Skip to content

No FASTQ File Generated After Successful Guppy Basecalling #56

@Echo-0301

Description

@Echo-0301

I successfully ran Guppy for basecalling, and the process completed without any errors. However, I noticed that no FASTQ files were generated in the output directory.

Here is the output from the run:

ONT Guppy duplex basecalling software version 6.0.6+8a98bbc
config file:        /input/model.cfg
model file:         /input/model.jsn
input path:         /input/demo
save path:          output/call_res
chunk size:         2000
chunks per runner:  256
minimum qscore:     0
records per file:   5000
num basecallers:    4
gpu device:         cuda:1
kernel path:        
runners per device: 12
Found 2 fast5 files to process.
Init time: 1676 ms
0%   10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************
Caller time: 2102 ms, Samples called: 465044, samples/s: 221239
Finishing up any open output files.
Failed to send ping to https://ping-dev.oxfordnanoportal.com/basecall: Failed to connect to ping-dev.oxfordnanoportal.com port 443: No route to host: Couldn't connect to server
Basecalling completed successfully.

Here is the generated sequencing_summary.txt:

filename	read_id	duplex_pair_read_id	run_id	batch_id	channel	mux	start_time	duration	num_events	passes_filtering	template_start	num_events_template	template_duration	sequence_length_template	mean_qscore_template	strand_score_template	median_template	mad_template	scaling_median_template	scaling_mad_template
temps_labd.fast5	read_channel1_cp0	read_channel1_cp1	PC28	0	1	1	42.594400	78.329800	78329	TRUE	42.620400	78303	78.303800	5060	6.228380	0	0.572205	0.076294	0.572205	0.076294

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions