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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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Methcounts: problem with chrom order in mapped reads #177

Closed shashwatsahay closed 3 years ago

shashwatsahay commented 3 years ago

I have been trying to run methcounts and I have divided the dataset chromosome wise for faster run computation on our cluster but every time I run the command I get the error "problem with chrom order in mapped reads" what I don't understand if there is not more than a single chromosome in the file being processed how can this be an error?

terencewtli commented 3 years ago

Hi, which version of Methpipe are you using? And would you be able to provide the files for me to test?

shashwatsahay commented 3 years ago

I am using the current version of methpipe. But I solved the issue by directly providing individual chromosome file instead of the whole genome

hchetia commented 3 years ago

Hi, I am not sure if I need to open a new issue or not, but my problem is the same. I am getting the error "problem with chrom order in mapped reads" despite using the individual chromosome fasta files. I am using the v4.1.2-alpha version. The steps prior to the methcount step were ran with the fullmoonlizard version. Please help.