Hi,
I am trying to run Metawatt in MacOS X 10.6.8, but I have some dependency errors.
"Dependency problems:
Blast: ERROR (No annotation possible)
Glimer: ERROR (No IMM/final binning possible)
Batik: OK"
I am sure that I installed the latest version of BLAST+, it is in the PATH, and it works fine. Is there an option to specify the path in case this error appears?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Lizbeth,
MacOS is experimental for me - I never tested it on this platform.
What is the output when you type "blastn -h" in a terminal/commandline?
Marc
Lizbeth Sayavedra wrote:
Hi,
I am trying to run Metawatt in MacOS X 10.6.8, but I have some
dependency errors.
"Dependency problems:
Blast: ERROR (No annotation possible)
Glimer: ERROR (No IMM/final binning possible)
Batik: OK"
I am sure that I installed the latest version of BLAST+, it is in the
PATH, and it works fine. Is there an option to specify the path in
case this error appears?
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Lizbeth,
the output shows that indeed blast is working and that the arguments are
the same as for unix. This means the problem is (a) either in java not
finding the path or (b) IOS does not like the way Metawatt calls the
blast. I would very much like to solve this problem but I do not have a
mac. What would be possible is if you would install netbeans
(http://netbeans.org/downloads/), a java programming environment, and
let me work on your mac for a few hours I should be able to solve the
problem and then we can make the program compatible to IOS.
Would that work for you?
Best wishes,
Marc
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I am trying to run Metawatt in Ubuntu 10.04, but I have some dependency errors.
"Dependency problems:
Blast: ERROR (No annotation possible)
Glimer: ERROR (No IMM/final binning possible)
Batik: OK"
I am sure that I installed the latest version of BLAST+, it is in the PATH, and it works fine, the same for Glimmer3. I also tried specifying where to find them as >java -jar path/to/jar/metawatt.jar -blast=/PATH/TO/BLAST/PROGRAMS -glimmer=/PATH/TO/GLIMMER, but it is not working...
Could you give me any advise of how to solve that problem?
Many thanks in advance!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Ana,
Thanks for your interest in metwatt...
(1) What version did you download?
(2) could you write exactly what you typed, eg:
java -jar path/to/jar/metawatt.jar ...
(3) What is output when you type ">blastn -h"
Best wishes,
Marc
Ana Suárez wrote:
Hello Marc,
I am trying to run Metawatt in Ubuntu 10.04, but I have some
dependency errors.
"Dependency problems:
Blast: ERROR (No annotation possible)
Glimer: ERROR (No IMM/final binning possible)
Batik: OK"
I am sure that I installed the latest version of BLAST+, it is in the
PATH, and it works fine, the same for Glimmer3. I also tried
specifying where to find them as >java -jar path/to/jar/metawatt.jar
-blast=/PATH/TO/BLAST/PROGRAMS -glimmer=/PATH/TO/GLIMMER, but it is
not working...
Could you give me any advise of how to solve that problem?
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I tried what you suggested but I get the same error. Here a copy of how I entered it and the output I got at the terminal.
ana@dell:~$ java -jar /home/ana/Programas/Metawatt.1.5/metawatt.jar -blast=/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin -glimmer=/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin
This is Metawatt version 1.4
Logging to /home/ana/metawatt.logbook.txt
added Compute N4 frequencies at 1
added Annotate at 7
added Bin with tetranucleotides at 9
added Bin with Markov models at 16
SST
Metawatt [INFO|6:29:19] /home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h
Metawatt [INFO|6:29:19] makeblastdb -h
Metawatt [INFO|6:29:19] simple-score -h
Dear Ana,
No the 1.4 is not relevant - I forgot to update this for version 1.5, but
its no problem.
From the output I see that the line is still not totally correct, there is
a space between the "-" and "glimmer", remove the space, this may help for
the glimmer dependency. For the blast dependency, quite frankly, I am
clueless, and it is difficult to say what exactly goes wrong. How did you
set the path, did you set it in the terminal or did you add it in your
.profile or whatever file? Somehow, Java encounters a problem when it
executes an external program on your system, it seems that it can still not
execute blast even though you can execute it on the command line. Could it
be a typo? What happens when you type
"/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h" on the
command line? Could it be the "+" in the path to blast? Are the blast
programs flagged executable?
