guppy basecalling failing with a pod5 file

[igor-stevanovski]

Hey,

I am trying to run guppy (v6.3.7) basecalling on our HPC on a pod5 file. The job finishes without crashing after like 5 seconds. No error message thrown. No output is created.

[0x55555555]

Hi @igor-stevanovski ,

Can you try on guppy 6.4.6 please?

Thanks,

• George

[igor-stevanovski]

Hi @jorj1988,

I have tried guppy 6.4.6. It said basecalling finished successfully, but no fastq was found. Here is the log file.

[igoste@brenner basecall_output]$ cat guppy_basecaller_log-2023-03-20_16-26-22.log 
2023-03-20 16:26:22.807514 [guppy/message] ONT Guppy basecalling software version 6.4.6+ae70e8f, minimap2 version 2.24-r1122
config file:        /share/ScratchGeneral/igoste/ont-guppy_6.4.6/data/dna_r9.4.1_450bps_fast_prom.cfg
model file:         /share/ScratchGeneral/igoste/ont-guppy_6.4.6/data/template_r9.4.1_450bps_fast_prom.jsn
input path:         /share/ScratchGeneral/igoste/NA12878_pod5_0_1_11
save path:          /scratch_local/3384184.1.long.q/basecall_output
chunk size:         2000
chunks per runner:  240
minimum qscore:     8
records per file:   4000
num basecallers:    4
gpu device:         cuda:0,1,2,3
kernel path:        
runners per device: 20

Use of this software is permitted solely under the terms of the end user license agreement (EULA).
By running, copying or accessing this software, you are demonstrating your acceptance of the EULA.
The EULA may be found in /share/ScratchGeneral/igoste/ont-guppy_6.4.6/bin
2023-03-20 16:26:22.808725 [guppy/info] crashpad_handler successfully launched.
2023-03-20 16:26:23.352446 [guppy/info] CUDA device 0 (compute 7.0) initialised, memory limit 16945512448B (16624123904B free)
2023-03-20 16:26:23.496961 [guppy/info] CUDA device 1 (compute 7.0) initialised, memory limit 16945512448B (16624123904B free)
2023-03-20 16:26:23.622812 [guppy/info] CUDA device 2 (compute 7.0) initialised, memory limit 16945512448B (16624123904B free)
2023-03-20 16:26:23.760764 [guppy/info] CUDA device 3 (compute 7.0) initialised, memory limit 16945512448B (16624123904B free)
2023-03-20 16:26:26.785665 [guppy/message] Found 1 input read file to process.
2023-03-20 16:26:26.793424 [guppy/message] Init time: 3984 ms
2023-03-20 16:26:26.800501 [guppy/info] Error attempting to open file "/share/ScratchGeneral/igoste/NA12878_pod5_0_1_11/NA12878.pod5": Failed to open source file: /share/ScratchGeneral/igoste/NA12878_pod5_0_1_11/NA12878.pod5 with error IOError: Memory mapping file failed: Cannot allocate memory
2023-03-20 16:26:26.894297 [guppy/message] Caller time: 101 ms, Samples called: 0, samples/s: 0
2023-03-20 16:26:26.894349 [guppy/message] There were fast5 file loading problems! Failed to load 1 out of 1 fast5 files. Check log file for details.
2023-03-20 16:26:26.894363 [guppy/message] Finishing up any open output files.
2023-03-20 16:26:26.941460 [guppy/info] Stats for model /share/ScratchGeneral/igoste/ont-guppy_6.4.6/data/template_r9.4.1_450bps_fast_prom.jsn, 20 runners/device, 240 chunks/run, 2000 blocks/chunk, lifetime 2.993 s
CUDA device 0: 0 runs with 0 chunks (-nan%), 0 samples (-nan%), avg max size -nan, avg size -nan (-nan% of max), 0 samples/s
CUDA device 1: 0 runs with 0 chunks (-nan%), 0 samples (-nan%), avg max size -nan, avg size -nan (-nan% of max), 0 samples/s
CUDA device 2: 0 runs with 0 chunks (-nan%), 0 samples (-nan%), avg max size -nan, avg size -nan (-nan% of max), 0 samples/s
CUDA device 3: 0 runs with 0 chunks (-nan%), 0 samples (-nan%), avg max size -nan, avg size -nan (-nan% of max), 0 samples/s
2023-03-20 16:26:27.276740 [guppy/message] Basecalling completed successfully.

Thanks

[0x55555555]

Hi @igor-stevanovski ,

Interesting, that looks familiar to an issue we have fixed internally - give me a moment to investigate.

Thanks,

• George

[0x55555555]

Hi @igor-stevanovski , pod5 0.1.13 is now live with a fix for this issue, I'll get builds of dorado and guppy available asap.

• George

[iiSeymour]

Dorado updated on master in https://github.com/nanoporetech/dorado/commit/27c8a2efbcbabc689eda0817e6a572cb9f2887c6.

[igor-stevanovski]

Thank you George, I will check when the binaries are released.