 #include "mkl.h"

          ^~~~~~~

compilation terminated.

make: *** [Makefile:107: release/birthdeath.o] Error 1

:~/Scaricati/CAFE$

 

It seems like a never ending story.

 

--

Giuseppe

 

 

 

 

Da: Gregg Thomas <greg...@gmail.com>
Inviato: giovedì 22 aprile 2021 20:54


A: Giuseppe Andolfo <giusepp...@hotmail.com>
Oggetto: Re: CAFE software

 

Yup, we'll be able to figure this out! An install issue would certainly be a problem, but let's check some other things first:

 

1) You have your path to cafe set as cafe in the first line of your shell script. This assumes that the cafe executable is in a directory that is in your system path. Can you check if this is true by simply typing cafe into your terminal from any directory and showing me the output? If CAFE starts correctly, you should be taken to the cafe shell, indicated by the # at the beginning of the command prompt. Simply type exit to exit the CAFE shell and return to your regular bash shell. If you get an error that might tell us that something is wrong with the installation!

 

2) Next I would check if your shell script can be run directly with CAFE. You got part of the way there, so let's get the rest of it:

 

    i)   Change directory to the location of your CAFE shell script (Script.sh) and input data file (OGs.txt): cd <directory name>

    ii)  Make the CAFE shell script executable (you already did this I think): chmod +x Script.sh

    iii) Run the shell script: ./Script.sh

 

3) I may not have coded the pathing very well when I wrote caferror, so I think it would be best to have all of caferror.py, your input data file (OGs.txt), and your CAFE shell script (Script.sh) in the same directory. Try moving them all to the same directory and re-running caferror.py.

 

Try these three things and report the outputs to me and that should give us a lot more info about what's going on. If you get an error/unexpected output from any of them, simply report that to me before moving on to the other steps. Hope this helps!

-Gregg

 

On Thu, Apr 22, 2021 at 6:16 AM Giuseppe Andolfo <giusepp...@hotmail.com> wrote:

Gregg,

 

probably, my problem is linked to the compiling.

I move to the CAFE folder, and run 

:$ make

 

It's not ran, becouse...  No target specified and no makefile found.

 

Maybe, now we can do something ... at least I hope so.

 

--

Giuseppe

 

 

 

 

Da: Gregg Thomas <greg...@gmail.com>
Inviato: giovedì 22 aprile 2021 00:52


A: Giuseppe Andolfo <giusepp...@hotmail.com>
Oggetto: Re: CAFE software

 

Yea, if they are in the same directory it should be able to find it. I would need to know more about your file system to fix that. Are you sure caferror.sh is generated in the same folder and not in the data folder? That might mess it up. I can try to recreate this behavior.

What happens when you just run your input script through CAFE directly with chmod +x Script.sh and then source Script.sh . ? Like I said, the error correcting may not be worth it with so few families.

-Gregg

 

On Wed, Apr 21, 2021 at 1:32 AM Giuseppe Andolfo <giusepp...@hotmail.com> wrote:

Hi Gregg,

 

here a screenshot of my shell.

It's included the CAFE's error message. I hope it will be helpful to fix the problem.

 

I'm sorry, I was completely certain that the error message was salved in the output.

It seems that, CAFE does not find cafeeros.sh file, but I can assure you that it is located in the same folder of caferror.py file.

 

Thanks.

--

Giuseppe

 

 

 

 

Da: Gregg Thomas <greg...@gmail.com>
Inviato: mercoledì 21 aprile 2021 06:42


A: Giuseppe Andolfo <giusepp...@hotmail.com>
Oggetto: Re: CAFE software

 

Hi Giuseppe,

How long did caferror.py run? Did any errors print to your screen? My suggestion is to run the input script through CAFE manually (rather than using caferror). This can be done simply by first changing the script to be an executable with chmod +x Script.sh and then executing it with source Script.sh . This will run CAFE without error model estimation and correction. Please do this and tell me what is printed to the screen and/or log file.

 

With so few orthogroups estimating error may be unreliable, so using caferror may be unnecessary. My suggestion is to run it without caferror (as outlined above) and with caferror to see how the results change and if the error estimates are reasonable. Then you can decide whether you want to include the error correction or not.

 

Hope this helps!

-Gregg

 

On Tue, Apr 20, 2021 at 4:55 AM Giuseppe Andolfo <giusepp...@hotmail.com> wrote:

Dear Gregg,

 

 

first of all thank you for your time and support.

