pod5 convert fast5 does not gracefully exit after an error when using "strict"

[billytcl]

Python 3.7, pod5 0.2.4

Using this command to catch exceptions on a SLURM HPC cluster:

pod5 convert fast5 --strict -f -o pod5/converted.pod5 -r -t 20 ./Seq_Output/

It catches an error early on, but seems to hang and not end the job:

(base) [billylau@sh02-ln04 login /scratch/groups/hanleeji/20221104_PRM_1295]$ cat slurm-30777430.out
Converting 30037 Fast5s:   5%|4         | 5752514/120088914 [10:27<3:27:59, 9161.58Reads/s]ERROR:pod5:Input PAM91900_pass_barcode01_9bb047c3_5303.fast5 is not a multi-read fast5
Converting 30037 Fast5s:   5%|4         | 5752914/120088914 [10:28<3:28:01, 9160.68Reads/s]ERROR:pod5:Encountered an exception in Seq_Output/20221104_1730_3B_PAM91900_1eee8ef4/fast5_pass/barcode01/PAM91900_pass_barcode01_9bb047c3_5303.fast5 - Seq_Output/20221104_1730_3B_PAM91900_1eee8ef4/fast5_pass/barcode01/PAM91900_pass_barcode01_9bb047c3_5303.fast5 is not a multi-read fast5 file.
NoneType: None
Seq_Output/20221104_1730_3B_PAM91900_1eee8ef4/fast5_pass/barcode01/PAM91900_pass_barcode01_9bb047c3_5303.fast5 is not a multi-read fast5 file.
Converting 30037 Fast5s:   5%|4         | 5753314/120088914 [10:28<3:28:01, 9160.76Reads/s]
CRITICAL:pod5:Exception raised and --strict set
An unexpected error occurred: Seq_Output/20221104_1730_3B_PAM91900_1eee8ef4/fast5_pass/barcode01/PAM91900_pass_barcode01_9bb047c3_5303.fast5 is not a multi-read fast5 file.

POD5 has encountered an error: 'Seq_Output/20221104_1730_3B_PAM91900_1eee8ef4/fast5_pass/barcode01/PAM91900_pass_barcode01_9bb047c3_5303.fast5 is not a multi-read fast5 file.'

For detailed information set POD5_DEBUG=1'

It's hung for about 30 minutes with no change to the pod5 file. SSHing into the node itself shows that the CPU is not doing anything, and the job hasn't exited.

[HalfPhoton]

Thanks for reporting this @billytcl , we'll take a look at improving the error handling of the converter