From aitsai at smail.nchu.edu.tw  Sat Jul  3 03:43:43 2021
From: aitsai at smail.nchu.edu.tw (An-I Tsai)
Date: Sat, 3 Jul 2021 17:43:43 +0800
Subject: [maker-devel] MAKER - error in gene prediction of SNAP
Message-ID: <CAAZyMnkxNnxM=NgB3VZpAbLp6WN8sgJ+yxeytJt2UUJ79GjcvQ@mail.gmail.com>

Dear MAKER support team,

I am using MAKER 3.01.03 to do gene prediction. But the error about SNAP
occurred.
There is no further error in previous files and the STDERR.
Besides, MAKER could work successfully with augustus parameter provided,
but the error would occur with SNAP hmm file specified.
SNAP could also work successfully individually.  I am not sure my guess is
right or not, bur It seems that the problem was triggered between MAKER and
SNAP.

Can't locate object method "add_entry" via package "1" (perhaps you forgot
to load "1"?) at /home/aitsai/anaconda3/envs/maker/bin/../lib/Widget/snap.pm
line 540.
--> rank=4, hostname=origo
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:000004F

I am wondering what is package "1" specified in the error message.

Appreciate a lot if you have any ideas in solving this problem.
Thank you.

Best regards,
An-I
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From carsonhh at gmail.com  Mon Jul 19 11:58:10 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 11:58:10 -0600
Subject: [maker-devel] Extract CDS sequences without UTRs
In-Reply-To: <CAO-Y8RnP-_uXJ5hxiMxq8iSE08EtJ4A845=61i5wSeX9fenNGw@mail.gmail.com>
References: <CAO-Y8RnP-_uXJ5hxiMxq8iSE08EtJ4A845=61i5wSeX9fenNGw@mail.gmail.com>
Message-ID: <AA59C044-5E02-4C89-8148-1138E58246A5@gmail.com>

fasta_tool with the ?trim_maker_utr option.

?Carson



> On Jun 27, 2021, at 7:55 PM, Sarah Baker <vireofeathers at gmail.com> wrote:
> 
> Hello,
> 
> I have annotated several genomes using the Maker2 pipeline with the goal of estimating dN/dS ratios for many genes. 
> 
> I have been using the fasta_merge script to extract the coding sequences, but I just noticed that the nucleotide sequences that it outputs (in *.all.maker.transcripts.fasta) sometimes include the 5' and 3' UTRs and they are not always in the correct reading frame. Is there a way to output CDS sequences in-frame and without UTRs (eg. so that the contents of *.all.maker.transcripts.fasta could be directly translated to the *.all.maker.proteins.fasta output by fasta_merge)?
> 
> Thank you for this great program!
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Mon Jul 19 12:35:59 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 12:35:59 -0600
Subject: [maker-devel] ERROR: Failed while processing all repeats
In-Reply-To: <CA+Lut46JA8VFt29fXCPwcPaor=7TCiWs-8b5Eu0u0yXcpbV1Fg@mail.gmail.com>
References: <CA+Lut46JA8VFt29fXCPwcPaor=7TCiWs-8b5Eu0u0yXcpbV1Fg@mail.gmail.com>
Message-ID: <9125C3A6-F67E-4903-B92D-DD203B1027F7@gmail.com>

Sorry for the slow reply.  This issue gat lost.  It was caused by RepeatMasker reporting invalid coordinate for one of it?s results. Make sure to install the most recent MAKER release. It knows how to fix and ignore these odd results.

?Carson


> On Mar 18, 2021, at 6:58 PM, Inf Bio <bioinf49 at gmail.com> wrote:
> 
> Dear Developers,
> 
> I've researched all available forums and tried to resolve this recurring error in maker: 
> 
> processing all repeats
> in cluster::shadow_cluster...
> Died at /home/user/bin/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=19, hostname=m30g4
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> 
> So far, I have tried: reformatting my gff file including purify script from Carson, Daren Card's script, and agat; uninstalled and reinstalled ncbi-blast+ and updated path; reinstated RMBlast path in repeatmasker; changed max_dna_length to 300000; set clean_try=1; replaced RepeatMasker.pm.
> 
> However, none of the above helped get rid of the issue. I cannot see what is wrong with my gff. Can you please help?
> 
> thank you.
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Mon Jul 19 15:00:35 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 15:00:35 -0600
Subject: [maker-devel] Error using ab intio gene predictor with gffs
In-Reply-To: <CAMcZUz9BAyQcEEQXgpLALW1nTArLP7p6H5Q4CVFYaoeNxL40fg@mail.gmail.com>
References: <CAMcZUz9BAyQcEEQXgpLALW1nTArLP7p6H5Q4CVFYaoeNxL40fg@mail.gmail.com>
Message-ID: <0DD674DB-6D6E-4C14-92B4-BF1407A5AC64@gmail.com>

Can you install 3.01.04 and see if you still have the error?