In the next version I will add more code to report what exactly goes wrong
in your case.
I tried what you suggested but I get the same error. Here a copy of how I
entered it and the output I got at the terminal.
ana@dell:~$ java -jar /home/ana/Programas/Metawatt.1.5/metawatt.jar
-blast=/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin
-glimmer=/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin
This is Metawatt version 1.4
Logging to /home/ana/metawatt.logbook.txt
added Compute N4 frequencies at 1
added Annotate at 7
added Bin with tetranucleotides at 9
added Bin with Markov models at 16
SST
Metawatt [INFO|6:29:19]
/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h
Metawatt [INFO|6:29:19] makeblastdb -h
Metawatt [INFO|6:29:19] simple-score -h
I was checking the line but I could not find the space between “-” and glimmer.
I had created a short-cut (by ln -s) to blastn that was working properly. I also tried adding the directories to glimmer and blastn to the PATH by editing my .bashrc and I checked that everything worked well by:
ana@dell:~$ echo $PATH
/home/ana/Programas/arb/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/ana/Programas:/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin:/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27/bin
Wait one second: metawatt also requires "makeblastdb", so you should
also link (ln) makeblastdb, like you did for blast.
The reason I think there was a space between - and glimmer is the output
you sent me yesterday:
ana@dell:~$ java -jar /home/ana/Programas/Metawatt.1.5/metawatt.jar
-blast=/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin
-glimmer=/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin
This is Metawatt version 1.4
Logging to /home/ana/metawatt.logbook.txt
added Compute N4 frequencies at 1
added Annotate at 7
added Bin with tetranucleotides at 9
added Bin with Markov models at 16
SST
Metawatt [INFO|6:29:19]http://sourceforge.net/../INFO%7C6:29:19
/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h
Metawatt [INFO|6:29:19]http://sourceforge.net/../INFO%7C6:29:19
makeblastdb -h
Metawatt [INFO|6:29:19]http://sourceforge.net/../INFO%7C6:29:19
simple-score -h
You see that it accepted your path to blast because it correctly calls
"/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h".
However, for the glimmer program it did not accept the path you
specified. It called "simple-score -h" but it should have called
"/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin/simple-score -h"
I arranged an Ubuntu 10 system for tomorrow so that I can check your
problem... myself, I'm working on arch linux.
Thanks for your perseverance!
Marc
Ana Suárez wrote:
Hi Marc,
I was checking the line but I could not find the space between “-” and
glimmer.
I had created a short-cut (by ln -s) to blastn that was working
properly. I also tried adding the directories to glimmer and blastn to
the PATH by editing my .bashrc and I checked that everything worked
well by:
ana@dell:~$ echo $PATH
/home/ana/Programas/arb/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/ana/Programas:/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin:/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27/bin
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I am trying to run Metawatt in MacOS X 10.6.8, but I have some dependency errors.
"Dependency problems:
Blast: ERROR (No annotation possible)
Glimer: ERROR (No IMM/final binning possible)
Batik: OK"
I am sure that I installed the latest version of BLAST+, it is in the PATH, and it works fine. Is there an option to specify the path in case this error appears?
Dear Lizbeth,
MacOS is experimental for me - I never tested it on this platform.
What is the output when you type "blastn -h" in a terminal/commandline?
Marc
Lizbeth Sayavedra wrote:
--
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de
http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
$ blastn -h
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-negative_gilist filename]
[-mask_subjects filtering_algorithms] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-perc_identity float_value]
[-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value] [-penalty penalty]
[-reward reward] [-no_greedy] [-min_raw_gapped_score int_value]
[-template_type type] [-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-window_size int_value]
[-use_index boolean] [-index_name string] [-lcase_masking]
[-query_loc range] [-parse_deflines] [-strand strand] [-outfmt format]
[-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
[-html] [-max_target_seqs num_sequences] [-num_threads int_value]
[-remote] [-version]
DESCRIPTION
Nucleotide-Nucleotide BLAST 2.2.18+
Use '-help' to print detailed descriptions of command line arguments
Dear Lizbeth,
the output shows that indeed blast is working and that the arguments are
the same as for unix. This means the problem is (a) either in java not
finding the path or (b) IOS does not like the way Metawatt calls the
blast. I would very much like to solve this problem but I do not have a
mac. What would be possible is if you would install netbeans
(http://netbeans.org/downloads/), a java programming environment, and
let me work on your mac for a few hours I should be able to solve the
problem and then we can make the program compatible to IOS.
