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"sqm_annot.pl" doesn't use optional parameters #540
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Hello Puspendu
Change these accordingly. Best, |
Hello @jtamames, Thank you very much for your reply and the suggestion. Regards, |
No, restart will not work for sqm_annot. Which step it is now in, 04? |
Yes. blastx is running with nr db. |
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. |
Thank you very much, @jtamames. |
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 thesqm_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
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