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jotech / gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
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Could not use find-transport function using '-m' option for specific metabolite. #203

Closed ashish193006 closed 10 months ago

ashish193006 commented 10 months ago

for bug reports and errors please report the output of: ./gapseq test The command './gapseq find-transport -m nitrogen genome.fasta' does not work. How can I solve this issue?

Waschina commented 10 months ago

There was a bug in the transporter prediction script. Thanks for reporting!

FWIW, the option -m nitrogen won't work, because there's no metabolite to test here. The molecule $N_2$ (Dinitrogen) readily crosses cell membranes without the need for a specific transporter. If you have a specific nitrogenous compound to test you can for instance use:

gapseq find-transport -b 200 -m Ammonia genome.fasta (testing for $NH_3$).

ashish193006 commented 10 months ago

Thank you for the reply and you time. I used 'nitrogen' keyword because I used the same for 'find' function. However, I think I might have to use different keywords for all nitrate, nitrite and ammonia as per your suggestion.

Regards, Ashish Singh

On Sat, 13 Jan, 2024, 6:31 pm Silvio Waschina, @.***> wrote:

There was a bug in the transporter prediction script. Thanks for reporting!

FWIW, the option -m nitrogen won't work, because there's no metabolite to test here. The molecule $N_2$ (Dinitrogen) readily crosses cell membranes without the need for a specific transporter. If you have a specific nitrogenous compound to test you can for instance use:

gapseq find-transport -b 200 -m Ammonia genome.fasta (testing for $NH_3$).

— Reply to this email directly, view it on GitHub https://github.com/jotech/gapseq/issues/203#issuecomment-1890451741, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVQ7NI53VFNBCF4ZKPRJ5DLYOKAUFAVCNFSM6AAAAABBZGAGVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJQGQ2TCNZUGE . You are receiving this because you authored the thread.Message ID: @.***>

ashish193006 commented 10 months ago

Dear Silvio, it's still not working even after the suggested corrections. Kindly suggest the needful.

Regards, Ashish Kumar Singh CSIR-Senior Research Fellow EBGD, CSIR-NEERI

---------- Forwarded message --------- From: Ashish Kumar Singh @.> Date: Sat, 13 Jan, 2024, 6:59 pm Subject: Re: [jotech/gapseq] Could not use find-transport function using '-m' option for specific metabolite. (Issue #203) To: jotech/gapseq < @.>

Dear Silvio, it's still not working even after the suggested corrections. I have attached the screenshot for your reference. Kindly suggest the needful.

Regards, Ashish Kumar Singh CSIR-Senior Research Fellow EBGD, CSIR-NEERI

On Sat, 13 Jan, 2024, 6:52 pm Ashish Kumar Singh, < @.***> wrote:

Thank you for the reply and you time. I used 'nitrogen' keyword because I used the same for 'find' function. However, I think I might have to use different keywords for all nitrate, nitrite and ammonia as per your suggestion.

Regards, Ashish Singh

On Sat, 13 Jan, 2024, 6:31 pm Silvio Waschina, @.***> wrote:

There was a bug in the transporter prediction script. Thanks for reporting!

FWIW, the option -m nitrogen won't work, because there's no metabolite to test here. The molecule $N_2$ (Dinitrogen) readily crosses cell membranes without the need for a specific transporter. If you have a specific nitrogenous compound to test you can for instance use:

gapseq find-transport -b 200 -m Ammonia genome.fasta (testing for $NH_3$ ).

— Reply to this email directly, view it on GitHub https://github.com/jotech/gapseq/issues/203#issuecomment-1890451741, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVQ7NI53VFNBCF4ZKPRJ5DLYOKAUFAVCNFSM6AAAAABBZGAGVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJQGQ2TCNZUGE . You are receiving this because you authored the thread.Message ID: @.***>

Waschina commented 10 months ago

Hi @ashish193006

It's working as expected on the two Linux systems I tested.

Did you update gapseq to the latest development version (e.g. via git pull)?

Please provide the output of gapseq test and the exact command you used.

ashish193006 commented 10 months ago

Hello, Jotech/gapseq

The application works fine with 'find-transport all' option. But it does not takes any other option for find-transport.

