search

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
348 stars 81 forks source link

Error in LoadSQM #667

Closed afsanarupa closed 1 year ago

afsanarupa commented 1 year ago

Hi, I have recently updated R packages which automatically updated SQMtools. After that I'm having this issue. I have tried 19.getcontigs /media/bioinfo/hdd2/Metagenome_jute/metagenom_run_final. I also tried to remove and downgrade the package using "remove.packages("SQMtools")" and "install.packages("SQMtools", version = "0.7.1", repos = "http://cran.us.r-project.org")" but I end up getting version 1.6.2.

met_jute = loadSQM('/media/bioinfo/hdd2/Metagenome_jute/metagenom_run_final', engine = 'data.table') 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 In addition: Warning message: In loadSQM("/media/bioinfo/hdd2/Metagenome_jute/metagenom_run_final", : Your project was created with SqueezeMeta v1.5, while this is SQMtools v1.6.2. You can ignore this message if things are working fine for you, but if you experience any issue consider using the right version of SQMtools for this project

fpusan commented 1 year ago

Hi! Yes, you can fix it by activating the SqueezeMeta environment and running 19.getcontigs.pl /path/to/project. Afterwards the project should load correctly in SQMtools v1.6.2.

afsanarupa commented 1 year ago

Hi, I have done that but i'm still getting the same error in R.

fpusan commented 1 year ago

Ah yes, I didn't read your first message correctly. Then you will need to install the latest version of SqueezeMeta in a different environment, activate it and then run the new version of script 19.

fpusan commented 1 year ago

(here I am assuming that you ran the script without previously updating your SqueezeMeta version, correct me otherwise)

afsanarupa commented 1 year ago

Hi, Thanks. It worked after I ran 19.getcontigs.pl after downloading new version of SqueezeMeta in a different envrionment.