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asadprodhan / GPU-accelerated-guppy-basecalling

GPU-accelerated guppy basecalling and demultiplexing on Linux
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Guppy does not recognise pod5 #4

Open yamkela-mg opened 6 days ago

yamkela-mg commented 6 days ago

Hi there,

I am trying to basecall pod5 files using guppy and it seems like it does not recognise the pod5 files. I am using version 6.1.7

Here is my script:

guppy_basecaller --input_path /mnt/lustre/groups/CBBI1133/03_Genomes_MinION_Raw/26_genome_Promethion_Ligation/26-2_genome_prometh/no_sample/20240423_1538_P2S-00927-A_PAS50468_e1be549b/pod5 --save_path /mnt/lustre/groups/CBBI1133/03_Genomes_MinION_Raw/26_genome_Promethion_Ligation/26-2_genome_prometh/no_sample/20240423_1538_P2S-00927-A_PAS50468_e1be549b/pod_basecalled --config dna_r10.4.1_e8.2_400bps_hac_prom.cfg --device cuda:0,1

And here is the output message:

Found 0 fast5 files to process. Init time: 4334 ms

0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|

Caller time: 101 ms, Samples called: 0, samples/s: 0 Finishing up any open output files. Basecalling completed successfully.

Kindly assist.

yamkela-mg commented 6 days ago

The same script worked for fast5 files

asadprodhan commented 6 days ago

The error message says that the Guppy couldn’t find any fast5 file! You need to convert the files from pod5 to fast5.

However, why wouldn’t you use the Nanopore latest basecaller, Dorado?

In my experience, it works better. See my study:

https://x.com/asad_prodhan/status/1797129339122991600?s=46&t=iIG0iaNKvjgscaPw9UaaiA

-----

Dr Asad Prodhan

Laboratory Scientist

Department of Primary Industries and Regional Development

3 Baron-Hay Court, South Perth WA 6151

&

Adjunct Research Fellow

School of Biological Sciences

University of Western Australia

35 Stirling Hwy, Crawley WA 6009

On Sun, 23 Jun 2024 at 7:12 am, yamkela-mg @.***> wrote:

Hi there,

I am trying to basecall pod5 files using guppy and it seems like it does not recognise the pod5 files. I am using version 6.1.7

Here is my script:

guppy_basecaller --input_path /mnt/lustre/groups/CBBI1133/03_Genomes_MinION_Raw/26_genome_Promethion_Ligation/26-2_genome_prometh/no_sample/20240423_1538_P2S-00927-A_PAS50468_e1be549b/pod5 --save_path /mnt/lustre/groups/CBBI1133/03_Genomes_MinION_Raw/26_genome_Promethion_Ligation/26-2_genome_prometh/no_sample/20240423_1538_P2S-00927-A_PAS50468_e1be549b/pod_basecalled --config dna_r10.4.1_e8.2_400bps_hac_prom.cfg --device cuda:0,1

And here is the output message:

Found 0 fast5 files to process. Init time: 4334 ms

0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|

Caller time: 101 ms, Samples called: 0, samples/s: 0 Finishing up any open output files. Basecalling completed successfully.

Kindly assist.

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