Jared Simpson
Jared Simpson
Hi @JesseBNL, I need a bit more information - what did `call-methylation` print at the end of the run? Did `nanopolish index` work correctly? How much coverage do you have...
If you only get a header line, and no line that says `[post-run summary]` then the process is probably still running, or failed (possibly ran out of memory?)
Can you paste the exact command you ran, and all the messages printed to the terminal?
If it terminates right after that line its probably running out of memory. Try to monitor the memory usage in another terminal window using `top` and see if the memory...
CPU usage of 99% is normal, I don't think that is the issue
Without some diagnostic information its pretty hard to debug. Can you try running this command, and paste all messages printed to the terminal result? ``` /usr/bin/time -v nanopolish/nanopolish call-methylation -t...
I just noticed that the region (`chr19:35600-203300`) is very close to the end of the chromosome so may be repetitive. Do you have any reads with MAPQ >20 there?
Do you have any other regions to try? I believe the most likely explanation is that nanopolish couldn't use any of your data
could you provide me with the BAM file for this region? On Thu, Aug 27, 2020 at 9:18 AM JesseBNL wrote: > Hmm, no this is all we captured. And...
If you can temporarily host on dropbox or google drive it would be best On Thu, Aug 27, 2020 at 9:46 AM JesseBNL wrote: > Yes, how can I send...