From carsonhh at gmail.com Fri Nov 2 11:56:35 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 10:56:35 -0600 Subject: [maker-devel] MAKER not running properly after installation, help needed In-Reply-To: References: Message-ID: Hi Nikolay, If you can provide the exact error, that would allow me to know more of what you are seeing. Normally the system perl should be fine (you can check the perl version using 'perl -v' on the command line). There was an issue with forks.pm that I believe the authors have fixed by now if you update to the latest version (more info here ?> https://groups.google.com/forum/#!msg/maker-devel/2kYQ90TCuXA/FxPaM45YGdoJ ). Also updarte to the current CPAN version of BioPerl if there are doubts about that. ?Caerson > On Oct 31, 2018, at 8:27 AM, Nikolay Alabi <17na34 at queensu.ca> wrote: > > Hello, > > I am attempting to annotate a garlic mustard genome using maker on a cluster at Queen?s University. I have been following the tutorial on wiki and was attempting to use the practice data to see if the program is running properly and to learn how to train the gene predicting system. Maker is now installed and is working to an extent, however when in use it is not working properly and cannot read/annotate a genome. I suspect two problems that is causing this to occur, first, anytime any maker command is called, it shows that an argument in forks.pm in perl5 is not correct, after trying to fix the problem, I see that the code should be correct, but the error line still occurs. Then every time a maker command Is called another error saying there is an error flow occurring somewhere in perl again. For instance when I command: maker -h, or maker -CTL or anything to do with maker, the error lines occur. Would you advise me to reinstall perl and bioperl? Other than that I believe everything else is properly installed and I do not understand why the program is not running properly. I have even tried using different data genomes, however the same problem occurs of the run never finishing, then retrying, and ultimately failing. Please let me know if there is another possible source of error in the problem. > > Best regards, Nikolay > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 12:06:59 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 11:06:59 -0600 Subject: [maker-devel] Issue with maker In-Reply-To: References: Message-ID: Try updating BioPerl. This is caused by an attempt to improve certain indexing performance in BioPerl by using C code that compiles on the fly during runtime. It?s semi-unstable and really needs to be removed from BioPerl especially since a simple perl translation operator (tr///d) already fixed the need for the performance change anyways. Caused by lines 249-273 in this BioPerl code ?> https://github.com/bioperl/bioperl-live/blob/master/lib/Bio/DB/IndexedBase.pm Alternatively edit the file in BioPerl and comment out lines 249-273 yourself with ?#? signs (also get the trailing bracket on line 280). ?Carson > On Oct 25, 2018, at 3:22 PM, Pallavi Gupta wrote: > > Hi Team MAKER, > > I am using maker for my research for genome annotation process. But when I run maker I am getting a weird error. I tried finding a work around on the internet by scrolling through various bioinformatics forum but I was unsuccessful. I will really appreciate if you can help me in this regard. I have attached my nohup.out log. Please let me know if you need anything else. > > Thanks, > Pallavi Gupta > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 12:18:52 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 11:18:52 -0600 Subject: [maker-devel] Problem compiling MAKER with Intel MPI In-Reply-To: References: Message-ID: <2D4E1EFA-CE98-4FC2-B65E-81E0D7911E3A@gmail.com> The problem is your perl perl installation. It?s broken. I?m guessing it?s a version installed by conda? The sys/types.h file is internal to perl itself (and will be bound to the version of perl you are using - i.e. don?t use sys/types.h from a different perl version). It?s used to map datatypes between perl and C. If you search /powerapps/share/centos7/miniconda/ you may be able to find it somewhere internally. You may be able to set it with C_INCLUDE_PATH or CPLUS_INCLUDE_PATH once you find it . There may be other environmental variables that must be set as well. The line inside the C code perl is running internally is something like ?