I was able to run the analysis with CAFE, but the results file is empty.

Attached are the files I used and the output of analysis.

 

Can you help me to run correctlly CAFE? 

Thank you very much.

 

G.

 

P.S.

Have you any suggestion to set my analysis, on the base of my datset?

I'm analysing the orthogroups of a specific gene family in 4 species.

 

 

 

 

Da: Gregg Thomas <greg...@gmail.com>
Inviato: lunedì 19 aprile 2021 19:52
A: Hahn, Matthew <m...@indiana.edu>
Cc: Giuseppe Andolfo <giusepp...@hotmail.com>; hahnlab-cafe <hahnl...@googlegroups.com>
Oggetto: Re: CAFE software

 

Fulton, Ben

unread,
Apr 26, 2021, 11:23:15 AM4/26/21
to Giuseppe Andolfo, Gregg Thomas, hahnlab-cafe

For some reason the BLAS math library isn’t being found properly. Open the file config.h, and remove the line

 

#define HAVE_BLAS 1

 

Then run

 

$ make clean

$ make

 

That should allow you to compile.

--

Ben Fulton

Research Applications and Deep Learning

Research Technologies

Indiana University

E-Mail: befu...@iu.edu

 

From: Giuseppe Andolfo <giusepp...@hotmail.com>
Sent: Monday, April 26, 2021 10:52 AM
To: Fulton, Ben <befu...@iu.edu>; Gregg Thomas <greg...@gmail.com>; hahnlab-cafe <hahnl...@googlegroups.com>
Subject: R: CAFE software

 

Dear Ben,

 

here is the output of your commands....

 

(base) antimo@antimo-system:~/Scaricati/CAFE$ make clean

rm -f release/cafe release/cafe_family.o release/cafe_main.o release/cafe_report.o release/cafe_tree.o release/cafe_shell.o release/birthdeath.o release/chooseln_cache.o release/phylogeny.o release/tree.o release/grpcmp.o release/histogram.o release/input_values.o release/matrix_exponential.o release/regexpress.o release/utils_string.o release/gmatrix.o release/hashtable.o release/mathfunc.o release/memalloc.o release/utils.o release/branch_cutting.o release/cafe_commands.o release/conditional_distribution.o release/cross_validator.o release/error_model.o release/fminsearch.o release/gene_family.o release/Globals.o release/lambda.o release/lambdamu.o release/log_buffer.o release/reports.o release/likelihood_ratio.o release/pvalue.o release/simerror.o release/viterbi.o debug/cafe debug/cafe_family.o debug/cafe_main.o debug/cafe_report.o debug/cafe_tree.o debug/cafe_shell.o debug/birthdeath.o debug/chooseln_cache.o debug/phylogeny.o debug/tree.o debug/grpcmp.o debug/histogram.o debug/input_values.o debug/matrix_exponential.o debug/regexpress.o debug/utils_string.o debug/gmatrix.o debug/hashtable.o debug/mathfunc.o debug/memalloc.o debug/utils.o debug/branch_cutting.o debug/cafe_commands.o debug/conditional_distribution.o debug/cross_validator.o debug/error_model.o debug/fminsearch.o debug/gene_family.o debug/Globals.o debug/lambda.o debug/lambdamu.o debug/log_buffer.o debug/reports.o debug/likelihood_ratio.o debug/pvalue.o debug/simerror.o debug/viterbi.o test/runtests test/command_tests.o test/error_model_tests.o test/family_tests.o test/lambda_tests.o test/report_tests.o test/test.o test/cafe_family.o test/cafe_main.o test/cafe_report.o test/cafe_tree.o test/cafe_shell.o test/birthdeath.o test/chooseln_cache.o test/phylogeny.o test/tree.o test/grpcmp.o test/histogram.o test/input_values.o test/matrix_exponential.o test/regexpress.o test/utils_string.o test/gmatrix.o test/hashtable.o test/mathfunc.o test/memalloc.o test/utils.o test/branch_cutting.o test/cafe_commands.o test/conditional_distribution.o test/cross_validator.o test/error_model.o test/fminsearch.o test/gene_family.o test/Globals.o test/lambda.o test/lambdamu.o test/log_buffer.o test/reports.o test/likelihood_ratio.o test/pvalue.o test/simerror.o test/viterbi.o debug/main.o release/main.o

