"sqm_annot.pl" doesn't use optional parameters

[PuspenduSardar]

Hello!

I have used the sqm_annot.pl script for functional annotation of an assembly file. The script runs fine, but the problem is it uses the default parameters ONLY. For example, I wanted to use 86 threads with no COG annotation. According to the sqm_annot.pl help message, I used -t 86 --nocog flags. SqueezeMeta still uses the default 12 threads and produces COG annotation. Could you please let me know if there is a way to make use of these non-default parameters? It would be great if there is a way to declare the percentage of identity for the diamond and evalue.

I am using SqueezeMeta v1.5.2

Many thanks!
Regards,
Puspendu

[jtamames]

Hello Puspendu
You are right, there is not a straightforward way to specify these parameters in sqm_annot.pl. I am taking this into account to fix in in upcoming versions. What sqm_annot.pl does is calling SqueezeMeta and some SqueezeMeta scripts. SqueezeMeta uses the file parameters.txt to define its settings. You can find there the ones controlling the behavior of the Diamond homology search:

$minidentax4=40;	  #-- STEP4: Minimum identity for Diamond, for tax only (also for STEP8)
$evaluefun4=1e-03;	  #-- STEP4: evalue for Diamond, for functions only (also for STEP8)
$minidenfun4=30;	  #-- STEP4: Minimum identity for Diamond, for functions only (also for STEP8)

Change these accordingly.
The -t option is not implemented in sqm_annot.pl (it takes the default of 12 threads. For changing it, please edit line 111:
my $command="perl $scriptdir/SqueezeMeta.pl -s $tempsample -f $aadir -m sequential $blockoption --nopfam -c 0 --empty";
to:
my $command="perl $scriptdir/SqueezeMeta.pl -s $tempsample -f $aadir -m sequential $blockoption -t 86 --nocog --nopfam -c 0 --empty";
This will include also the --nocog option

Best,
J

[PuspenduSardar]

Hello @jtamames,

Thank you very much for your reply and the suggestion.
I have already started an analysis, and it's running for 3 days now. Would you recommend stopping it and using restart.pl script after editing the SqueezeMeta_conf.pl that has been generated during the run? (I am not sure though if restart would work in this case).
Many thanks,

Regards,
Puspendu

[jtamames]

No, restart will not work for sqm_annot. Which step it is now in, 04?

[PuspenduSardar]

Yes. blastx is running with nr db.

[jtamames]

Unfortunately there is no good way to know the progress of the blastx step. That is the most demanding step (blastx/nr), the rest of the pipeline will take less time. Consider if you want to wait a bit or rerun it setting higher number of threads.

[PuspenduSardar]

Thank you very much, @jtamames.
I'll close the issue now.