Can't open perl script "NOVOPlasty4.2.pl": No such file or directory

Giovani1981 commented 2 years ago

Dear ndierckx,

I am trying running NOVOPlast, however, after hours of trying to figure out what it's going on, I gave up. I created a Conda env called "Plant" and downloaded novoplasty from Conda using the command:

conda install -c bioconda novoplasty

After running this command, I got the following information:

Collecting package metadata (current_repodata.json): done Solving environment: done Package Plan environment location: /home/student/anaconda3/envs/Plant added / updated specs:

novoplasty The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17 libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17 novoplasty bioconda/noarch::novoplasty-4.2-pl5262hdfd78af_1 perl pkgs/main/linux-64::perl-5.26.2-h14c3975_0 Proceed ([y]/n)? Preparing transaction: done Verifying transaction: done Executing transaction: done

After it, I checked to see if Novoplast was installed, using the command conda list. See below:

packages in environment at /home/student/anaconda3/envs/Plant:

Name Version Build Channel _libgcc_mutex. 0.1 main
_openmp_mutex 4.5 1_gnu
libgcc-ng 9.3.0 h5101ec6_17
libgomp 9.3.0 h5101ec6_17
novoplasty 4.2 pl5262hdfd78af_1 bioconda perl 5.26.2 h14c3975_0

The files config.txt and rbcl_seed.fasta are in the directory ~/Plant-genome/shotgun-dna/chloroplast/. I am trying to run Novoplasty as shown below: (Plant) student@landingvm:~/Plant-genome/shotgun-dna/chloroplast$ perl NOVOPlasty.4.3 -c config.txt

The output for the command above is the message: Can't open perl script "NOVOPlasty4.3.pl": No such file or directory A friend told me to use 4.2 instead of 4.3 in the command because 4.3 was a typo. It also didn't work.

I tried many different ways to accomplish it, by reading the GitHub page, manuals... but I just couldn’t figure out how to overcome it. Could you help to figure it out? Sincerely,

Giovani

ndierckx commented 2 years ago

Hi,

perl NOVOPlasty4.3.pl -c config.txt is the command if you just download the script from github, no installation required the latest version on conda is 4.2. To run it you need to use this command: NOVOPlasty4.2.pl -c config.txt

I will update conda version to 4.3 and the installation instructions of conda on this github

Giovani1981 commented 2 years ago

Dear Mr. Dierckxsens, Thanks a lot. I was able to run NOVOPlasty after reading your instructions. Thanks also for have developed this amazing tool! Sincerely,

Giovani

Heba383 commented 2 years ago

i have perl 5 on my pc and still can not run NOVOPlasty it alywase can not read perl script

ndierckx commented 2 years ago

Which platform and with conda or without?

Heba383 commented 2 years ago

Which platform and with conda or without?

ndierckx commented 2 years ago

Are you sure your perl script is in that folder...

Heba383 commented 2 years ago

Are you sure your perl script is in that folder... i have check that thanks for helping me

ndierckx commented 2 years ago

That error has nothing to do with NOVOPlasty You must be doing something wrong, can you show a screenshot of your folder

Heba383 commented 2 years ago

hello, sir i have run a config.txt and every time said invalid seeds and i didnot know what i can do and can i used my reference in input seeds thanks in advance

On Fri, Nov 12, 2021 at 1:14 AM Nicolas Dierckxsens < @.***> wrote:

That error has nothing to do with NOVOPlasty You must be doing something wrong, can you show a screenshot of your folder

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ndierckx/NOVOPlasty/issues/182#issuecomment-966691347, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATW7OTCBS2ZBYDI5VPRHLCLULRE53ANCNFSM5GFHYPTQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Heba Abd El Aziz Moussa Abd Alla, MSc Assistant Researcher of plant biotechnology. Botany Department,National Research center, Dokki,Giza, 12622 00201020091978 lap phone 0202_33371362! Ext.1159 fax:0020233370931 @. @.> @.*** http://www.nrc.sci.eg/

Project:
-----------------------
Project name          = M. peregrina
Type                  = chloro
Genome Range          = 160000-180000
K-mer                 = 39
Max memory            = 0
Extended log          = 0
Save assembled reads  = no
Seed Input            = C:\Users\ASUS-MCC\Desktop\novo\M.P\Seed_RUBP.fasta 
Extend seed directly  = no
Reference sequence    =  C:\Users\ASUS-MCC\Desktop\novo\M.P\Moringa_oleifera .fasta
Variance detection    = 
Chloroplast sequence  = 