(base) antimo@antimo-system:~/Scaricati/CAFE$ ./configure

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether /home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ accepts -g... yes

checking whether we are using the GNU C compiler... yes

checking whether /home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc accepts -g... yes

checking for /home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed

checking for /home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ option to support OpenMP... -fopenmp

checking for library containing sgemm... -lmkl_intel_lp64

checking for library containing cblas_dgemm... no

checking how to run the C++ preprocessor... /home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -E

checking for grep that handles long lines and -e... /bin/grep

checking for egrep... /bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking for dirent.h... yes

checking for ndir.h... no

checking for a readline compatible library... -lreadline

checking readline.h usability... no

checking readline.h presence... no

checking for readline.h... no

checking readline/readline.h usability... yes

checking readline/readline.h presence... yes

checking for readline/readline.h... yes

checking whether readline supports history... yes

checking history.h usability... no

checking history.h presence... no

checking for history.h... no

checking readline/history.h usability... yes

checking readline/history.h presence... yes

checking for readline/history.h... yes

configure: creating ./config.status

config.status: creating Makefile

config.status: creating config.h

config.status: config.h is unchanged

(base) antimo@antimo-system:~/Scaricati/CAFE$ make

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_family.o cafe/cafe_family.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_main.o cafe/cafe_main.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_report.o cafe/cafe_report.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_tree.o cafe/cafe_tree.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_shell.o cafe/cafe_shell.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/birthdeath.o libtree/birthdeath.c

libtree/birthdeath.c:17:10: fatal error: mkl.h: No such file or directory

 #include "mkl.h"

          ^~~~~~~

compilation terminated.

make: *** [Makefile:107: release/birthdeath.o] Error 1

(base) antimo@antimo-system:~/Scaricati/CAFE$

 

 

 

--

Giuseppe 

 

 

 

 

 

Da: Fulton, Ben <befu...@iu.edu>
Inviato: lunedì 26 aprile 2021 14:24
A: Gregg Thomas <greg...@gmail.com>; Giuseppe Andolfo <giusepp...@hotmail.com>; hahnlab-cafe <hahnl...@googlegroups.com>
Oggetto: RE: CAFE software

 

Fulton, Ben

unread,
Apr 27, 2021, 8:17:04 AM4/27/21
to Giuseppe Andolfo, Gregg Thomas, hahnlab-cafe

Wow, the configure failed rather badly at analyzing your system. What OS and version is it? It appears the compiler you’re using comes from Anaconda – how do you have your Conda environment set up? Please send the config.log file that was generated.

 

You can get around the immediate problem by removing the line

 

#define HAVE_LIBREADLINE 1

 

From config.h.

 

--

Ben Fulton

Research Applications and Deep Learning

Research Technologies

Indiana University

E-Mail: befu...@iu.edu

 

From: Giuseppe Andolfo <giusepp...@hotmail.com>
Sent: Tuesday, April 27, 2021 4:12 AM
To: Fulton, Ben <befu...@iu.edu>; Gregg Thomas <greg...@gmail.com>; hahnlab-cafe <hahnl...@googlegroups.com>
Subject: R: CAFE software

 

Dear Ben,

 

here is the new error message:

 

(base) antimo@antimo-system:~/Scaricati/CAFE$ make clean

rm -f release/cafe release/cafe_family.o release/cafe_main.o release/cafe_report.o release/cafe_tree.o release/cafe_shell.o release/birthdeath.o release/chooseln_cache.o release/phylogeny.o release/tree.o release/grpcmp.o release/histogram.o release/input_values.o release/matrix_exponential.o release/regexpress.o release/utils_string.o release/gmatrix.o release/hashtable.o release/mathfunc.o release/memalloc.o release/utils.o release/branch_cutting.o release/cafe_commands.o release/conditional_distribution.o release/cross_validator.o release/error_model.o release/fminsearch.o release/gene_family.o release/Globals.o release/lambda.o release/lambdamu.o release/log_buffer.o release/reports.o release/likelihood_ratio.o release/pvalue.o release/simerror.o release/viterbi.o debug/cafe debug/cafe_family.o debug/cafe_main.o debug/cafe_report.o debug/cafe_tree.o debug/cafe_shell.o debug/birthdeath.o debug/chooseln_cache.o debug/phylogeny.o debug/tree.o debug/grpcmp.o debug/histogram.o debug/input_values.o debug/matrix_exponential.o debug/regexpress.o debug/utils_string.o debug/gmatrix.o debug/hashtable.o debug/mathfunc.o debug/memalloc.o debug/utils.o debug/branch_cutting.o debug/cafe_commands.o debug/conditional_distribution.o debug/cross_validator.o debug/error_model.o debug/fminsearch.o debug/gene_family.o debug/Globals.o debug/lambda.o debug/lambdamu.o debug/log_buffer.o debug/reports.o debug/likelihood_ratio.o debug/pvalue.o debug/simerror.o debug/viterbi.o test/runtests test/command_tests.o test/error_model_tests.o test/family_tests.o test/lambda_tests.o test/report_tests.o test/test.o test/cafe_family.o test/cafe_main.o test/cafe_report.o test/cafe_tree.o test/cafe_shell.o test/birthdeath.o test/chooseln_cache.o test/phylogeny.o test/tree.o test/grpcmp.o test/histogram.o test/input_values.o test/matrix_exponential.o test/regexpress.o test/utils_string.o test/gmatrix.o test/hashtable.o test/mathfunc.o test/memalloc.o test/utils.o test/branch_cutting.o test/cafe_commands.o test/conditional_distribution.o test/cross_validator.o test/error_model.o test/fminsearch.o test/gene_family.o test/Globals.o test/lambda.o test/lambdamu.o test/log_buffer.o test/reports.o test/likelihood_ratio.o test/pvalue.o test/simerror.o test/viterbi.o debug/main.o release/main.o

