Process termination at Step 5/5 in flair correct without error messages

[kataksk]

Copy and paste the exact command you tried to run

flair correct \
-q /bed_data/$query_bed12 \
-f /genome_data/$annotation \
-g /genome_data/$genome \
--output /bed_data \
--threads 16 \
--print_check

How did you install Flair?

2. docker pull brookslab/flair:latest

What happened?

The process proceeds through the steps as expected but terminates at Step 5/5 without generating the output files. The temporary directories that were created during the process also disappear upon termination. Below is the output from the command:

Step 1/5: Splitting junctions from GTF by chromosome: 100%|█████████████████████████████████████████████████████████████████████████████████████████████| 15883/15883 [00:00<00:00, 180360.98it/s]
Step 3/5: Preparing annotated junctions to use for correction: 100%|███████████████████████████████████████████████████████████████████████████████████████| 161/161 [00:00<00:00, 197.97it/s]
Step 4/5: Preparing reads for correction: 78145763it [17:46, 73243.85it/s]█████████████████████████████████████████████████████████████▊                       | 120/161 [00:00<00:00, 276.89it/s]
Step 5/5: Correcting Splice Sites: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 158/158 [07:56<00:00,  3.01s/it]
Step 5/5: Correcting Splice Sites:   1%|██                                                                                                                                                                    | 2/158 [07:56<9:06:29, 210.19s/it]

What else do we need to know? I am working with non-model organism gene models and using Nanopore cDNA-seq reads mapped to the genome, converted to BED12 format. I have tried this several times, but the process always terminates at Step 5/5 without any error messages. Additionally, the temporary directories created during the process are removed upon termination.

[kataksk]

I initially included the --output /bed_data option, but this seemed to cause the output files to disappear upon process termination. After removing this option, the process generated flair_all_inconsistent.bed, flair_all_corrected.bed, and flair.err. However, the standard output error still appears to terminate midway through Step 5/5, as shown below:

Step 1/5: Splitting junctions from GTF by chromosome: 100%|██████████| 15883/15883 [00:00<00:00, 209080.70it/s]
Step 3/5: Preparing annotated junctions to use for correction: 100%|██████████| 161/161 [00:00<00:00, 391.18it/s]
Step 4/5: Preparing reads for correction: 78145763it [03:03, 426078.55it/s]   | 72/161 [00:00<00:00, 250.14it/s]
Step 5/5: Correcting Splice Sites: 100%|██████████| 158/158 [02:35<00:00,  1.02it/s]
Step 5/5: Correcting Splice Sites:   1%|▏         | 2/158 [02:35<3:02:55, 70.35s/it]

Is this the expected behavior, or is there something wrong with the process?

Best regards,