sqm2tables.py - All fixes in one place :-)

[biobrad]

Not an issue - i had a couple of problems and found this data in separate places. Adding here for the next person who needs it.

If you have run SqueezeMeta on a HPC and are now working with the results locally...

Fix SqueezeMeta sqm2tables.py issue:

In the file in the analysis folder - SqueezeMeta_conf.pl - Change path to results folder and db to match your install and db locations
$installpath = "/home/harbj019/miniconda3/envs/newsqueezemeta/SqueezeMeta";
$databasepath = "/home/harbj019/dbs/db";

If you have upgraded your SqueezeMeta Install to a later version (after 1.2) and want to work with
data from a version 1.2 or earlier:

Fix SqueezeMeta sqm2tables.py issue:

In the file in the analysis folder - SqueezeMeta_conf.pl -

below line 55 add:
$mappingstat = "$resultpath/10.$projectname.mappingstat";

Run step 9 again (perl 09.summarycontigs3.pl /path/to/your/project). (use full path)
Remove the /path/to/your/project/results/tables, if present.

Save and run sqm2tables again.
sqm2tables.py /<project> /<projectname>/table

[fpusan]

Great, thanks for compiling this! :)

[biobrad]

Thank you for squeezemeta! You have done a lot for the research community!

…

On Thu, 20 Jan 2022, 8:20 pm Fernando Puente-Sánchez, < ***@***.***> wrote: Great, thanks for compiling this! :) — Reply to this email directly, view it on GitHub <#416 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANITBGQ43UUTSAWJ2AE56MTUW7LHLANCNFSM5MMC6X5A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[fpusan]

If you are trying to run SQMtools (loadSQM in particular) in Windows without having run sqm2tables.py in your Linux computer, the command will fail complaining about sqm2tables.py.

If this is the case, make sure you run sqm2tables.py in your Linux environment before migrating the data to Windows, with
sqm2tables.py /path/to/project/ /path/to/project/results/tables

Find more details in
https://github.com/jtamames/SqueezeMeta/wiki/Using-SQMtools-in-a-Windows-environment

[fpusan]

... and note that you also have sqm2zip.py to easily transfer your project to a different machine.
Also installing SQMtools has become much easier in Windows and Mac (see ReadMe!)

[srz11d]

Hello,
I am having issues with loading my files too.

I have my files in 10 separate folders (10 samples), every folder contains the following files:

I tried to load the files in RStudio but I seemed to fail:
I read other comments and I tried:

library('SQMtools')
Indoor1 = loadSQM('/Users/user/Documents/SQM_Ponds1')

But then I got:

Error in loadSQM("/Users/user/Documents/SQM_Ponds1") : 
  Directory "/Users/user/Documents/SQM_Ponds1" does not seem to contain a valid SqueezeMeta project

Are there any missing files?

Thanks!

[fpusan]

did you rename your SqueezeMeta_conf.pl files?
I see one of them is named SqueezeMeta_conf_Indoor1.pl

[srz11d]

I did change the name to identify the samples, but after reading other comments, I decided to load every single folder. The folder results contains a folder named tables. I haven't changed any tables or files, the format looks like this (for each file):

I ran:
Outdoor2 = loadSQM('/Volumes/Intenso/Hazda/Outdoor.2')

and I got:

Outdoor2 = loadSQM('/Volumes/Intenso/Hazda/Outdoor.2')
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("/Volumes/Intenso/Hazda/Outdoor.2") :
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

Could the version of SQM be the reason my files are not processed?

[fpusan]

yes, you should be using the SQMtools version that was shipped with SqueezeMeta v1.5