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Rob Kudyba
11/17/23
[maker-devel] container for MAKER v3.01.03 on HPC systems Singularity/Apptainer?
I found an older Docker container at https://hub.docker.com/r/cgwyx/maker/dockerfile but the Perl
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[maker-devel] container for MAKER v3.01.03 on HPC systems Singularity/Apptainer?
I found an older Docker container at https://hub.docker.com/r/cgwyx/maker/dockerfile but the Perl
11/17/23
Rob Kudyba
11/10/23
[maker-devel] location of example folders from MAKER tutorial 2013?
Hello, Is there a place I can download the 4 directories and files mentioned in http://gmod.org/wiki/
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[maker-devel] location of example folders from MAKER tutorial 2013?
Hello, Is there a place I can download the 4 directories and files mentioned in http://gmod.org/wiki/
11/10/23
Hayley Mangelson
, …
Carson Hinton Holt
10
9/26/23
[maker-devel] MAKER Commercial User -- Install and run issues
What does the error say? One thing you can do is run on a single thread (ie no mpiexec, just call
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[maker-devel] MAKER Commercial User -- Install and run issues
What does the error say? One thing you can do is run on a single thread (ie no mpiexec, just call
9/26/23
Maggie Sudo
6/1/23
[maker-devel] Pre-masked Genome for MAKER annotation
Dear Sir /Madam, I am using MAKER to annotate my genome. I have created a custom repeat library for
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[maker-devel] Pre-masked Genome for MAKER annotation
Dear Sir /Madam, I am using MAKER to annotate my genome. I have created a custom repeat library for
6/1/23
Cerda, Juan Daniel
6/1/23
[maker-devel] Fw: Help with Maker installation
-- Juan D. Cerda Graduate Student in Bioinformatics and Genomics Huck Institute of the Life Sciences
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[maker-devel] Fw: Help with Maker installation
-- Juan D. Cerda Graduate Student in Bioinformatics and Genomics Huck Institute of the Life Sciences
6/1/23
Brett A Milash
,
Carson Holt
2
2/9/23
[maker-devel] Ran into unknown state (hex char: 29) at ... ../lib/Proc/Signal.pm line 177
Hi Brett, The specific module is seeing a weird character returned form the system signals table (it
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[maker-devel] Ran into unknown state (hex char: 29) at ... ../lib/Proc/Signal.pm line 177
Hi Brett, The specific module is seeing a weird character returned form the system signals table (it
2/9/23
Carson Holt
,
yuxi hu
3
2/2/23
Re: [maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error
Hi, Carson I change the TMP directory to an NFS location, but it still gave the same error message as
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Re: [maker-devel] maker error message: DBD::SQLite::db commit failed: disk I/O error
Hi, Carson I change the TMP directory to an NFS location, but it still gave the same error message as
2/2/23
Alam,Elissar
,
Jason Stajich
4
11/26/22
[maker-devel] Augustus predictions within MAKER2
I'd check the documentation and the raw files in the run folder if you aren't sure but The
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[maker-devel] Augustus predictions within MAKER2
I'd check the documentation and the raw files in the run folder if you aren't sure but The
11/26/22
WIIE AY
,
Carson Holt
2
11/3/22
[maker-devel] Maker always fails to run on a particular chromosome.
You have a number of initial GFF3 related errors. I think one of your input files has an issue
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[maker-devel] Maker always fails to run on a particular chromosome.
You have a number of initial GFF3 related errors. I think one of your input files has an issue
11/3/22
Jingyin Yu
11/1/22
[maker-devel] ERROR: Unknown strand in GFFDB::_sort_exons!
Hello All, I ran maker3 and got the error message, but did not get way how to solve it, #############
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[maker-devel] ERROR: Unknown strand in GFFDB::_sort_exons!
Hello All, I ran maker3 and got the error message, but did not get way how to solve it, #############
11/1/22
Kyle Keepers
,
Carson Holt
2
6/28/22
[maker-devel] Installation failing due to pg_config
Say no to the optional dependencies question —> Checking optional dependencies: Install DBD::Pg? [
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[maker-devel] Installation failing due to pg_config
Say no to the optional dependencies question —> Checking optional dependencies: Install DBD::Pg? [
6/28/22
莫东鑫
6/25/22
[maker-devel] Maker MPI problems
Hello, maker development team Few questions when I using maker with MPI. I had a genome file with
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[maker-devel] Maker MPI problems
Hello, maker development team Few questions when I using maker with MPI. I had a genome file with
6/25/22
chen wang
6/25/22
[maker-devel] blast error in maker
Dear professor maker is a great annotation software, when i using it, i have some strange problems. i
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[maker-devel] blast error in maker
Dear professor maker is a great annotation software, when i using it, i have some strange problems. i
6/25/22
Taslim, Cenny
, …
Fields, Christopher J
4
3/23/22
[maker-devel] Repbase subscription
This is good to know. Unfortunately our university library does not have a Repbase license. From:
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[maker-devel] Repbase subscription
This is good to know. Unfortunately our university library does not have a Repbase license. From:
3/23/22
michel argonauta
3/14/22
[maker-devel] MAKER V 2.28
Dear Developers: I am a graduate student at INECOL AC in Mexico. We want to run a pipeline to
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[maker-devel] MAKER V 2.28
Dear Developers: I am a graduate student at INECOL AC in Mexico. We want to run a pipeline to
3/14/22
Upendra Bhattarai
1/24/22
[maker-devel] How to solve Non-unique top level ID error in Maker annotation pipeline ?
