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mutation_analysis Undefined subroutine &analysis::read_motifs #2

Closed aciernia closed 5 years ago

aciernia commented 6 years ago

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 commented 6 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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aciernia commented 5 years ago

This fixed it! Thanks so much!