#include?, so make sure the path you give to C_INCLUDE_PATH is the directory right before the /sys folder. Alternatively you may need to do this outside of conda. ?Carson > On Oct 17, 2018, at 8:27 AM, Lior Glick wrote: > > Hello, > I am trying to compile MAKER with Intel MPI. > We are using a cluster based on Intel x86_64 architecture and using lmod for environment variables. > All required dependencies have already been installed and the initial 'perl Build.PL' passes without issues (see attached). > When running './Build install' it always fails to find 'sys/types.h' and exits (see additional attachment). > The Build command probably searches for the '/usr/include/sys/types.h' file, but no matter which variable (INCLUDE, PERL5LIB etc...) I update with the required path (either '/usr/include' or '/usr/include/sys') - it keeps failing. > I would appreciate your input. > Thanks a lot! > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From 17na34 at queensu.ca Mon Nov 5 11:34:06 2018 From: 17na34 at queensu.ca (Nikolay Alabi) Date: Mon, 5 Nov 2018 17:34:06 +0000 Subject: [maker-devel] fasta_merge and gff3_merge commands not working Message-ID: Is there any prerequisites I must adhere to ensure the commands gff3_merge and fasta_merge work. I was following the Wiki tutorial and when I wanted to execute the commands in the data directory in order to make a clean out version of the files for later use, the computer did not recognize the commands. Please help. Thanks, Nikolay -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 14 13:35:52 2018 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 14 Nov 2018 12:35:52 -0700 Subject: [maker-devel] fasta_merge and gff3_merge commands not working In-Reply-To: References: Message-ID: Sorry for the slow reply. If you put ?/maker/bin in your PATH environmental variable, then all MAKER executables can be executed directly without having to call the full path. This is covered in the MAKER install instructions. You can learn more about PATH here ?> https://opensource.com/article/17/6/set-path-linux ?Carson > On Nov 5, 2018, at 10:34 AM, Nikolay Alabi <17na34 at queensu.ca> wrote: > > Is there any prerequisites I must adhere to ensure the commands gff3_merge and fasta_merge work. I was following the Wiki tutorial and when I wanted to execute the commands in the data directory in order to make a clean out version of the files for later use, the computer did not recognize the commands. Please help. > > Thanks, Nikolay -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytshen at genetics.ac.cn Thu Nov 29 21:24:48 2018 From: ytshen at genetics.ac.cn (ytshen at genetics.ac.cn) Date: Fri, 30 Nov 2018 11:24:48 +0800 Subject: [maker-devel] RNA-seq gff file cause MAKER running arrest Message-ID: <2018113011234848442023@genetics.ac.cn> Dears, I am trying to run MAKER for a plant genome and want to use RNA-seq information for my annotation. For this purpose, I alignment RNA-seq reads to my genome by using Hisat2 and assemble transcripts by using Stringtie, and transfer the Stringtie gtf output file into gff file by using Cufflinks2gff script provided by MAKER (ver 2.31.10). When I set the gff file as est_gff in maker_opts.ctl file, the MAKER running will stop at some point, but it didn't provide any error or warning information and also didn't exist. But when I transfer the gff file into fasta file, and set it as est_fasta in maker_opts.ctl file, the MAKER can run successfully. Has this phenomenon happened to someone else? How I can fix it? Hope your reply! Thank you very much! Best! Sinceraly, Yanting ??? ???????????????? ???010-64801362 ?????????????1?? ???100101 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 10:56:35 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 10:56:35 -0600 Subject: [maker-devel] MAKER not running properly after installation, help needed In-Reply-To: References: Message-ID: Hi Nikolay, If you can provide the exact error, that would allow me to know more of what you are seeing. Normally the system perl should be fine (you can check the perl version using 'perl -v' on the command line). There was an issue with forks.pm that I believe the authors have fixed by now if you update to the latest version (more info here ?