EGA-archive / ont2cram

Oxford Nanopore HDF/Fast5 to CRAM conversion tool
Apache License 2.0
22 stars 2 forks source link

Does this work with 2021 files? #21

Open lunakd opened 3 years ago

lunakd commented 3 years ago

I'm trying to convert multi-fast 5 files that I recently generated from a MinION. I only have fast5 but the code is asking for fastq also. It's giving this error. What should I do?

vml@Legion:~$ ont2cram converter -i '/media/vml/Seagate/2021 runs/Test_ont2cram' -o '/media/vml/Seagate/2021 runs/Test_ont2cram/test.cram' -m 'skip' -p -v Check input files Pre-processing Fast5 files from: '/media/vml/Seagate/2021 runs/Test_ont2cram' 100%|████████████████████████████████████████████████████████████████████████| 1.00/1.00 [00:53<00:00, 53.4s/ files] Writing CRAM to: '/media/vml/Seagate/2021 runs/Test_ont2cram/test.cram' 0%| | 0.00/1.00 [00:00<?, ? files/s] fast5 files found: 1 reads found in fast5: 1

Traceback (most recent call last): File "/home/vml/miniconda3/envs/ont2cram/bin/ont2cram", line 8, in sys.exit(main()) File "/home/vml/miniconda3/envs/ont2cram/lib/python3.8/site-packages/ont2cram/main.py", line 65, in main args.func(**vars(args)) File "/home/vml/miniconda3/envs/ont2cram/lib/python3.8/site-packages/ont2cram/converter.py", line 106, in converter write_cram( File "/home/vml/miniconda3/envs/ont2cram/lib/python3.8/site-packages/ont2cram/converter.py", line 389, in write_cram read_name, read_seq, sep ,read_qual = read_group[fastq_path].value.splitlines() AttributeError: 'Dataset' object has no attribute 'value'