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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Error in loadSQM #577

Closed astromecki closed 1 year ago

astromecki commented 1 year ago

Hello,

First off, thank you for the excellent pipeline and documentation. I have run SqueezeMeta on my data and generated tabular outputs, and am now in the analysis phase.

I keep getting this error when trying to load my project into SQMtools in R:

> IRL_Moose_2013 = loadSQM('/data/amstromecki/Moose_MG_reads/116195/2013_reads/IRL_Moose_MG_2013/')
Loading total reads
Loading orfs
    table...
|--------------------------------------------------|
|==================================================|
    abundances...
    sequences
|--------------------------------------------------|
|==================================================|
    taxonomy...
|--------------------------------------------------|
|==================================================|
Loading contigs
    table...
    abundances...
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent

Could you please advise?

Thank you! Amanda

fpusan commented 1 year ago

Hi! I assume that you are using SqueezeMeta 1.5. That bug was fixed in the latest version, so I'd recommend updating to it. Once you activate the new environment (make sure to re-link the databases after updating, as shown in the ReadMe), you will need to run 19.getcontigs.pl /data/amstromecki/Moose_MG_reads/116195/2013_reads/IRL_Moose_MG_2013/. Hopefully everything works after that. Fernando

astromecki commented 1 year ago

Hi Fernando,

This worked great - I am now able to analyze my data in R. Thanks so much for your help and prompt reply!

All the best, Amanda

On Nov 9, 2022, at 7:05 AM, Fernando Puente-Sánchez @.***> wrote:

Hi! I assume that you are using SqueezeMeta 1.5. That bug was fixed in the latest version, so I'd recommend updating to it. Once you activate the new environment (make sure to re-link the databases after updating, as shown in the ReadMe), you will need to run 19.getcontigs.pl /data/amstromecki/Moose_MG_reads/116195/2013_reads/IRL_Moose_MG_2013/. Hopefully everything works after that. Fernando

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fpusan commented 1 year ago

Glad to hear! Closing issue