error in loadSQM

[Nykolazzo72]

Hello, We' ve succesfully processed 6 metagenomic samples with SqueezeMeta (sequential mode), and we are experiencing some troubles while trying to further analyze our results using SQMtools through rstudio. After invoking rstudio in SqueezeMeta conda environment and loading the SQMtools library, we ran the following command and were greeted with this error message:

N77 = loadSQM('/home/usuario/N77/', engine = 'data.table') Loading total reads Loading orfs table... abundances... sequences taxonomy... Loading contigs table... abundances... Error in [.data.frame(x, i, j, drop) : undefined columns selected Además: Warning message: In sprintf("%s/results/tables/%s.superkingdom.%s.abund.tsv", project_path, : one argument not used by format '%s/results/tables/%s.superkingdom.%s.abund.tsv'

Thanks in advance for your assistance!

[fpusan]

I suspect your project was generated with an older version of SqueezeMeta. What version did you use for generating the project, and what version of SQMtools are you using to load it?

[Nykolazzo72]

Hi Fernando,

Thanks for your prompt response. Answering your question, the project was generated using SqueezeMeta v 1.6.0 and the SQMtools version is 0.8.0. Greetings,

Nicolás.

El vie, 17 feb 2023 a las 9:16, Fernando Puente-Sánchez (< @.***>) escribió:

I suspect your project was generated with an older version of SqueezeMeta. What version did you use for generating the project, and what version of SQMtools are you using to load it?

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[fpusan]

Try using SQMtools version 1.6.0 or 1.6.1

[Nykolazzo72]

Thanks, I'll check it out.

El vie., 17 de feb. de 2023 17:59, Fernando Puente-Sánchez < @.***> escribió:

Try using SQMtools version 1.6.0 or 1.6.1

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[Nykolazzo72]

Hi Fernando,

I finally reinstalled SqueezeMeta (albeit a newer version) and that did the trick! Thanks a bunch for your help!

Nicolás.

El vie, 17 feb 2023 a las 18:55, Nicolas Cordeiro @.***>) escribió:

Thanks, I'll check it out.

El vie., 17 de feb. de 2023 17:59, Fernando Puente-Sánchez < @.***> escribió:

Try using SQMtools version 1.6.0 or 1.6.1

— Reply to this email directly, view it on GitHub https://github.com/jtamames/SqueezeMeta/issues/627#issuecomment-1435260798, or unsubscribe https://github.com/notifications/unsubscribe-auth/A56EA5IU2SIAPXI6C66PM4TWX7RDBANCNFSM6AAAAAAU6KRVZQ . You are receiving this because you authored the thread.Message ID: @.***>

[fpusan]

glad to hear. clossing issue!