Regards, Ashish Kumar Singh CSIR-Senior Research Fellow EBGD, CSIR-NEERI

On Mon, 15 Jan, 2024, 10:29 pm Silvio Waschina, @.***> wrote:

Hi @ashish193006 https://github.com/ashish193006

It's working as expected on the two Linux systems I tested.

Did you update gapseq to the latest development version (e.g. via git pull )?

Please provide the output of gapseq test and the exact command you used.

— Reply to this email directly, view it on GitHub https://github.com/jotech/gapseq/issues/203#issuecomment-1892519621, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVQ7NIZH5JY4XFWDHO7YDCLYOVN6PAVCNFSM6AAAAABBZGAGVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJSGUYTSNRSGE . You are receiving this because you were mentioned.Message ID: @.***>

jotech commented 10 months ago

hi @ashish193006 Could you please try ./gapseq find-transport -b 200 -m Ammonia toy/myb71.fna.gz? And if this fails, can you copy and paste the output of ./gapseq test?

ashish193006 commented 10 months ago

Dear Jotech/Gapseq, I apologize for the late reply as I occupied my work. Here is the './gapseq test' run output you asked for below: gapseq version: 1.2 f96e1272 linux-gnu

40-Ubuntu SMP PREEMPT_DYNAMIC Tue Nov 14 14:18:00 UTC 2023

#######################

Checking dependencies

####################### ldconfig (Ubuntu GLIBC 2.37-0ubuntu2.2) 2.37 libsbml.so.5 -> libsbml.so.5.17.0 libsbml.so.5 -> libsbml.so.5.19.7 libglpk.so.40 -> libglpk.so.40.3.1 awk: not an option: --version awk NOT FOUND sed (GNU sed) 4.9 grep (GNU grep) 3.8 This is perl 5, version 32, subversion 1 (v5.32.1) built for x86_64-linux-thread-multi tblastn: 2.14.0+ exonerate from exonerate version 2.4.0 bedtools v2.31.0 barrnap 0.9 - rapid ribosomal RNA prediction R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting" git version 2.39.2 GNU parallel 20230922 HMMER 3.3.2 (Nov 2020); http://hmmer.org/ bc 1.07.1

Missing dependencies: 1

#####################

Checking R packages

##################### data.table 1.14.10 stringr 1.5.1 sybil 2.2.0 getopt 1.20.4 doParallel 1.0.17 foreach 1.5.2 R.utils 2.12.3 stringi 1.8.3 glpkAPI 1.3.4 BiocManager 1.30.22 Biostrings 2.66.0 jsonlite 1.8.8 CHNOSZ 2.0.0 httr 1.4.7

Missing R packages: 0

##############################

Checking basic functionality

############################## Optimization test: OK Building full model: OK Blast test: OK

Passed tests: 3/3

I see the missing dependency 'awk'. Is this the reason I couldn't run the 'find-transport' option? And even though I couldn't get what I was looking for, the 'gapseq' tool helped me with some unexpected discoveries in research work. I am grateful to the team who made this application.

On Tue, Jan 23, 2024 at 3:25 PM jo @.***> wrote:

hi @ashish193006 https://github.com/ashish193006 Could you please try ./gapseq find-transport -b 200 -m Ammonia toy/myb71.fna.gz? And if this fails, can you copy and paste the output of ./gapseq test?

— Reply to this email directly, view it on GitHub https://github.com/jotech/gapseq/issues/203#issuecomment-1905688767, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVQ7NI2XRYV6XKO5RYDBRXLYP6CJ7AVCNFSM6AAAAABBZGAGVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBVGY4DQNZWG4 . You are receiving this because you were mentioned.Message ID: @.***>

-- Regards, Ashish Kumar Singh CSIR-SRF EBGD, CSIR-NEERI, Mob. no. +91 8888485812

jotech commented 8 months ago

hi I'm sorry for the late response!

It seems it didn't work because you forgot to update to the newest version after the initial problem was fixed. If it is still a problem, please update to the latest gapseq version (e.g., via git pull) and try again.