Error in Make.file

1

Below is the error I recieved. I used my current version of Mothur (1.48.0) 3 weeks ago to process some data and everything went smoothly. This week I am processing a much smaller set of data. Below is the input and error output.

There are a few other make.file topics. I read through them to troubleshoot my problem with no resolution.

Please advise, Thanks!

mothur > make.file(inputdir=mothurhome, type=fastq, prefix=stability)

[ERROR]: basic_string::replace: __pos (which is 4294967295) > this->size() (which is 173)RAM used: 12.032Gigabytes . Total Ram: 15.672Gigabytes.

has occurred in the InteractEngine class function getCommand. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry

‘make.file’ is not recognized as an internal or external command,
operable program or batch file.

2

Hi Jsabo01,

Can you post the first 10 or so lines from your mothur session? It should look something like this…

Mac version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.48.0
Last updated: 5/20/22
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

I’m worried that you are accidentally using an older version of mothur since it’s complaining about not knowing what the make.file function is

Pat

3

Hi Pat,

Here you go.

Microsoft Windows [Version 10.0.19045.4412]
(c) Microsoft Corporation. All rights reserved.

C:\Users\SABOJA> cd OneDrive - Idaho National Laboratory\Desktop\Works in progress\Battery gene contamination_Kris Egan\Mothur

C:\Users\SABOJA\OneDrive - Idaho National Laboratory\Desktop\Works in progress\Battery gene contamination_Kris Egan\Mothur>Mothur.exe
Windows version

Using Boost
mothur v.1.48.1
Last updated: 5/15/24
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type ‘help()’ for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type ‘quit()’ to exit program

[NOTE]: Setting random seed to 19760620.

Interactive Mode

mothur > make.file(inputdir=., type=fastq, prefix=stability)

Setting input directories to:
C:\Users\SABOJA\OneDrive - Idaho National Laboratory\Desktop\Works in progress\Battery gene contamination_Kris Egan\Mothur\

3

Output File Names:
C:\Users\SABOJA\OneDrive - Idaho National Laboratory\Desktop\Works in progress\Battery gene contamination_Kris Egan\Mothur\stability.files

mothur > make.file(inputdir=mothurhome, type=fastq, prefix=stability)

[ERROR]: basic_string::replace: __pos (which is 4294967295) > this->size() (which is 173)RAM used: 11.6713Gigabytes . Total Ram: 15.672Gigabytes.

has occurred in the InteractEngine class function getCommand. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry

C:\Users\SABOJA\OneDrive - Idaho National Laboratory\Desktop\Works in progress\Battery gene contamination_Kris Egan\Mothur>

4

Thanks for reporting this bug. I have created a GitHub issue where you can track it’s progress.

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