hi，I ran into difficulties building the index in the first step:

[yzyupup]

this in my command: tombo resquiggle /home/yzy/ont-data/MinION_CP_NAT/fin/ CP.fasta --processes 4 --num-most-common-errors 5 The program keeps showing 5 most common unsuccessful read types (approx. %):--corrected-group] and [--overwrite] is not set Did I make a mistake? Thank you！！！

[SycamoreLeaf]

Hi @yzyupup . Add the --overwrite flag.

[yzyupup]

Hi @yzyupup . Add the --overwrite flag.

Hi，thank you for your attention , add the --overwrite in the end? tombo resquiggle /home/yzy/data/NAT_single_fast5/5/ CP.fasta --processes 4 --num-most-common-errors 5 --overwrite The result of this is the same as before. Did I add it wrong?

[SycamoreLeaf]

@yzyupup can you share a screenshot showing both the command you typed and the output you saw?

[yzyupup]

@yzyupup can you share a screenshot showing both the command you typed and the output you saw?

tombo resquiggle /home/ywj/fang_lab/NAT_single_fast5/3 CP.fasta --processes 4 --num-most-common-errors 5 --overwrite thanks！ tombo resquiggle /home/ywj/fang_lab/NAT_single_fast5/3 CP.fasta --processes 4 --num-most-common-errors 5 --overwrite thanks！

[SycamoreLeaf]

Based on the text in your screenshots, it appears Tombo is working correctly.

[yzyupup]

Based on the text in your screenshots, it appears Tombo is working correctly.

Hello, with your help, I completed the first step index construction. But after comparing the two sets of data to find the methylation sites, I encountered new troubles. Whenever I run to this step, the program will stop and the interface will remain motionless. Is this something I made a mistake or is it because my data is too large? The following is a screenshot of my operation, the interface has been stopped in this state thanks！

[marcus1487]

This is an issue with a newer version of numpy. A downgrade with pip install "numpy<1.20" should resolve this issue.