Error in explore_basecaller_and_fast5type with object 'model'

[yeroslaviz]

Hi, I'm having problems running the find_tails command with my fast5 files.

> fast5 <- "rawData/Nanopore_06.2022/fast5/fast5_pass/"
> df <- find_tails(fast5_dir = fast5,
+                  save_dir = "Analysis/Nanopore_06.2022/tailfindr",
+                  csv_filename = 'FAT11673_tailfindr.csv',
+                  num_cores = 8,
+                  basecall_group = 'Basecall_1D_000'
+                  )
── Started tailfindr (version 1.3) 
☰ You have configured tailfindr as following:
❯ fast5_dir:         rawData/Nanopore_06.2022/fast5/fast5_pass/
❯ save_dir:          Analysis/Nanopore_06.2022/tailfindr
❯ csv_filename:      FAT11673_tailfindr.csv
❯ num_cores:         8
❯ basecall_group:    Basecall_1D_000
❯ save_plots:        FALSE
❯ plot_debug_traces: FALSE
❯ plotting_library:  rbokeh
── Processing started at 2022-08-26 11:40:43 

• Searching for all Fast5 files...
  Done! Found 585 Fast5 files.
• Analyzing a single Fast5 file to assess if your data 
  is in an acceptable format...
Error in explore_basecaller_and_fast5type(fast5_files_list[1], basecall_group = basecall_group) : 
  object 'model' not found

I have tried with both Basecall_1D_000 and Basecall_1D_001.

Can you please have a look at my fast5 files. You can download them from here. The link contains a zipped file with a few fast5 samples

(I would love to avoid needing to re-run base calling, but if it is unavoidable, would this be the way?

INPUT="Path to my raw fast5"
OUTPUT="ouput"
$guppy_basecaller \
    --flowcell FLO-MIN106 \
    --kit SQK-RNA002 \
    --input_path $INPUT \
    --save_path $OUTPUT \
    --device cuda:0 \
    --recursive \
    --fast5_out

thanks

Assa

[adnaniazi]

Hi,

Yeah rebasecall the data with the command that you wrote and then try tailfindr again on rebasecalled data.

Adnan

[yeroslaviz]

Hi, thanks for the help,

I have rerun guppy and now it works

• Searching for all Fast5 files...
  Done! Found 585 Fast5 files.
• Analyzing a single Fast5 file to assess if your data 
  is in an acceptable format...
  ✔ The data has been basecalled using Guppy.
  ✔ Flipflop model was used during basecalling.
  ✔ The reads are packed in multi-fast5 file(s).
  ✔ The experiment type is RNA, so we will search
    for poly(A) tails.
  ✔ The reads are 1D reads.
• Starting a parallel compute cluster...
  Done!
• Discovering reads in the 585 multifast5 files...