Dataset 1:
-----------------------
Read Length           = 151
Insert size           = 300
Platform              = illumina
Single/Paired         = PE
Combined reads        = 
Forward reads         = C:\Users\ASUS-MCC\Desktop\novo\M.P\M_per_1.fq
Reverse reads         = C:\Users\ASUS-MCC\Desktop\novo\M.P\M_per_2.fq
Store Hash            =

Heteroplasmy:
-----------------------
MAF                   = 
HP exclude list       = 
PCR-free              = 

Optional:
-----------------------
Insert size auto      = yes
Use Quality Scores    = no
Output path           =

NOVOPlasty: The Organelle Assembler Version 4.3.1 Author: Nicolas Dierckxsens, (c) 2015-2020

Input parameters from the configuration file: Verify if everything is correct

Project:

Project name = M. peregrina Type = chloro Genome range = 160000-180000 K-mer = 39 Max memory = 0 Extended log = 0 Save assembled reads = no Seed Input = C:\Users\ASUS-MCC\Desktop\novo\M.P\Seed_RUBP.fasta Extend seed directly = no Reference sequence = C:\Users\ASUS-MCC\Desktop\novo\M.P\Moringa_oleifera .fasta Variance detection = Chloroplast sequence =

Dataset 1:

Read Length = 151 Insert size = 300 Platform = illumina Single/Paired = PE Combined reads = Forward reads = C:\Users\ASUS-MCC\Desktop\novo\M.P\M_per_1.fq Reverse reads = C:\Users\ASUS-MCC\Desktop\novo\M.P\M_per_2.fq Store Hash =

Heteroplasmy:

Heteroplasmy = HP exclude list = PCR-free =

Optional:

Insert size auto = yes Use Quality Scores = Output path =

Subsampled fraction: 0.00 %

Retrieve Seed...

INVALID SEED, PLEASE TRY AGAIN WITH A NEW ONE

ndierckx commented 2 years ago

Can you send your log file

Heba383 commented 2 years ago

thanks sir for your response, i ask one friend and help me in that thanks for your programe much

On Sun, Nov 21, 2021 at 2:51 PM Nicolas Dierckxsens < @.***> wrote:

Can you send your log file

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-- Heba Abd El Aziz Moussa Abd Alla, MSc Assistant Researcher of plant biotechnology. Botany Department,National Research center, Dokki,Giza, 12622 00201020091978 lap phone 0202_33371362! Ext.1159 fax:0020233370931 @. @.> @.*** http://www.nrc.sci.eg/

timurrxxcd commented 1 year ago

Hi sir I'm doing plastid genome assembly. But, it says this error. Please help me! Can you response to my email if possible. asatullayevtemurrr@gmail.com , .

Heba383 commented 1 year ago

Hello, dear Sorry for the late reply, i was outside and did not open my email CdspacesDesktop\NOVOPlasty-master PerlspacesNOVOPlasty4.0.plspaces_cspacesConfig.txt. If you need anything please let me know

On Mon, Apr 24, 2023 at 9:48 PM timurrxxcd @.***> wrote:

Hi sir I'm doing plastid genome assembly. But, it says this error. Please help me! [image: image] https://user-images.githubusercontent.com/86943771/234016000-4889aa5c-b292-4d81-87d0-8748699f8635.png , [image: image] https://user-images.githubusercontent.com/86943771/234016114-67d006f0-5430-46cb-8234-4974ae7e3018.png

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timurrxxcd commented 1 year ago

Hello, dear

Thanks for responding. I ran your code. But, I had another problem in the picture. I'm not sure what's wrong here. Also, this is plastid genome, should I filter for adapters before assembling by NOVOPlasty?

вт, 25 апр. 2023 г. в 11:41, Heba383 @.***>:

Hello, dear Sorry for the late reply, i was outside and did not open my email CdspacesDesktop\NOVOPlasty-master PerlspacesNOVOPlasty4.0.plspaces_cspacesConfig.txt. If you need anything please let me know

On Mon, Apr 24, 2023 at 9:48 PM timurrxxcd @.***> wrote:

Hi sir I'm doing plastid genome assembly. But, it says this error. Please help me! [image: image] < https://user-images.githubusercontent.com/86943771/234016000-4889aa5c-b292-4d81-87d0-8748699f8635.png

, [image: image] < https://user-images.githubusercontent.com/86943771/234016114-67d006f0-5430-46cb-8234-4974ae7e3018.png

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Heba383 commented 1 year ago

Hello, I think the problem is with Perl. You have first correct install and make sure in the control prompt, then you can write my codes and no need for filtrate just choose good seeds for your work The last thing be patience and keep trying it will work do not worry

On Tue, Apr 25, 2023 at 1:12 PM timurrxxcd @.***> wrote:

Hello, dear

Thanks for responding. I ran your code. But, I had another problem in the picture. I'm not sure what's wrong here. Also, this is plastid genome, should I filter for adapters before assembling by NOVOPlasty?

