Could not use find-transport function using '-m' option for specific metabolite.

[ashish193006]

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]

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]

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

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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 <#203 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVQ7NI53VFNBCF4ZKPRJ5DLYOKAUFAVCNFSM6AAAAABBZGAGVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJQGQ2TCNZUGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ashish193006]

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

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---------- 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 > <#203 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AVQ7NI53VFNBCF4ZKPRJ5DLYOKAUFAVCNFSM6AAAAABBZGAGVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJQGQ2TCNZUGE> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

[Waschina]

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]

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

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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 <#203 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVQ7NIZH5JY4XFWDHO7YDCLYOVN6PAVCNFSM6AAAAABBZGAGVWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJSGUYTSNRSGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[jotech]

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]

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 f96e127 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.

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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 <#203 (comment)>, 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]

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.