(base) antimo@antimo-system:~/Scaricati/CAFE$ make

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_family.o cafe/cafe_family.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_main.o cafe/cafe_main.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_report.o cafe/cafe_report.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_tree.o cafe/cafe_tree.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_shell.o cafe/cafe_shell.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/birthdeath.o libtree/birthdeath.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/chooseln_cache.o libtree/chooseln_cache.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/phylogeny.o libtree/phylogeny.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/tree.o libtree/tree.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/grpcmp.o libcommon/grpcmp.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/histogram.o libcommon/histogram.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/input_values.o libtree/input_values.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/matrix_exponential.o libcommon/matrix_exponential.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/regexpress.o libcommon/regexpress.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/utils_string.o libcommon/utils_string.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/gmatrix.o libcommon/gmatrix.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/hashtable.o libcommon/hashtable.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/mathfunc.o libcommon/mathfunc.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/memalloc.o libcommon/memalloc.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc -c -Wall -std=c11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/utils.o libcommon/utils.c

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/branch_cutting.o cafe/branch_cutting.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cafe_commands.o cafe/cafe_commands.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/conditional_distribution.o cafe/conditional_distribution.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/cross_validator.o cafe/cross_validator.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/error_model.o cafe/error_model.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/fminsearch.o libcommon/fminsearch.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/gene_family.o cafe/gene_family.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/Globals.o cafe/Globals.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/lambda.o cafe/lambda.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/lambdamu.o cafe/lambdamu.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/log_buffer.o cafe/log_buffer.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/reports.o cafe/reports.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/likelihood_ratio.o cafe/likelihood_ratio.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/pvalue.o cafe/pvalue.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/simerror.o cafe/simerror.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/viterbi.o cafe/viterbi.cpp

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -c -Wall -std=c++11 -I cafe -I libtree -I libcommon -fopenmp -O3 -DNDEBUG -o release/main.o main.cpp

main.cpp:18:10: fatal error: readline/history.h: No such file or directory

 #include <readline/history.h>

          ^~~~~~~~~~~~~~~~~~~~

compilation terminated.

make: *** [Makefile:113: release/main.o] Error 1

(base) antimo@antimo-system:~/Scaricati/CAFE$

 

 

Thanks for your help.

 

--

Giuseppe

 

 

 

Da: Fulton, Ben <befu...@iu.edu>
Inviato: lunedì 26 aprile 2021 17:22
A: Giuseppe Andolfo <giusepp...@hotmail.com>; Gregg Thomas <greg...@gmail.com>; hahnlab-cafe <hahnl...@googlegroups.com>
Oggetto: RE: CAFE software

 

Fulton, Ben

unread,
Apr 29, 2021, 8:07:59 AM4/29/21
to Giuseppe Andolfo, hahnlab-cafe

Correct.

 

--

Ben Fulton

Research Applications and Deep Learning

Research Technologies

Indiana University

E-Mail: befu...@iu.edu

 

From: Giuseppe Andolfo <giusepp...@hotmail.com>
Sent: Tuesday, April 27, 2021 9:43 AM
To: Fulton, Ben <befu...@iu.edu>

Subject: R: CAFE software

 

Ben, 

here the tree of /home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc

 

I'm sorry but not being a computer scientist, it takes me a while to understand what you are saying.