> https://groups.google.com/forum/#!msg/maker-devel/2kYQ90TCuXA/FxPaM45YGdoJ ). Also updarte to the current CPAN version of BioPerl if there are doubts about that. ?Caerson > On Oct 31, 2018, at 8:27 AM, Nikolay Alabi <17na34 at queensu.ca> wrote: > > Hello, > > I am attempting to annotate a garlic mustard genome using maker on a cluster at Queen?s University. I have been following the tutorial on wiki and was attempting to use the practice data to see if the program is running properly and to learn how to train the gene predicting system. Maker is now installed and is working to an extent, however when in use it is not working properly and cannot read/annotate a genome. I suspect two problems that is causing this to occur, first, anytime any maker command is called, it shows that an argument in forks.pm in perl5 is not correct, after trying to fix the problem, I see that the code should be correct, but the error line still occurs. Then every time a maker command Is called another error saying there is an error flow occurring somewhere in perl again. For instance when I command: maker -h, or maker -CTL or anything to do with maker, the error lines occur. Would you advise me to reinstall perl and bioperl? Other than that I believe everything else is properly installed and I do not understand why the program is not running properly. I have even tried using different data genomes, however the same problem occurs of the run never finishing, then retrying, and ultimately failing. Please let me know if there is another possible source of error in the problem. > > Best regards, Nikolay > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 11:06:59 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 11:06:59 -0600 Subject: [maker-devel] Issue with maker In-Reply-To: References: Message-ID: Try updating BioPerl. This is caused by an attempt to improve certain indexing performance in BioPerl by using C code that compiles on the fly during runtime. It?s semi-unstable and really needs to be removed from BioPerl especially since a simple perl translation operator (tr///d) already fixed the need for the performance change anyways. Caused by lines 249-273 in this BioPerl code ?> https://github.com/bioperl/bioperl-live/blob/master/lib/Bio/DB/IndexedBase.pm Alternatively edit the file in BioPerl and comment out lines 249-273 yourself with ?#? signs (also get the trailing bracket on line 280). ?Carson > On Oct 25, 2018, at 3:22 PM, Pallavi Gupta wrote: > > Hi Team MAKER, > > I am using maker for my research for genome annotation process. But when I run maker I am getting a weird error. I tried finding a work around on the internet by scrolling through various bioinformatics forum but I was unsuccessful. I will really appreciate if you can help me in this regard. I have attached my nohup.out log. Please let me know if you need anything else. > > Thanks, > Pallavi Gupta > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 11:18:52 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 11:18:52 -0600 Subject: [maker-devel] Problem compiling MAKER with Intel MPI In-Reply-To: References: Message-ID: <2D4E1EFA-CE98-4FC2-B65E-81E0D7911E3A@gmail.com> The problem is your perl perl installation. It?s broken. I?m guessing it?s a version installed by conda? The sys/types.h file is internal to perl itself (and will be bound to the version of perl you are using - i.e. don?t use sys/types.h from a different perl version). It?s used to map datatypes between perl and C. If you search /powerapps/share/centos7/miniconda/ you may be able to find it somewhere internally. You may be able to set it with C_INCLUDE_PATH or CPLUS_INCLUDE_PATH once you find it . There may be other environmental variables that must be set as well. The line inside the C code perl is running internally is something like ?#include?, so make sure the path you give to C_INCLUDE_PATH is the directory right before the /sys folder. Alternatively you may need to do this outside of conda. ?Carson > On Oct 17, 2018, at 8:27 AM, Lior Glick wrote: > > Hello, > I am trying to compile MAKER with Intel MPI. > We are using a cluster based on Intel x86_64 architecture and using lmod for environment variables. > All required dependencies have already been installed and the initial 'perl Build.PL' passes without issues (see attached). > When running './Build install' it always fails to find 'sys/types.h' and exits (see additional attachment). > The Build command probably searches for the '/usr/include/sys/types.h' file, but no matter which variable (INCLUDE, PERL5LIB etc...) I update with the required path (either '/usr/include' or '/usr/include/sys') - it keeps failing. > I would appreciate your input. > Thanks a lot! > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From 17na34 at queensu.ca Mon Nov 5 10:34:06 2018 From: 17na34 at queensu.ca (Nikolay Alabi) Date: Mon, 5 Nov 2018 17:34:06 +0000 Subject: [maker-devel] fasta_merge and gff3_merge commands not working Message-ID: Is there any prerequisites I must adhere to ensure the commands gff3_merge and fasta_merge work. I was following the Wiki tutorial and when I wanted to execute the commands in the data directory in order to make a clean out version of the files for later use, the computer did not recognize the commands. Please help. Thanks, Nikolay -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 14 12:35:52 2018 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 14 Nov 2018 12:35:52 -0700 Subject: [maker-devel] fasta_merge and gff3_merge commands not working In-Reply-To: References: Message-ID: Sorry for the slow reply. If you put ?