Closed aciernia closed 5 years ago
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
On Aug 28, 2018, at 11:26 PM, Annie Vogel Ciernia notifications@github.com 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!
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This fixed it! Thanks so much!
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!