Installation

[hpyle50]

Hi, Could someone please tell me the code I should enter into terminal in order to install MetONTIIME? I already have most up-to-date conda and qiime2-2021.11 environments installed. I have tried to go thru the install.sh page without any success. Thank you for your help, I really appreciate it.

[MaestSi]

Hi, have you already run this?

git clone https://github.com/MaestSi/MetONTIIME.git
cd MetONTIIME
chmod 755 *
./install.sh

Did you get any errors? If yes, please report them. Moreover, which operative system are you working with? Simone

[hpyle50]

Thank you for the quick reply. I was using MAC OS but am going to try downloading virtual machine and using Ubuntu. I will update you on my progress and whether that fixes things. Thanks again!

H

[sulheim]

I also encounter several issues with the installation. At least, the installation does not seem to install R and neccessary libraries. Second, the error in the nohup files says the the R files can't be found...

[MaestSi]

Hi @sulheim , what OS are you running on? Which R files are you referring to? Please list the command you pasted and the error you got. Thanks, Simone

[sulheim]

I use Ubuntu 20 in WSL2. I run bash Launch_MinION_mobile_lab.sh test_MetONTIIME/fast5. After installing the required R packages, the nohup file says:

Welcome to MinION meta-barcoding mobile laboratory!

Raw reads directory: /root/git/MetONTIIME/test_MetONTIIME/fast5
Basecalled reads directory: /root/git/MetONTIIME/test_MetONTIIME/fast5_analysis/basecalling
Preprocessing directory: /root/git/MetONTIIME/test_MetONTIIME/fast5_analysis/preprocessing
Analysis and results directory: /root/git/MetONTIIME/test_MetONTIIME/fast5_analysis/analysis
Flow-cell: FLO-MIN106
Kit: SQK-RAB204
Expected amplicon length [bp]: 1400
Barcodes used in this experiment: BC01, BC02, BC03, BC04, BC05, BC06, BC07, BC08, BC09, BC10, BC11, BC12
Basecalling is going to be performed by : Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 6.0.1+652ffd179
Basecalling model: fast
Demultiplexing is going to be performed by guppy_barcoder after basecalling
Taxonomic classifier: Vsearch

Basecalling started at Fri Jan 21 10:05:31 2022
[40:40:20220121,100534.944921:ERROR exception_handler_server.cc:361] getsockopt: Invalid argument (22)
nohup.out (END)

[MaestSi]

Hi, that is a guppy_basecaller error. What Guppy version are you using? I can install the same version and do a quick test, it seems parameters may have changed. In the meanwhile, you could use Guppy v5.0, which I previously tested with the pipeline. EDIT: I just tested it with the newest Guppy 6.0.11 version, and it works, so I guess it has to be a problem due to WSL2 running Guppy. Please try running standalone Guppy on the test dataset and let me know if you succeed. Simone

[hpyle50]

Hi Simone, I have virtual machine and am now using ubuntu. I have installed conda, created metontiime environment. I have downloaded reference database (bioproject 33175) and am trying to use Import_database.sh command to import but am receiving error message "Import_database.sh: command not found"

Thank you for your help!

[MaestSi]

Hi, did you specify the path to the script? If you are already in MetONTIIME directory, just add ./ before the script name. Simone

[hpyle50]

Thanks again. Just ran script. Looks like it go to the last step before there was an error: Invalid value for '--input-path': Path '/home/qiime2/MetONTIIME/database_accession_taxonomy.txt' does not exist.

[MaestSi]

Hi, what is the full command you ran? Did you also specify the full path to the fasta file? Do not activate che MetONTIIME conda environment before running this instruction, since a different conda environment is created for this particular script. Simone

[tamara-nano]

Hey, I also have an issue with launching the Metontiime script: I've installed conda environment, guppy and metontiime in a docker container and call it via bitvise terminal on win10 and when I want to run it I get following error: bash Launch_MinION_mobile_lab.sh /data/nanopore/16S/fast5_pass/
(base) root@tamara:/MetONTIIME# nohup: appending output to 'nohup.out'

I just don't understand the issue and what could be a problem to cause that?

Edit: I've seen here that extra R-packages/libraries are required? Which ones would I need to install extra? Maybe this could be an issue for my nohup problem?

Thank you in advance :) Tamara

[hpyle50]

Hi, the full command that I ran, while in the MetONTIIME directory and starting in the base conda environment, is: ./Import_database.sh "database"

Please note that the database file is also in the same MetONTIIME directory

I have tried the 2 times, and each time receive the error message:

(1/1) Invalid value for '--input-path': Path '/home/qiime2/MetONTIIME/database_accession_taxonomy.txt' does not exist.

Thanks again Simone.

[MaestSi]

Is “database” a fasta file, or is it just a placeholder? It seems it is not able to find it...please try specifying the full path to the fasta file. SM

[MaestSi]

@tamara-nano : that doesn’t look like an error, it just tells you that the script is run in background, and that standard output and standard error are redirected to the nohup.out file. Please have a look inside the file to see if you had any errors. Ps: since the output is appended at each execution of the program, it may be easier to delete the file together with the output directory, stop the process (if running) and run it again, to better identify the error messages. SM

[tamara-nano]

@MaestSi : Thank you very much, I could work it out now and it is running! :)

[MaestSi]

Hi @hpyle50 , I'm closing the issue due to inactivity. In case you face any other issues with the installation, please reopen it. Simone