If I understand correctly, you want me to remove the file config.h, located in the CAFE directory?

 

 

 

--

Andolfo Giuseppe

 

 

 

 

Da: Fulton, Ben <befu...@iu.edu>
Inviato: martedì 27 aprile 2021 15:04
A: Giuseppe Andolfo <giusepp...@hotmail.com>
Oggetto: RE: CAFE software

 

What packages are in your Conda environment that set up the use of

 

/home/antimo/anaconda3/bin/x86_64-conda_cos6-linux-gnu-cc

 

As your C++ compiler?

 

The config log seems to indicate that the readline library is not being found, which contradicts what is in the config.h file. I suspect that ./configure is not overwriting your config.h properly. I would try deleting that file, then make clean, ./configure, and make again.

 

--

Ben Fulton

Research Applications and Deep Learning

Research Technologies

Indiana University

E-Mail: befu...@iu.edu

 

From: Giuseppe Andolfo <giusepp...@hotmail.com>
Sent: Tuesday, April 27, 2021 8:32 AM
To: Fulton, Ben <befu...@iu.edu>

Subject: R: CAFE software

 

Hi Ben,

 

here the config.log file.

 

What OS and version is it?

 

Ubuntu 16.04.4 LTS

 

It appears the compiler you’re using comes from Anaconda – how do you have your Conda environment set up?

 

conda 4.9.2

 

 

I removed #define HAVE_LIBREADLINE 1 from config.h file..., but the problem persists...

Ben, thanks for your help and time...

Giuseppe. 

 

 

 

 

Da: Fulton, Ben <befu...@iu.edu>
Inviato: martedì 27 aprile 2021 14:16

Fulton, Ben

unread,
Apr 30, 2021, 8:07:32 AM4/30/21
to Giuseppe Andolfo, hahnlab-cafe

I’m out of ideas. You might be able to modify config.h and remove the line

 

#define HAVE_READLINE_HISTORY_H 1

 

But that will likely lead to another configuration problem. If that doesn’t work, my suggestions would be, in order:

 

* Delete the entire CAFE directory, download it again, and start over;

* Uninstall Conda;

* Upgrade your operating system to Ubuntu 18 or Ubuntu 20.

 

--

Ben Fulton

Research Applications and Deep Learning

Research Technologies

Indiana University

E-Mail: befu...@iu.edu

 

From: Giuseppe Andolfo <giusepp...@hotmail.com>
Sent: Friday, April 30, 2021 3:13 AM
To: Fulton, Ben <befu...@iu.edu>; hahnlab-cafe <hahnl...@googlegroups.com>
Subject: R: CAFE software

 

Hi Ben,

 

here the usual error message

 

what do we do?

Thanks.

 

--

Giuseppe

 

 

 

Da: Fulton, Ben <befu...@iu.edu>
Inviato: giovedì 29 aprile 2021 14:07
A: Giuseppe Andolfo <giusepp...@hotmail.com>; hahnlab-cafe <hahnl...@googlegroups.com>
Oggetto: RE: CAFE software

 

Gregg Thomas

unread,
Apr 30, 2021, 12:22:22 PM4/30/21
to Fulton, Ben, Giuseppe Andolfo, hahnlab-cafe
Since they have conda installed, would it make sense for them to try installing through the conda package? https://anaconda.org/bioconda/cafe
This has worked for me in the past.
-Gregg

To view this discussion on the web visit https://groups.google.com/d/msgid/hahnlabcafe/DM5PR0801MB3703A705567E0F159AA73F23B15E9%40DM5PR0801MB3703.namprd08.prod.outlook.com.

Dan Vanderpool

unread,
Apr 30, 2021, 4:13:26 PM4/30/21
to Gregg Thomas, Fulton, Ben, Giuseppe Andolfo, hahnlab-cafe
Yeah, that would probably work.  Also, if you run “find” for the missing libraries across the system, do they exist?  I am guessing your conda install of the compiler might not have the right "include” paths specified.  If you find the libraries  you can add the path to the make file with the -I flag.  I have had to do this building with conda installs.

dv


__________________________
Dan Vanderpool
Postdoctoral Scholar
Department of Biology
Indiana University
Hahn Lab, Jordan Hall 249B
1001 East Third Street
Bloomington, IN 47405
Email: ddvand...@gmail.com

Reply all
Reply to author
Forward
0 new messages