/maker/bin in your PATH environmental variable, then all MAKER executables can be executed directly without having to call the full path. This is covered in the MAKER install instructions. You can learn more about PATH here ?> https://opensource.com/article/17/6/set-path-linux ?Carson > On Nov 5, 2018, at 10:34 AM, Nikolay Alabi <17na34 at queensu.ca> wrote: > > Is there any prerequisites I must adhere to ensure the commands gff3_merge and fasta_merge work. I was following the Wiki tutorial and when I wanted to execute the commands in the data directory in order to make a clean out version of the files for later use, the computer did not recognize the commands. Please help. > > Thanks, Nikolay -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytshen at genetics.ac.cn Thu Nov 29 20:24:48 2018 From: ytshen at genetics.ac.cn (ytshen at genetics.ac.cn) Date: Fri, 30 Nov 2018 11:24:48 +0800 Subject: [maker-devel] RNA-seq gff file cause MAKER running arrest Message-ID: <2018113011234848442023@genetics.ac.cn> Dears, I am trying to run MAKER for a plant genome and want to use RNA-seq information for my annotation. For this purpose, I alignment RNA-seq reads to my genome by using Hisat2 and assemble transcripts by using Stringtie, and transfer the Stringtie gtf output file into gff file by using Cufflinks2gff script provided by MAKER (ver 2.31.10). When I set the gff file as est_gff in maker_opts.ctl file, the MAKER running will stop at some point, but it didn't provide any error or warning information and also didn't exist. But when I transfer the gff file into fasta file, and set it as est_fasta in maker_opts.ctl file, the MAKER can run successfully. Has this phenomenon happened to someone else? How I can fix it? Hope your reply! Thank you very much! Best! Sinceraly, Yanting ??? ???????????????? ???010-64801362 ?????????????1?? ???100101 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 10:56:35 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 10:56:35 -0600 Subject: [maker-devel] MAKER not running properly after installation, help needed In-Reply-To: References: Message-ID: Hi Nikolay, If you can provide the exact error, that would allow me to know more of what you are seeing. Normally the system perl should be fine (you can check the perl version using 'perl -v' on the command line). There was an issue with forks.pm that I believe the authors have fixed by now if you update to the latest version (more info here ?> https://groups.google.com/forum/#!msg/maker-devel/2kYQ90TCuXA/FxPaM45YGdoJ ). Also updarte to the current CPAN version of BioPerl if there are doubts about that. ?Caerson > On Oct 31, 2018, at 8:27 AM, Nikolay Alabi <17na34 at queensu.ca> wrote: > > Hello, > > I am attempting to annotate a garlic mustard genome using maker on a cluster at Queen?s University. I have been following the tutorial on wiki and was attempting to use the practice data to see if the program is running properly and to learn how to train the gene predicting system. Maker is now installed and is working to an extent, however when in use it is not working properly and cannot read/annotate a genome. I suspect two problems that is causing this to occur, first, anytime any maker command is called, it shows that an argument in forks.pm in perl5 is not correct, after trying to fix the problem, I see that the code should be correct, but the error line still occurs. Then every time a maker command Is called another error saying there is an error flow occurring somewhere in perl again. For instance when I command: maker -h, or maker -CTL or anything to do with maker, the error lines occur. Would you advise me to reinstall perl and bioperl? Other than that I believe everything else is properly installed and I do not understand why the program is not running properly. I have even tried using different data genomes, however the same problem occurs of the run never finishing, then retrying, and ultimately failing. Please let me know if there is another possible source of error in the problem. > > Best regards, Nikolay > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 11:06:59 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 11:06:59 -0600 Subject: [maker-devel] Issue with maker In-Reply-To: References: Message-ID: Try updating BioPerl. This is caused by an attempt to improve certain indexing performance in BioPerl by using C code that compiles on the fly during runtime. It?s semi-unstable and really needs to be removed from BioPerl especially since a simple perl translation operator (tr///d) already fixed the need for the performance change anyways. Caused by lines 249-273 in this BioPerl code ?