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orzechoj / piq-single

PIQ DNA footprinting. Cloned from https://bitbucket.org/thashim/piq-single
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Issue running PIQ #4

Open shankar2318 opened 1 year ago

shankar2318 commented 1 year ago

I am trying to run PIQ for the 139 Jaspar motif on my dataset. However, I am getting an error during the clustering step. The previous steps ran without a problem i.e. 'PWM hits across the genome' & 'BAM to internal binary format'. I am not sure how I proceed further so any help is greatly appreciated! Command used:

Rscript pertf.r /home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/common.djap.r /home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/motif_match_files/ /home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/tempo/ /home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/output/139.mm10.d0hr/ /home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/bamfiles/d0hr.Rdata 139

Error message:

Error in UseMethod("sofia") : error during clustering
Error msg: no applicable method for 'sofia' applied to an object of class "character"
 Args:/home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/common.djap.r:/home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/motif_match_files/:/home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/tempo/:/home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/output/139.mm10.d0hr/:/home/shankar2318/dj_atac/bowtie_align/bowtie_with_piwi/piq/piq-single/bamfiles/d0hr.Rdata:139
Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
AndrewHardigan commented 1 year ago

Same issue with RSofia happening for me. Not sure how to fix or if the issue, or if the issue is with Sofia in pert.r is with an intermediate file generated by prior steps.Any luck fixing this?

shankar2318 commented 1 year ago

Same issue with RSofia happening for me. Not sure how to fix or if the issue, or if the issue is with Sofia in pert.r is with an intermediate file generated by prior steps.Any luck fixing this?

I contacted the authors and they said they haven't seen the issue before either so I gave up on trying to solve it.

I would suggest you to look into "TOBIAS". It does the same analysis much better and is well maintained on github.