SQMtools issue with running sqm2tables.py

[mefeeney]

Having issues working with my data in r using SQMtools. Seen other users with similar issues but the fixes associated with #416 do not seem to be helping and I'm not sure what I'm doing wrong.
I ran squeezemeta in a hpc/computing cluster. Downloaded the resulting project folder locally to a windows computer.
Both cluster and local windows squeezemeta installs are version 1.5.1. and are the same version as far as I am aware.
I have R (v 4.1.3) and R studio (2021.09.1 Build 372) currently installed.
I installed SQMtools in R with the following:
install.packages("reshape2")
install.packages("pathviewr")
install.packages("data.table")
install.packages("BiocManager")
BiocManager::install("pathview")
install.packages("H:/Cluster_backup/SqueezeMeta/lib/SQMtools", repos = NULL, type = "source")
library(SQMtools)
library(reshape2)
library(data.table)
library(BiocManager)
library(pathview)

• Note I installed pathview with BiocManager because install.packages("pathview") gives an error along the lines of 'pathview is not available for this version of R). Followed instructions from here.

SQMtools will load, and I can run 'loadSQMlite' on the outputs I generated from sqm2tables.py however I cannot use 'subsetTax' on the resulting object because The first argument must be a SQM object.

I cannot run loadSQM when I give it the path to my squeezemeta analysis folder. (project.large=loadSQM("H:/Cluster_backup/water500test3"))
I get the following error:
Error in loadSQM("H:/Cluster_backup/water500test3") :
An error occurred while running sqm2tables.py
In addition: 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'

I tried the solution in #416 , changing the following:
$installpath = "/home/zeiss/anaconda3/envs/SqueezeMeta/SqueezeMeta";
#$databasepath = "/mnt/h/Cluster_backup/SqueezeMeta/makedb/db";
$databasepath = "/mnt/h/Cluster_backup/SqueezeMeta/makedb/db";

I added $mappingstat = "$resultpath/10.$projectname.mappingstat"; to line 55,

I tried re-running step 9 perl script for my project

I still get the error?

[fpusan]

Hi!
Did you follow
https://github.com/jtamames/SqueezeMeta/wiki/Using-SQMtools-in-a-Windows-environment
?
You need to run sqm2tables.py manually in the Linux environment before migrating the data to Windows.
Try:
sqm2tables.py /path/to/project /path/to/project/results/tables
And then move the project to your Windows computer (you don't need all the files, the needed files are listed in the wiki article I linked).
Let me know if this works for you.

[mefeeney]

Hello,

Thank you for pointing this out, the issue was I put the wrong output path for sqm2tables.py when I ran it on the cluster.
I ran sqm2tables.py with /path/to/project/results/tables, and running SQMtools locally worked fine.

[fpusan]

Glad to hear it works!