Would that work for you?
Best wishes,
Marc
Lizbeth Sayavedra wrote:
--
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de
http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
Dear Marc,
Sounds great! I already installed the NetBeans.
Best,
Lizbeth
Would tomorrow morning be ok for you?
Marc
Lizbeth Sayavedra wrote:
--
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de
http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
Hello Marc,
I am trying to run Metawatt in Ubuntu 10.04, but I have some dependency errors.
"Dependency problems:
Blast: ERROR (No annotation possible)
Glimer: ERROR (No IMM/final binning possible)
Batik: OK"
I am sure that I installed the latest version of BLAST+, it is in the PATH, and it works fine, the same for Glimmer3. I also tried specifying where to find them as >java -jar path/to/jar/metawatt.jar -blast=/PATH/TO/BLAST/PROGRAMS -glimmer=/PATH/TO/GLIMMER, but it is not working...
Could you give me any advise of how to solve that problem?
Many thanks in advance!
Dear Ana,
Thanks for your interest in metwatt...
(1) What version did you download?
(2) could you write exactly what you typed, eg:
Best wishes,
Marc
Ana Suárez wrote:
--
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de
http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
Hi Marc,
Many thanks for the fast replay! Sorry for the double mail, I had not seen your answer here..
I downloaded Metawatt 1.5.
I type:
Here the >blastn -h output:
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-entrez_query entrez_query]
[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
[-subject subject_input_file] [-subject_loc range] [-query input_file]
[-out output_file] [-evalue evalue] [-word_size int_value]
[-gapopen open_penalty] [-gapextend extend_penalty]
[-perc_identity float_value] [-xdrop_ungap float_value]
[-xdrop_gap float_value] [-xdrop_gap_final float_value]
[-searchsp int_value] [-max_hsps_per_subject int_value] [-penalty penalty]
[-reward reward] [-no_greedy] [-min_raw_gapped_score int_value]
[-template_type type] [-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-remote] [-version]
DESCRIPTION
Nucleotide-Nucleotide BLAST 2.2.27+
Dear Ana,
try:
java -jar /home/ana/Programas/Metawat.1.5/metawatt.jar
-blast=/home/ana/Programas/Metawat.1.5/ncbi-blast-2.2.27+/bin
-glimmer=home/ana/Programas/Metawat.1.5/glimmer3.02/bin
(you need to provide the folder that contains the blast programs and the
folder that contains the glimmer programs)
Let me know if it works!
Best wishes,
Marc
Ana Suárez wrote:
--
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de
http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center
Hi Marc,
I tried what you suggested but I get the same error. Here a copy of how I entered it and the output I got at the terminal.
ana@dell:~$ java -jar /home/ana/Programas/Metawatt.1.5/metawatt.jar -blast=/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin -glimmer=/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin
This is Metawatt version 1.4
Logging to /home/ana/metawatt.logbook.txt
added Compute N4 frequencies at 1
added Annotate at 7
added Bin with tetranucleotides at 9
added Bin with Markov models at 16
SST
Metawatt [INFO|6:29:19] /home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h
Metawatt [INFO|6:29:19] makeblastdb -h
Metawatt [INFO|6:29:19] simple-score -h
I had downloaded the last version (1.5) at https://sourceforge.net/projects/metawatt/, but now it says that it is the 1.4. Could that be relevant somehow?
Best regards,
Ana
Last edit: Ana Suárez 2013-01-21
Dear Ana,
No the 1.4 is not relevant - I forgot to update this for version 1.5, but
its no problem.
