FORUMNot getting any output from ‘maker_map_ids’
sjossey asked 3 months ago



Hi,
I finished running Maker for annotation and want to change the IDs. I am using the command
$ module load nixpkgs/16.09 gcc/5.4.0 openmpi/2.1.1 maker/2.31.9
$ maker_map_ids –prefix BMM1_ –justify 8 Maker_GFF.all.gff > Maker_GFF.all.id.map
This gives me a empty file ‘ Maker_GFF.all.id.map’
The file ‘Maker_GFF.all.gff’  was produced at the end of Maker using ‘gff3_merge’ so the format should be correct.
Hope someone can help me with this!
Thanks,
Sushma

2 Answers
jrosner Staff answered 2 months ago



Hi Sushma,
Were you able to figure out the problem yet?
My inclination is to think there is in fact an issue with the input file… i.e. some kind of formatting problem.  Even if it was produced by gff3_merge, it’s still a possibility.
Perhaps you could try running one of the input files prior to merging to see if that gives some output?

sjossey answered 2 months ago



Well, I just could not run it so just had to change the ids in excel and made a  “Maker_GFF.all.id.map’ looking at the format online and then was able to run the subsequent commands using the  Maker_GFF.all.id.map
Thanks,
Sushma