Thanks,
Carson
 

> On Jun 15, 2021, at 3:31 AM, Megan Aylward <aylward.megan at gmail.com> wrote:
> 
> Hi,
> 
> After running one round of Maker, I am trying to run a second round using the outputs from the first as inputs for the different evidence for EST, proteins, and repeats in gff format.
> 
> I am receiving the following error:
> 
> Can't locate object method "add_entry" via package "1" (perhaps you forgot to load "1"?) at maker-3.01.03/bin/../lib/Widget/snap.pm <http://snap.pm/> line 540.
> 
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> 
> There are not any other errors prior to this one. As I understand it may be an issue with one of the feature files. Could this be the issue, and if so do you have any suggestions of how to detect what is causing the error?
> 
> Many thanks,
> 
> Megan
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From aitsai at smail.nchu.edu.tw  Sat Jul  3 03:43:43 2021
From: aitsai at smail.nchu.edu.tw (An-I Tsai)
Date: Sat, 3 Jul 2021 17:43:43 +0800
Subject: [maker-devel] MAKER - error in gene prediction of SNAP
Message-ID: <CAAZyMnkxNnxM=NgB3VZpAbLp6WN8sgJ+yxeytJt2UUJ79GjcvQ@mail.gmail.com>

Dear MAKER support team,

I am using MAKER 3.01.03 to do gene prediction. But the error about SNAP
occurred.
There is no further error in previous files and the STDERR.
Besides, MAKER could work successfully with augustus parameter provided,
but the error would occur with SNAP hmm file specified.
SNAP could also work successfully individually.  I am not sure my guess is
right or not, bur It seems that the problem was triggered between MAKER and
SNAP.

Can't locate object method "add_entry" via package "1" (perhaps you forgot
to load "1"?) at /home/aitsai/anaconda3/envs/maker/bin/../lib/Widget/snap.pm
line 540.
--> rank=4, hostname=origo
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:000004F

I am wondering what is package "1" specified in the error message.

Appreciate a lot if you have any ideas in solving this problem.
Thank you.

Best regards,
An-I
-------------- next part --------------
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From carsonhh at gmail.com  Mon Jul 19 11:58:10 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 11:58:10 -0600
Subject: [maker-devel] Extract CDS sequences without UTRs
In-Reply-To: <CAO-Y8RnP-_uXJ5hxiMxq8iSE08EtJ4A845=61i5wSeX9fenNGw@mail.gmail.com>
References: <CAO-Y8RnP-_uXJ5hxiMxq8iSE08EtJ4A845=61i5wSeX9fenNGw@mail.gmail.com>
Message-ID: <AA59C044-5E02-4C89-8148-1138E58246A5@gmail.com>

fasta_tool with the ?trim_maker_utr option.

?Carson



> On Jun 27, 2021, at 7:55 PM, Sarah Baker <vireofeathers at gmail.com> wrote:
> 
> Hello,
> 
> I have annotated several genomes using the Maker2 pipeline with the goal of estimating dN/dS ratios for many genes. 
> 
> I have been using the fasta_merge script to extract the coding sequences, but I just noticed that the nucleotide sequences that it outputs (in *.all.maker.transcripts.fasta) sometimes include the 5' and 3' UTRs and they are not always in the correct reading frame. Is there a way to output CDS sequences in-frame and without UTRs (eg. so that the contents of *.all.maker.transcripts.fasta could be directly translated to the *.all.maker.proteins.fasta output by fasta_merge)?
> 
> Thank you for this great program!
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Mon Jul 19 12:35:59 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 12:35:59 -0600
Subject: [maker-devel] ERROR: Failed while processing all repeats
In-Reply-To: <CA+Lut46JA8VFt29fXCPwcPaor=7TCiWs-8b5Eu0u0yXcpbV1Fg@mail.gmail.com>
References: <CA+Lut46JA8VFt29fXCPwcPaor=7TCiWs-8b5Eu0u0yXcpbV1Fg@mail.gmail.com>
Message-ID: <9125C3A6-F67E-4903-B92D-DD203B1027F7@gmail.com>

Sorry for the slow reply.  This issue gat lost.  It was caused by RepeatMasker reporting invalid coordinate for one of it?s results. Make sure to install the most recent MAKER release. It knows how to fix and ignore these odd results.

