I'm running FAIREseq data through the most basic DiffBind pipeline in the tutorial and dba.analyze successfully goes through making final dispersion estimates, then never finishes. I don't think it's still running, it's been over an hour and R is using 0% of my CPU. Did I do something stupid and obvious or is some dependency not working properly, or something else? I'm not using any input control, which I've read is optional, is that causing an issue? Here's some details

contents of sample_sheet.csv
SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,Peaks,PeakCaller
DzSG_FAIRE_Rep1,DzSG,Dazao,none,FAIRE,1,../bam/Bmori_Dazao_SG_FAIRE_Rep1_std.bam,../macs2/Bmori_Dazao_SG_FAIRE_Rep1/Bmori_Dazao_SG_FAIRE_Rep1_peaks.narrowPeak,bed
DzSG_FAIRE_Rep2,DzSG,Dazao,none,FAIRE,2,../bam/Bmori_Dazao_SG_FAIRE_Rep2_std.bam,../macs2/Bmori_Dazao_SG_FAIRE_Rep2/Bmori_Dazao_SG_FAIRE_Rep2_peaks.narrowPeak,bed
DzSG_FAIRE_Rep3,DzSG,Dazao,none,FAIRE,3,../bam/Bmori_Dazao_SG_FAIRE_Rep3_std.bam,../macs2/Bmori_Dazao_SG_FAIRE_Rep3/Bmori_Dazao_SG_FAIRE_Rep3_peaks.narrowPeak,bed
D872SG_FAIRE_Rep1,D872SG,D872,none,FAIRE,1,../bam/Bmori_D872_SG_FAIRE_Rep1_std.bam,../macs2/Bmori_D872_SG_FAIRE_Rep1/Bmori_D872_SG_FAIRE_Rep1_peaks.narrowPeak,bed
D872SG_FAIRE_Rep2,D872SG,D872,none,FAIRE,2,../bam/Bmori_D872_SG_FAIRE_Rep2_std.bam,../macs2/Bmori_D872_SG_FAIRE_Rep2/Bmori_D872_SG_FAIRE_Rep2_peaks.narrowPeak,bed
D872SG_FAIRE_Rep3,D872SG,D872,none,FAIRE,3,../bam/Bmori_D872_SG_FAIRE_Rep3_std.bam,../macs2/Bmori_D872_SG_FAIRE_Rep3/Bmori_D872_SG_FAIRE_Rep3_peaks.narrowPeak,bed
DzBmE_FAIRE_Rep1,DzBmE,Dazao,none,FAIRE,1,../bam/Bmori_Dazao_BmE_FAIRE_Rep1_std.bam,../macs2/Bmori_Dazao_BmE_FAIRE_Rep1/Bmori_Dazao_BmE_FAIRE_Rep1_peaks.narrowPeak,bed
DzBmE_FAIRE_Rep2,DzBmE,Dazao,none,FAIRE,2,../bam/Bmori_Dazao_BmE_FAIRE_Rep2_std.bam,../macs2/Bmori_Dazao_BmE_FAIRE_Rep2/Bmori_Dazao_BmE_FAIRE_Rep2_peaks.narrowPeak,bed
DzBmE_FAIRE_Rep3,DzBmE,Dazao,none,FAIRE,3,../bam/Bmori_Dazao_BmE_FAIRE_Rep3_std.bam,../macs2/Bmori_Dazao_BmE_FAIRE_Rep3/Bmori_Dazao_BmE_FAIRE_Rep3_peaks.narrowPeak,bed

commands in R:

library(DiffBind)

library(rtracklayer)

bm_faire <- dba(sampleSheet="sample_sheet.csv")

bm_faire <- dba.count(bm_faire)

bm_faire <- dba.normalize(bm_faire)

bm_faire <- dba.contrast(bm_faire, categories=DBA_TISSUE)

bm_faire <- dba.analyze(bm_faire)

output from final line:

Applying Blacklist/Greylists...

No genome detected.

Analyzing...
gene-wise dispersion estimates

mean-dispersion relationship

final dispersion estimates

Has anyone else experienced this? Any ideas?



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