вт, 25 апр. 2023 г. в 11:41, Heba383 @.***>:

Hello, dear Sorry for the late reply, i was outside and did not open my email CdspacesDesktop\NOVOPlasty-master PerlspacesNOVOPlasty4.0.plspaces_cspacesConfig.txt. If you need anything please let me know

On Mon, Apr 24, 2023 at 9:48 PM timurrxxcd @.***> wrote:

Hi sir I'm doing plastid genome assembly. But, it says this error. Please help me! [image: image] <

https://user-images.githubusercontent.com/86943771/234016000-4889aa5c-b292-4d81-87d0-8748699f8635.png

, [image: image] <

https://user-images.githubusercontent.com/86943771/234016114-67d006f0-5430-46cb-8234-4974ae7e3018.png

— Reply to this email directly, view it on GitHub <

https://github.com/ndierckx/NOVOPlasty/issues/182#issuecomment-1520196291

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-- Heba Abd El Aziz Moussa Abd Alla, MSc Assistant Researcher of plant biotechnology. Botany Department,National Research center, Dokki,Giza, 12622 00201020091978 lap phone 0202_33371362! Ext.1159 fax:0020233370931 @. @.> @.*** http://www.nrc.sci.eg/

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ndierckx commented 1 year ago

Hi, no trimming adapter is usually not necessary, but can't harm

You are trying to run 4.3, while in your folder you have version 4.3.1

Heba383 commented 1 year ago

Thank you for your response. But that is not me someone just ask me

On Sun, May 7, 2023 at 2:07 PM Nicolas Dierckxsens @.***> wrote:

Hi, no trimming adapter is usually not necessary, but can't harm

You are trying to run 4.3, while in your folder you have version 4.3.1

— Reply to this email directly, view it on GitHub https://github.com/ndierckx/NOVOPlasty/issues/182#issuecomment-1537302030, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATW7OTCMRZ6T2EIBHASH7TTXE432NANCNFSM5GFHYPTQ . You are receiving this because you commented.Message ID: @.***>

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timurrxxcd commented 1 year ago

Hi dear. I'm trying to run Novoplasty for chloro assemble. But it says no such file or directory. everything is correct it seems. I'm attaching two pictures by this email. please find the problem if you have free time. Thanks!

вс, 7 мая 2023 г. в 14:17, Heba383 @.***>:

Thank you for your response. But that is not me someone just ask me

On Sun, May 7, 2023 at 2:07 PM Nicolas Dierckxsens @.***> wrote:

Hi, no trimming adapter is usually not necessary, but can't harm

You are trying to run 4.3, while in your folder you have version 4.3.1

— Reply to this email directly, view it on GitHub < https://github.com/ndierckx/NOVOPlasty/issues/182#issuecomment-1537302030 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ATW7OTCMRZ6T2EIBHASH7TTXE432NANCNFSM5GFHYPTQ

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-- Heba Abd El Aziz Moussa Abd Alla, MSc Assistant Researcher of plant biotechnology. Botany Department,National Research center, Dokki,Giza, 12622 00201020091978 lap phone 0202_33371362! Ext.1159 fax:0020233370931 @. @.> @.*** http://www.nrc.sci.eg/

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timurrxxcd commented 1 year ago

these fastq files are NGS clean data.

ср, 17 мая 2023 г. в 17:15, Temur Asatulloyev @.***

:

Hi dear. I'm trying to run Novoplasty for chloro assemble. But it says no such file or directory. everything is correct it seems. I'm attaching two pictures by this email. please find the problem if you have free time. Thanks!

вс, 7 мая 2023 г. в 14:17, Heba383 @.***>:

Thank you for your response. But that is not me someone just ask me

On Sun, May 7, 2023 at 2:07 PM Nicolas Dierckxsens @.***> wrote:

Hi, no trimming adapter is usually not necessary, but can't harm

You are trying to run 4.3, while in your folder you have version 4.3.1

— Reply to this email directly, view it on GitHub < https://github.com/ndierckx/NOVOPlasty/issues/182#issuecomment-1537302030 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ATW7OTCMRZ6T2EIBHASH7TTXE432NANCNFSM5GFHYPTQ

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-- Heba Abd El Aziz Moussa Abd Alla, MSc Assistant Researcher of plant biotechnology. Botany Department,National Research center, Dokki,Giza, 12622 00201020091978 lap phone 0202_33371362! Ext.1159 fax:0020233370931 @. @.> @.*** http://www.nrc.sci.eg/

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