Error running slide variants

[doshirLV]

Command:

python /path/to/EpiNano/misc/Slide_Variants.py sample.minus_strand.per.site.csv 5

Error:

Traceback (most recent call last): File "/path/to/EpiNano/misc/Slide_Variants.py", line 20, in <module> slide_per_site_var(per_site_var, kmer_len) File "/path/to/EpiNano/misc/../epinano_modules.py", line 861, in slide_per_site_var tmpfh = open (out_tmp,'r') FileNotFoundError: [Errno 2] No such file or directory: 'sample.minus_strand.per_site_var.5mer.tmp'

Notes:

• When I open the sample.minus_strand.per_site_var.5mer.csv file, which should be the output of the Slide_Variants.py function, it is empty with only a header.
• I could run it perfectly fine with the plus strand of the same sample.
• Also, when I observe the files as the script is running, a sample.minus_strand.per_site_var.5mer.tmp file definitely gets created in the directory, but something happens where it cannot be found when the script finishes.
• Any idea what might be causing this?

Thank you for the help, Raj

[Huanle]

Hi @doshirLV

I have requested to commit changes to the repo. The new script will be available very soon. Once you can clone it, give it a go and hit me up whenever you run into any problems.

Best, Huanle

[enovoa]

Can you please test the new slide_variants script from EpiNano 1.2.3? Thanks

[doshirLV]

Thank you for the new slide_variants script and for providing feedback on the non-consecutive-sites file @Huanle. Feel free to close that other issue, as I do not have any problems with the speed of this command or have errors in processing the plus/minus strand files.