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adnaniazi / tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
https://www.cbu.uib.no/valen/
GNU General Public License v3.0
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empty csv after analysis #33

Closed xcarmengrandix closed 1 year ago

xcarmengrandix commented 1 year ago

Hello,

I'm facing the same problem other people already reported, but cannot fix it. After running tailfindr the analysis ends without errors:

☰ You have configured tailfindr as following: ❯ fast5_dir: C:/data_nanopore/PA_CG1_081/HEK293T17_polyA_GFP50tail/20220719_1149_MN40636_FAT95703_19084a4c/basecalled_new/test ❯ save_dir: C:/data_nanopore/PA_CG1_081/HEK293T17_polyA_GFP50tail/20220719_1149_MN40636_FAT95703_19084a4c/tailfindr_test ❯ csv_filename: rna_tails.csv ❯ num_cores: 4 ❯ basecall_group: Basecall_1D_000 ❯ save_plots: TRUE ❯ plot_debug_traces: FALSE ❯ plotting_library: rbokeh ── Processing started at 2022-07-25 17:16:27 ─────────────────────────────────────────────────────────────────────────────────── • Searching for all Fast5 files... Done! Found 1 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 1 multifast5 files... Done! Found 4000 reads • Searching for Poly(A) tails... Processing chunk 1 of 1 • Formatting the tail data... Done! • Saving the data in the CSV file... Done! Below is the path of the CSV file: C:/data_nanopore/PA_CG1_081/HEK293T17_polyA_GFP50tail/20220719_1149_MN40636_FAT95703_19084a4c/tailfindr_test/rna_tails.csv • A logfile containing all this information has been saved in this path: C:/data_nanopore/PA_CG1_081/HEK293T17_polyA_GFP50tail/20220719_1149_MN40636_FAT95703_19084a4c/tailfindr_test/2022-07-25_17-16-27_tailfinder.log ── Processing ended at 2022-07-25 17:16:56 ✔ tailfindr finished successfully!

However the csv file doesn't contain any tail and I assume it's because of a wrong installation of the plugin VBZ. I installed it on Windows from nanopore: https://github.com/nanoporetech/vbz_compression/releases/tag/v1.0.1 I then export the path like this: set HDF5_PLUGIN_PATH=C:\Program Files\OxfordNanopore\ont-vbz-hdf-plugin\hdf5\lib\plugin but the output doesn't change.

I'm not sure if I'm doing something wrong in setting the path but I can't manage to make it work.

Thanks a lot in advance for your help!

adnaniazi commented 1 year ago

Hi,

Thank you for trying out tailfindr.

I am sorry; I am not a Windows user, so I dont know how to make the VBZ HDF plugin work in Windows. You can try asking the developers of VBZ plugin on their GitHub.

Adnan

xcarmengrandix commented 1 year ago

Hi,

I actually managed to solve the problem in a very simple way by installing the last version of HDF5 with Windows 10 64-bit pre-built binary (https://portal.hdfgroup.org/display/support/HDF5+1.10.9#files).

The link you provide in the readme redirects to a manual installation (https://github.com/mannau/h5-libwin). It was a bit confusing for me.

I'm now curious to analyse my data! :)