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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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SQM Tools 1.6.0 compatability with sqm_longreads.pl? #649

Closed mscarbor closed 1 year ago

mscarbor commented 1 year ago

Hello!

I used sqm_longreads.pl to analyze a large time series of nanopore data. I am using "SqueezeMeta on Long Reads v1.6.0, September 2022 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN" - The SQM job finished successfully, but SQMTools does not like the LoadSQM command:

Error in loadSQM("/users/m/s/mscarbor/Peyton_Landfill_sqm_longreads/") : Directory "/users/m/s/mscarbor/Peyton_Landfill_sqm_longreads/" does not seem to contain a valid SqueezeMeta project

The directory I am pointing loadSQM to contains a directory for each sample as well as: Peyton_Landfill_sqm_longreads.out.allreads Peyton_Landfill_sqm_longreads.out.allreads.funcog Peyton_Landfill_sqm_longreads.out.allreads.funkegg Peyton_Landfill_sqm_longreads.out.allreads.mcount Peyton_Landfill_sqm_longreads.out.allreads.stats Peyton_Landfill_sqm_longreads.out.mappingstat

Should I expect SQMTools to work with output from sqm_longreads.pl?

Thanks!

fpusan commented 1 year ago

Yes, but use sqmreads2tables.py to generate aggregated taxonomy/function tables (you can also select subsets at this stage) and then load the data into R/SQMtools with loadSQMlite.

mscarbor commented 1 year ago

Thank you!