From the output I see that the line is still not totally correct, there is
a space between the "-" and "glimmer", remove the space, this may help for
the glimmer dependency. For the blast dependency, quite frankly, I am
clueless, and it is difficult to say what exactly goes wrong. How did you
set the path, did you set it in the terminal or did you add it in your
.profile or whatever file? Somehow, Java encounters a problem when it
executes an external program on your system, it seems that it can still not
execute blast even though you can execute it on the command line. Could it
be a typo? What happens when you type
"/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h" on the
command line? Could it be the "+" in the path to blast? Are the blast
programs flagged executable?
In the next version I will add more code to report what exactly goes wrong
in your case.
Best wishes,
Marc
On Mon, 21 Jan 2013 17:34:51 +0000, "Ana Suárez" anasuarez@users.sf.net
wrote:
Hi Marc,
I was checking the line but I could not find the space between “-” and glimmer.
I had created a short-cut (by ln -s) to blastn that was working properly. I also tried adding the directories to glimmer and blastn to the PATH by editing my .bashrc and I checked that everything worked well by:
ana@dell:~$ echo $PATH
/home/ana/Programas/arb/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/home/ana/Programas:/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin:/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27/bin
I also removed symbols as + just in case...
Here the output from
ana@dell:~$ /home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27/bin/blastn -h
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-entrez_query entrez_query]
[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
[-subject subject_input_file] [-subject_loc range] [-query input_file]
[-out output_file] [-evalue evalue] [-word_size int_value]
[-gapopen open_penalty] [-gapextend extend_penalty]
[-perc_identity float_value] [-xdrop_ungap float_value]
[-xdrop_gap float_value] [-xdrop_gap_final float_value]
[-searchsp int_value] [-max_hsps_per_subject int_value] [-penalty penalty]
[-reward reward] [-no_greedy] [-min_raw_gapped_score int_value]
[-template_type type] [-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-remote] [-version]
DESCRIPTION
Nucleotide-Nucleotide BLAST 2.2.27+
I had been reviewing all the steps with other colleages with more experience in installation but we did not find any clue neither.
Do you know about other Ubuntu 10.04 users that were able to run it succesfully? Could I ask under which Linux SO are you running it?
Many thanks for your help. I hope we can find a solution because I am really looking forward to test it with my samples!!
Best,
Ana
Dear Ana,
Wait one second: metawatt also requires "makeblastdb", so you should
also link (ln) makeblastdb, like you did for blast.
The reason I think there was a space between - and glimmer is the output
you sent me yesterday:
ana@dell:~$ java -jar /home/ana/Programas/Metawatt.1.5/metawatt.jar
-blast=/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin
-glimmer=/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin
This is Metawatt version 1.4
Logging to /home/ana/metawatt.logbook.txt
added Compute N4 frequencies at 1
added Annotate at 7
added Bin with tetranucleotides at 9
added Bin with Markov models at 16
SST
Metawatt [INFO|6:29:19] http://sourceforge.net/../INFO%7C6:29:19
/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h
Metawatt [INFO|6:29:19] http://sourceforge.net/../INFO%7C6:29:19
makeblastdb -h
Metawatt [INFO|6:29:19] http://sourceforge.net/../INFO%7C6:29:19
simple-score -h
You see that it accepted your path to blast because it correctly calls
"/home/ana/Programas/Metawatt.1.5/ncbi-blast-2.2.27+/bin/blastn -h".
However, for the glimmer program it did not accept the path you
specified. It called "simple-score -h" but it should have called
"/home/ana/Programas/Metawatt.1.5/glimmer3.02/bin/simple-score -h"
I arranged an Ubuntu 10 system for tomorrow so that I can check your
problem... myself, I'm working on arch linux.
Thanks for your perseverance!
Marc
Ana Suárez wrote:
--
Prof. dr. ir. Marc Strous
Leader of the Max Planck Research Group "Microbial Fitness"
MPI for Marine Microbiology
28359 Bremen
Germany
mstrous@mpi-bremen.de
http://www.mpi-bremen.de/en/Microbial_Fitness.html
phone +49 421 20 28 822
fax +49 421 20 28 580
Professor of Sustainable Energy Production
Center for Biotechnology (CeBiTec)
University of Bielefeld
Professor of Fundamental Microbiology
Radboud University Medical Center