> https://github.com/bioperl/bioperl-live/blob/master/lib/Bio/DB/IndexedBase.pm Alternatively edit the file in BioPerl and comment out lines 249-273 yourself with ?#? signs (also get the trailing bracket on line 280). ?Carson > On Oct 25, 2018, at 3:22 PM, Pallavi Gupta wrote: > > Hi Team MAKER, > > I am using maker for my research for genome annotation process. But when I run maker I am getting a weird error. I tried finding a work around on the internet by scrolling through various bioinformatics forum but I was unsuccessful. I will really appreciate if you can help me in this regard. I have attached my nohup.out log. Please let me know if you need anything else. > > Thanks, > Pallavi Gupta > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 11:18:52 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 11:18:52 -0600 Subject: [maker-devel] Problem compiling MAKER with Intel MPI In-Reply-To: References: Message-ID: <2D4E1EFA-CE98-4FC2-B65E-81E0D7911E3A@gmail.com> The problem is your perl perl installation. It?s broken. I?m guessing it?s a version installed by conda? The sys/types.h file is internal to perl itself (and will be bound to the version of perl you are using - i.e. don?t use sys/types.h from a different perl version). It?s used to map datatypes between perl and C. If you search /powerapps/share/centos7/miniconda/ you may be able to find it somewhere internally. You may be able to set it with C_INCLUDE_PATH or CPLUS_INCLUDE_PATH once you find it . There may be other environmental variables that must be set as well. The line inside the C code perl is running internally is something like ?#include?, so make sure the path you give to C_INCLUDE_PATH is the directory right before the /sys folder. Alternatively you may need to do this outside of conda. ?Carson > On Oct 17, 2018, at 8:27 AM, Lior Glick wrote: > > Hello, > I am trying to compile MAKER with Intel MPI. > We are using a cluster based on Intel x86_64 architecture and using lmod for environment variables. > All required dependencies have already been installed and the initial 'perl Build.PL' passes without issues (see attached). > When running './Build install' it always fails to find 'sys/types.h' and exits (see additional attachment). > The Build command probably searches for the '/usr/include/sys/types.h' file, but no matter which variable (INCLUDE, PERL5LIB etc...) I update with the required path (either '/usr/include' or '/usr/include/sys') - it keeps failing. > I would appreciate your input. > Thanks a lot! > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From 17na34 at queensu.ca Mon Nov 5 10:34:06 2018 From: 17na34 at queensu.ca (Nikolay Alabi) Date: Mon, 5 Nov 2018 17:34:06 +0000 Subject: [maker-devel] fasta_merge and gff3_merge commands not working Message-ID: Is there any prerequisites I must adhere to ensure the commands gff3_merge and fasta_merge work. I was following the Wiki tutorial and when I wanted to execute the commands in the data directory in order to make a clean out version of the files for later use, the computer did not recognize the commands. Please help. Thanks, Nikolay -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 14 12:35:52 2018 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 14 Nov 2018 12:35:52 -0700 Subject: [maker-devel] fasta_merge and gff3_merge commands not working In-Reply-To: References: Message-ID: Sorry for the slow reply. If you put ?/maker/bin in your PATH environmental variable, then all MAKER executables can be executed directly without having to call the full path. This is covered in the MAKER install instructions. You can learn more about PATH here ?