Hi, I am trying to run a second round of Maker annotation job with a SNAP trained file. However, when
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[maker-devel] How to solve Non-unique top level ID error in Maker annotation pipeline ?
Hi, I am trying to run a second round of Maker annotation job with a SNAP trained file. However, when
1/24/22
Winter Sven
,
Marvin B Moore
2
1/23/22
[maker-devel] maker conda installation
Hi Sven, Sorry, the conda package was not created and is not maintained by the Yandell lab. Regards,
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[maker-devel] maker conda installation
Hi Sven, Sorry, the conda package was not created and is not maintained by the Yandell lab. Regards,
1/23/22
Kyungyong Seong
,
Carson Holt
5
1/21/22
[maker-devel] High memory consumption
I found out that high memory consumption was caused by BLAST or exonerate on incompletely masked
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[maker-devel] High memory consumption
I found out that high memory consumption was caused by BLAST or exonerate on incompletely masked
1/21/22
zc y
, …
Robert King
3
1/12/22
[maker-devel] cds error
If change second from last column to just . then that usually fixes this kind of problem or try
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[maker-devel] cds error
If change second from last column to just . then that usually fixes this kind of problem or try
1/12/22
Adam Stuckert
,
Carson Holt
2
1/3/22
[maker-devel] Maker predicts way too few genes/proteins
Make sure you are training either SNAP or Augustus and not just protein2genome or est2genome. You can
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[maker-devel] Maker predicts way too few genes/proteins
Make sure you are training either SNAP or Augustus and not just protein2genome or est2genome. You can
1/3/22
刘昱
,
Carson Holt
2
1/3/22
[maker-devel] part long scafflods finished,the others failed
You are out of RAM. If running on a scheduler like SLURM or PBS, depending on how you submit the job
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[maker-devel] part long scafflods finished,the others failed
You are out of RAM. If running on a scheduler like SLURM or PBS, depending on how you submit the job
1/3/22
Luca Peruzza
11/18/21
[maker-devel] Maker 3 stuck at "processing chunk output"
Dear Maker developers, I am posting here because we have a curious situation happening while using
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[maker-devel] Maker 3 stuck at "processing chunk output"
Dear Maker developers, I am posting here because we have a curious situation happening while using
11/18/21
Steven L. Miller
11/18/21
[maker-devel] Continuing problems
I just ran Maker on my 75507 unitig database. The maker_opts.ctl file included EST Evidence in the
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[maker-devel] Continuing problems
I just ran Maker on my 75507 unitig database. The maker_opts.ctl file included EST Evidence in the
11/18/21
Gezahegn Girma
11/3/21
[maker-devel] Request for support on maker pipeline
Hello, I am using maker for genome annotation of sorghum genotype. Maker is running and keep
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[maker-devel] Request for support on maker pipeline
Hello, I am using maker for genome annotation of sorghum genotype. Maker is running and keep
11/3/21
Marvin B Moore
,
Gezahegn Girma
2
11/3/21
Re: [maker-devel] Support on maker
Hi Barry, Thank you so much for the kind reply and suggestion to join mailing list. Looking forward
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Re: [maker-devel] Support on maker
Hi Barry, Thank you so much for the kind reply and suggestion to join mailing list. Looking forward
11/3/21
Macguigan, Daniel
11/3/21
[maker-devel] Maker Repeat Masking model_org option with D
Hello, I have a straightforward question, but I can't seem to find the answer anywhere. Is it
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[maker-devel] Maker Repeat Masking model_org option with D
Hello, I have a straightforward question, but I can't seem to find the answer anywhere. Is it
11/3/21
Carson Holt
10/20/21
Re: [maker-devel] How do I extract matrix from annotation
This is an older email that looks like never got an answer. Briefly you need to use Linux command
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Re: [maker-devel] How do I extract matrix from annotation
This is an older email that looks like never got an answer. Briefly you need to use Linux command
10/20/21
Steven L. Miller
, …
Carson Holt
6
10/20/21
[maker-devel] Adapting MAKER pipeline for my HPC
Funnanotate takes FASTA as input. But if you still choose the MAKER route, BUSCO can train Augustus
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[maker-devel] Adapting MAKER pipeline for my HPC
Funnanotate takes FASTA as input. But if you still choose the MAKER route, BUSCO can train Augustus
10/20/21
Steven L. Miller
,
Carson Holt
2
10/19/21
[maker-devel] failed to run MAKER tutorial test data
RepeatMasker seems to be the issue. You may need to install it manually instead of letting MAKER
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[maker-devel] failed to run MAKER tutorial test data
RepeatMasker seems to be the issue. You may need to install it manually instead of letting MAKER
10/19/21
Kevin Kocot
, …
Jacques Dainat
10
9/27/21
[maker-devel] Troubleshooting Maker failure
Hi all, Thank you again for the help! This solved my issue with the file formatting and I was able to
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[maker-devel] Troubleshooting Maker failure
Hi all, Thank you again for the help! This solved my issue with the file formatting and I was able to
9/27/21