?Carson


> On Mar 18, 2021, at 6:58 PM, Inf Bio <bioinf49 at gmail.com> wrote:
> 
> Dear Developers,
> 
> I've researched all available forums and tried to resolve this recurring error in maker: 
> 
> processing all repeats
> in cluster::shadow_cluster...
> Died at /home/user/bin/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=19, hostname=m30g4
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> 
> So far, I have tried: reformatting my gff file including purify script from Carson, Daren Card's script, and agat; uninstalled and reinstalled ncbi-blast+ and updated path; reinstated RMBlast path in repeatmasker; changed max_dna_length to 300000; set clean_try=1; replaced RepeatMasker.pm.
> 
> However, none of the above helped get rid of the issue. I cannot see what is wrong with my gff. Can you please help?
> 
> thank you.
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Mon Jul 19 15:00:35 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 15:00:35 -0600
Subject: [maker-devel] Error using ab intio gene predictor with gffs
In-Reply-To: <CAMcZUz9BAyQcEEQXgpLALW1nTArLP7p6H5Q4CVFYaoeNxL40fg@mail.gmail.com>
References: <CAMcZUz9BAyQcEEQXgpLALW1nTArLP7p6H5Q4CVFYaoeNxL40fg@mail.gmail.com>
Message-ID: <0DD674DB-6D6E-4C14-92B4-BF1407A5AC64@gmail.com>

Can you install 3.01.04 and see if you still have the error?

Thanks,
Carson
 

> On Jun 15, 2021, at 3:31 AM, Megan Aylward <aylward.megan at gmail.com> wrote:
> 
> Hi,
> 
> After running one round of Maker, I am trying to run a second round using the outputs from the first as inputs for the different evidence for EST, proteins, and repeats in gff format.
> 
> I am receiving the following error:
> 
> Can't locate object method "add_entry" via package "1" (perhaps you forgot to load "1"?) at maker-3.01.03/bin/../lib/Widget/snap.pm <http://snap.pm/> line 540.
> 
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> 
> There are not any other errors prior to this one. As I understand it may be an issue with one of the feature files. Could this be the issue, and if so do you have any suggestions of how to detect what is causing the error?
> 
> Many thanks,
> 
> Megan
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From aitsai at smail.nchu.edu.tw  Sat Jul  3 03:43:43 2021
From: aitsai at smail.nchu.edu.tw (An-I Tsai)
Date: Sat, 3 Jul 2021 17:43:43 +0800
Subject: [maker-devel] MAKER - error in gene prediction of SNAP
Message-ID: <CAAZyMnkxNnxM=NgB3VZpAbLp6WN8sgJ+yxeytJt2UUJ79GjcvQ@mail.gmail.com>

Dear MAKER support team,

I am using MAKER 3.01.03 to do gene prediction. But the error about SNAP
occurred.
There is no further error in previous files and the STDERR.
Besides, MAKER could work successfully with augustus parameter provided,
but the error would occur with SNAP hmm file specified.
SNAP could also work successfully individually.  I am not sure my guess is
right or not, bur It seems that the problem was triggered between MAKER and
SNAP.

Can't locate object method "add_entry" via package "1" (perhaps you forgot
to load "1"?) at /home/aitsai/anaconda3/envs/maker/bin/../lib/Widget/snap.pm
line 540.
--> rank=4, hostname=origo
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:000004F

I am wondering what is package "1" specified in the error message.

Appreciate a lot if you have any ideas in solving this problem.
Thank you.

