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No FASTQ File Generated After Successful Guppy Basecalling #56

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Echo-0301 opened this issue Aug 23, 2024 · 0 comments
Open

No FASTQ File Generated After Successful Guppy Basecalling #56

Echo-0301 opened this issue Aug 23, 2024 · 0 comments

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@Echo-0301
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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

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