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agshumate / Liftoff

An accurate GFF3/GTF lift over pipeline
GNU General Public License v3.0
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Use of -mm2_options gives usage error #111

Open sanyalab opened 2 years ago

sanyalab commented 2 years ago

Hello,

I am getting an error something like unrecognizable command for -p 0.9 when I use the -mm2_options.

My Command is as below: Please let me know if the syntax is accurate or not. I tried different ways of specifying -mm2_options (with single quotes) but the same error.

/mnt/common/rh6/annotate/Anaconda3/bin/liftoff -g Ref.gff3 -o Target_OUT.gff3 -u unmapped.txt -dir intermediate_files -p 24 -m /home/sanyalab/READ-ALIGNERS/minimap2-2.24_x64-linux/minimap2 -mm2_options="-a --end-bonus 5 --eqx -N 50 -p 0.9" -chroms chr.txt Target.fa Ref.fa

Thanks Abhijit

sanyalab commented 2 years ago

Hi,

I also tried with the option -mm2_options -a --end-bonus 5 --eqx -N 50 -p 0.9 without the =. it does not work. Please advice. Further here is the error that I get ERROR: failed to open file '=-a': No such file or directory

Thanks Abhijit

agshumate commented 2 years ago

Hello, apologies for the delayed response. can you specify which version of liftoff you are using?

sanyalab commented 2 years ago

Hello Alaina,

I am using the latest v1.6.3. Also at the beginning of every run I see the following warnings. But thats ok i guess.

(base) lxjh634:/home/sanyalab$ liftoff --version /mnt/common/rh6/annotate/Anaconda3/lib/python3.8/site-packages/Liftoff-1.6.3-py3.8.egg/liftoff/run_liftoff.py:45: SyntaxWarning: "is not" with a literal. Did you mean "!="? /mnt/common/rh6/annotate/Anaconda3/lib/python3.8/site-packages/Liftoff-1.6.3-py3.8.egg/liftoff/run_liftoff.py:45: SyntaxWarning: "is not" with a literal. Did you mean "!="? v1.6.3

Thanks Abhijit

sanyalab commented 2 years ago

HI Alaina,

Any update on the error?

Thanks Abhijit

agshumate commented 2 years ago

hi, i am not able to reproduce this. would you be able to share your data with me?

sanyalab commented 2 years ago

Hi,

I changed the system and I do not get the error messages. Seems to be working now. Sorry for the alarm.

On a separate subject, if I were to liftoff annotations from one line to another of the same species, which parameter in liftoff will have the best effect, since I know these lines are highly syntenic. Changing "-s" and/or "-a" to over 0.9 or changing the minimap options "-p" to 0.9.

Thanks a lot Abhijit