Best regards,
An-I
-------------- next part --------------
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From carsonhh at gmail.com  Mon Jul 19 11:58:10 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 11:58:10 -0600
Subject: [maker-devel] Extract CDS sequences without UTRs
In-Reply-To: <CAO-Y8RnP-_uXJ5hxiMxq8iSE08EtJ4A845=61i5wSeX9fenNGw@mail.gmail.com>
References: <CAO-Y8RnP-_uXJ5hxiMxq8iSE08EtJ4A845=61i5wSeX9fenNGw@mail.gmail.com>
Message-ID: <AA59C044-5E02-4C89-8148-1138E58246A5@gmail.com>

fasta_tool with the ?trim_maker_utr option.

?Carson



> On Jun 27, 2021, at 7:55 PM, Sarah Baker <vireofeathers at gmail.com> wrote:
> 
> Hello,
> 
> I have annotated several genomes using the Maker2 pipeline with the goal of estimating dN/dS ratios for many genes. 
> 
> I have been using the fasta_merge script to extract the coding sequences, but I just noticed that the nucleotide sequences that it outputs (in *.all.maker.transcripts.fasta) sometimes include the 5' and 3' UTRs and they are not always in the correct reading frame. Is there a way to output CDS sequences in-frame and without UTRs (eg. so that the contents of *.all.maker.transcripts.fasta could be directly translated to the *.all.maker.proteins.fasta output by fasta_merge)?
> 
> Thank you for this great program!
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Mon Jul 19 12:35:59 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 12:35:59 -0600
Subject: [maker-devel] ERROR: Failed while processing all repeats
In-Reply-To: <CA+Lut46JA8VFt29fXCPwcPaor=7TCiWs-8b5Eu0u0yXcpbV1Fg@mail.gmail.com>
References: <CA+Lut46JA8VFt29fXCPwcPaor=7TCiWs-8b5Eu0u0yXcpbV1Fg@mail.gmail.com>
Message-ID: <9125C3A6-F67E-4903-B92D-DD203B1027F7@gmail.com>

Sorry for the slow reply.  This issue gat lost.  It was caused by RepeatMasker reporting invalid coordinate for one of it?s results. Make sure to install the most recent MAKER release. It knows how to fix and ignore these odd results.

?Carson


> On Mar 18, 2021, at 6:58 PM, Inf Bio <bioinf49 at gmail.com> wrote:
> 
> Dear Developers,
> 
> I've researched all available forums and tried to resolve this recurring error in maker: 
> 
> processing all repeats
> in cluster::shadow_cluster...
> Died at /home/user/bin/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=19, hostname=m30g4
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> 
> So far, I have tried: reformatting my gff file including purify script from Carson, Daren Card's script, and agat; uninstalled and reinstalled ncbi-blast+ and updated path; reinstated RMBlast path in repeatmasker; changed max_dna_length to 300000; set clean_try=1; replaced RepeatMasker.pm.
> 
> However, none of the above helped get rid of the issue. I cannot see what is wrong with my gff. Can you please help?
> 
> thank you.
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
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From carsonhh at gmail.com  Mon Jul 19 15:00:35 2021
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 19 Jul 2021 15:00:35 -0600
Subject: [maker-devel] Error using ab intio gene predictor with gffs
In-Reply-To: <CAMcZUz9BAyQcEEQXgpLALW1nTArLP7p6H5Q4CVFYaoeNxL40fg@mail.gmail.com>
References: <CAMcZUz9BAyQcEEQXgpLALW1nTArLP7p6H5Q4CVFYaoeNxL40fg@mail.gmail.com>
Message-ID: <0DD674DB-6D6E-4C14-92B4-BF1407A5AC64@gmail.com>

Can you install 3.01.04 and see if you still have the error?

Thanks,
Carson
 

> On Jun 15, 2021, at 3:31 AM, Megan Aylward <aylward.megan at gmail.com> wrote:
> 
> Hi,
> 
> After running one round of Maker, I am trying to run a second round using the outputs from the first as inputs for the different evidence for EST, proteins, and repeats in gff format.
> 
> I am receiving the following error:
> 
> Can't locate object method "add_entry" via package "1" (perhaps you forgot to load "1"?) at maker-3.01.03/bin/../lib/Widget/snap.pm <http://snap.pm/> line 540.
> 
> ERROR: Failed while annotating transcripts
> ERROR: Chunk failed at level:1, tier_type:4
> 
> There are not any other errors prior to this one. As I understand it may be an issue with one of the feature files. Could this be the issue, and if so do you have any suggestions of how to detect what is causing the error?
> 
> Many thanks,
> 
> Megan
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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