> https://opensource.com/article/17/6/set-path-linux ?Carson > On Nov 5, 2018, at 10:34 AM, Nikolay Alabi <17na34 at queensu.ca> wrote: > > Is there any prerequisites I must adhere to ensure the commands gff3_merge and fasta_merge work. I was following the Wiki tutorial and when I wanted to execute the commands in the data directory in order to make a clean out version of the files for later use, the computer did not recognize the commands. Please help. > > Thanks, Nikolay -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytshen at genetics.ac.cn Thu Nov 29 20:24:48 2018 From: ytshen at genetics.ac.cn (ytshen at genetics.ac.cn) Date: Fri, 30 Nov 2018 11:24:48 +0800 Subject: [maker-devel] RNA-seq gff file cause MAKER running arrest Message-ID: <2018113011234848442023@genetics.ac.cn> Dears, I am trying to run MAKER for a plant genome and want to use RNA-seq information for my annotation. For this purpose, I alignment RNA-seq reads to my genome by using Hisat2 and assemble transcripts by using Stringtie, and transfer the Stringtie gtf output file into gff file by using Cufflinks2gff script provided by MAKER (ver 2.31.10). When I set the gff file as est_gff in maker_opts.ctl file, the MAKER running will stop at some point, but it didn't provide any error or warning information and also didn't exist. But when I transfer the gff file into fasta file, and set it as est_fasta in maker_opts.ctl file, the MAKER can run successfully. Has this phenomenon happened to someone else? How I can fix it? Hope your reply! Thank you very much! Best! Sinceraly, Yanting ??? ???????????????? ???010-64801362 ?????????????1?? ???100101 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 10:56:35 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 10:56:35 -0600 Subject: [maker-devel] MAKER not running properly after installation, help needed In-Reply-To: References: Message-ID: Hi Nikolay, If you can provide the exact error, that would allow me to know more of what you are seeing. Normally the system perl should be fine (you can check the perl version using 'perl -v' on the command line). There was an issue with forks.pm that I believe the authors have fixed by now if you update to the latest version (more info here ?> https://groups.google.com/forum/#!msg/maker-devel/2kYQ90TCuXA/FxPaM45YGdoJ ). Also updarte to the current CPAN version of BioPerl if there are doubts about that. ?Caerson > On Oct 31, 2018, at 8:27 AM, Nikolay Alabi <17na34 at queensu.ca> wrote: > > Hello, > > I am attempting to annotate a garlic mustard genome using maker on a cluster at Queen?s University. I have been following the tutorial on wiki and was attempting to use the practice data to see if the program is running properly and to learn how to train the gene predicting system. Maker is now installed and is working to an extent, however when in use it is not working properly and cannot read/annotate a genome. I suspect two problems that is causing this to occur, first, anytime any maker command is called, it shows that an argument in forks.pm in perl5 is not correct, after trying to fix the problem, I see that the code should be correct, but the error line still occurs. Then every time a maker command Is called another error saying there is an error flow occurring somewhere in perl again. For instance when I command: maker -h, or maker -CTL or anything to do with maker, the error lines occur. Would you advise me to reinstall perl and bioperl? Other than that I believe everything else is properly installed and I do not understand why the program is not running properly. I have even tried using different data genomes, however the same problem occurs of the run never finishing, then retrying, and ultimately failing. Please let me know if there is another possible source of error in the problem. > > Best regards, Nikolay > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 11:06:59 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 11:06:59 -0600 Subject: [maker-devel] Issue with maker In-Reply-To: References: Message-ID: Try updating BioPerl. This is caused by an attempt to improve certain indexing performance in BioPerl by using C code that compiles on the fly during runtime. It?s semi-unstable and really needs to be removed from BioPerl especially since a simple perl translation operator (tr///d) already fixed the need for the performance change anyways. Caused by lines 249-273 in this BioPerl code ?> https://github.com/bioperl/bioperl-live/blob/master/lib/Bio/DB/IndexedBase.pm Alternatively edit the file in BioPerl and comment out lines 249-273 yourself with ?