Hello,
thank you so much for developing this tool!! It's been working well for several different plant genomes (helping me to infer putative centromeres when I don't have access to Chip-seq or FISH data), but I've encountered a slight problem recently. I've been having two problems
The first one might be related with small chromosomes! I'm working with a plant genome that is ~180Mb with 34 chromosomes, and most chromosomes are <5Mb. So, I have edited the Setup_Run_Repeats.sh script to accept these chromosomes, but the summary files are not being generated. I started digging and I SUSPECT something with the 5Mb window from the Shannon_diversity plots. Because not all chromosomes are going through, the summary files might be stuck (???). Additionally, in the Summary_output/pdfs/ directory I only have cucu_H0-AT_Chr#_roll_mean_Shannon_1000.pdf for the chromosomes >5Mb.
This is just to highlight how smaller windows go through all chromosomes, except the 5Mb one.
In the end of the run, this is the error that I'm getting:
[1] "Summary_plots2.R starting"
[1] "plot all chromosomes roll_sum_histogram and Shannon starting"
Error in chr_list1[, 3] : subscript out of bounds
Calls: plot_all_chromosomes
Execution halted
./Summary_output/isochores
./Summary_output/pdfs/histograms
RepeatOBserverV1 complete
I initially thought it was something with the chromosome name parsing, but when I tested it, I do get the three expected columns... So I dunno...
Log:
repeat_observer_cucu_log.txt
The second problem I have less of a guess of what is going on. Big genome, big chromosomes, but the histograms are not being generated.
Log for this genome:
cerato_log.txt
Thank you so much,
Y
Hello,
thank you so much for developing this tool!! It's been working well for several different plant genomes (helping me to infer putative centromeres when I don't have access to Chip-seq or FISH data), but I've encountered a slight problem recently. I've been having two problems
The first one might be related with small chromosomes! I'm working with a plant genome that is ~180Mb with 34 chromosomes, and most chromosomes are <5Mb. So, I have edited the Setup_Run_Repeats.sh script to accept these chromosomes, but the summary files are not being generated. I started digging and I SUSPECT something with the 5Mb window from the Shannon_diversity plots. Because not all chromosomes are going through, the summary files might be stuck (???). Additionally, in the Summary_output/pdfs/ directory I only have cucu_H0-AT_Chr#_roll_mean_Shannon_1000.pdf for the chromosomes >5Mb.
This is just to highlight how smaller windows go through all chromosomes, except the 5Mb one.
In the end of the run, this is the error that I'm getting:
I initially thought it was something with the chromosome name parsing, but when I tested it, I do get the three expected columns... So I dunno...
Log:
repeat_observer_cucu_log.txt
The second problem I have less of a guess of what is going on. Big genome, big chromosomes, but the histograms are not being generated.
Log for this genome:
cerato_log.txt
Thank you so much,
Y