mutation_analysis Undefined subroutine &analysis::read_motifs

[aciernia]

I am trying to run a pairwise motif mutation analysis using MMARGE.pl mutation_analysis but am getting the following error: Undefined subroutine &analysis::read_motifs called at /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux/bin//analyze_ChIP_mutations_tree.pl line 264.

I ran the following commands:
#annotate peakfile for tag directories for samples 1-8 listed in Media_TagDirectories.txt
annotatePeaks.pl BTBRmedia_greater_C57media.mm10.bed mm10 -noann -nogene -dfile Media_TagDirectories.txt > BTBRmedia_greater_C57media.txt

#MMARGE.pl mutation_analysis
MMARGE.pl mutation_analysis -file BTBRmedia_greater_C57media.txt -ind BTBR_1,BTBR_2,BTBR_3,BTBR_4,C57_1,C57_2,C57_3,C57_4 -output output-BTBR_greater_C57media -plot plot-BTBR_greater_C57media -core 8

Undefined subroutine &analysis::read_motifs called at /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux/bin//analyze_ChIP_mutations_tree.pl line 264.

Any thoughts on how to fix this?

Thanks!

[vlink]

Hi Annie, Thanks for using MMARGE! I am sorry for that. Just add a line package analysis; in /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux/bin/analysis_tree.pm right above the line use config; That should fix this problem. I also updated the install script to fix the problem. Please let me know if you have any other problems. Best, Verena

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On Aug 28, 2018, at 11:26 PM, Annie Vogel Ciernia ***@***.***> wrote: I am trying to run a pairwise motif mutation analysis using MMARGE.pl mutation_analysis but am getting the following error: Undefined subroutine &analysis::read_motifs called at /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux/bin//analyze_ChIP_mutations_tree.pl line 264. I ran the following commands: #annotate peakfile for tag directories for samples 1-8 listed in Media_TagDirectories.txt annotatePeaks.pl BTBRmedia_greater_C57media.mm10.bed mm10 -noann -nogene -dfile Media_TagDirectories.txt > BTBRmedia_greater_C57media.txt #MMARGE.pl mutation_analysis MMARGE.pl mutation_analysis -file BTBRmedia_greater_C57media.txt -ind BTBR_1,BTBR_2,BTBR_3,BTBR_4,C57_1,C57_2,C57_3,C57_4 -output output-BTBR_greater_C57media -plot plot-BTBR_greater_C57media -core 8 Undefined subroutine &analysis::read_motifs called at /afs/.genomecenter.ucdavis.edu/software/mmarge/1.0/lssc0-linux/bin//analyze_ChIP_mutations_tree.pl line 264. Any thoughts on how to fix this? Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD8p6L5pXr9iIVdClKIpV-pgZdqE1gqRks5uVbWLgaJpZM4WQbJ_>.

[aciernia]

This fixed it! Thanks so much!