#? signs (also get the trailing bracket on line 280). ?Carson > On Oct 25, 2018, at 3:22 PM, Pallavi Gupta wrote: > > Hi Team MAKER, > > I am using maker for my research for genome annotation process. But when I run maker I am getting a weird error. I tried finding a work around on the internet by scrolling through various bioinformatics forum but I was unsuccessful. I will really appreciate if you can help me in this regard. I have attached my nohup.out log. Please let me know if you need anything else. > > Thanks, > Pallavi Gupta > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 2 11:18:52 2018 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 2 Nov 2018 11:18:52 -0600 Subject: [maker-devel] Problem compiling MAKER with Intel MPI In-Reply-To: References: Message-ID: <2D4E1EFA-CE98-4FC2-B65E-81E0D7911E3A@gmail.com> The problem is your perl perl installation. It?s broken. I?m guessing it?s a version installed by conda? The sys/types.h file is internal to perl itself (and will be bound to the version of perl you are using - i.e. don?t use sys/types.h from a different perl version). It?s used to map datatypes between perl and C. If you search /powerapps/share/centos7/miniconda/ you may be able to find it somewhere internally. You may be able to set it with C_INCLUDE_PATH or CPLUS_INCLUDE_PATH once you find it . There may be other environmental variables that must be set as well. The line inside the C code perl is running internally is something like ?#include?, so make sure the path you give to C_INCLUDE_PATH is the directory right before the /sys folder. Alternatively you may need to do this outside of conda. ?Carson > On Oct 17, 2018, at 8:27 AM, Lior Glick wrote: > > Hello, > I am trying to compile MAKER with Intel MPI. > We are using a cluster based on Intel x86_64 architecture and using lmod for environment variables. > All required dependencies have already been installed and the initial 'perl Build.PL' passes without issues (see attached). > When running './Build install' it always fails to find 'sys/types.h' and exits (see additional attachment). > The Build command probably searches for the '/usr/include/sys/types.h' file, but no matter which variable (INCLUDE, PERL5LIB etc...) I update with the required path (either '/usr/include' or '/usr/include/sys') - it keeps failing. > I would appreciate your input. > Thanks a lot! > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From 17na34 at queensu.ca Mon Nov 5 10:34:06 2018 From: 17na34 at queensu.ca (Nikolay Alabi) Date: Mon, 5 Nov 2018 17:34:06 +0000 Subject: [maker-devel] fasta_merge and gff3_merge commands not working Message-ID: Is there any prerequisites I must adhere to ensure the commands gff3_merge and fasta_merge work. I was following the Wiki tutorial and when I wanted to execute the commands in the data directory in order to make a clean out version of the files for later use, the computer did not recognize the commands. Please help. Thanks, Nikolay -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 14 12:35:52 2018 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 14 Nov 2018 12:35:52 -0700 Subject: [maker-devel] fasta_merge and gff3_merge commands not working In-Reply-To: References: Message-ID: Sorry for the slow reply. If you put ?/maker/bin in your PATH environmental variable, then all MAKER executables can be executed directly without having to call the full path. This is covered in the MAKER install instructions. You can learn more about PATH here ?> https://opensource.com/article/17/6/set-path-linux ?Carson > On Nov 5, 2018, at 10:34 AM, Nikolay Alabi <17na34 at queensu.ca> wrote: > > Is there any prerequisites I must adhere to ensure the commands gff3_merge and fasta_merge work. I was following the Wiki tutorial and when I wanted to execute the commands in the data directory in order to make a clean out version of the files for later use, the computer did not recognize the commands. Please help. > > Thanks, Nikolay -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytshen at genetics.ac.cn Thu Nov 29 20:24:48 2018 From: ytshen at genetics.ac.cn (ytshen at genetics.ac.cn) Date: Fri, 30 Nov 2018 11:24:48 +0800 Subject: [maker-devel] RNA-seq gff file cause MAKER running arrest Message-ID: <2018113011234848442023@genetics.ac.cn> Dears, I am trying to run MAKER for a plant genome and want to use RNA-seq information for my annotation. For this purpose, I alignment RNA-seq reads to my genome by using Hisat2 and assemble transcripts by using Stringtie, and transfer the Stringtie gtf output file into gff file by using Cufflinks2gff script provided by MAKER (ver 2.31.10). When I set the gff file as est_gff in maker_opts.ctl file, the MAKER running will stop at some point, but it didn't provide any error or warning information and also didn't exist. But when I transfer the gff file into fasta file, and set it as est_fasta in maker_opts.ctl file, the MAKER can run successfully. Has this phenomenon happened to someone else? How I can fix it? Hope your reply! Thank you very much! Best! Sinceraly, Yanting ??? ???????????????? ???010-64801362 ?????????????1?? ???100101 -------------- next part -------------- An HTML attachment was scrubbed... URL: