Trim intervall termination
Closed this issue · 1 comments
Hi,
I am running dorado 080 on macos M1 Pro.
I am running the following command:
./dorado basecaller hac input_dir/pod5/ --emit-fastq --kit-name SQK-RBK114-24 --output-dir /output_dir/
This results in a termination:
[2024-09-30 16:49:35.433] [info] - Note: FASTQ output is not recommended as not all data can be preserved.
[2024-09-30 16:49:35.671] [info] Assuming cert location is /etc/ssl/cert.pem
[2024-09-30 16:49:35.674] [info] - downloading dna_r10.4.1_e8.2_400bps_hac@v5.0.0 with foundation
[2024-09-30 16:49:50.220] [info] Normalised: chunksize 10000 -> 9996
[2024-09-30 16:49:50.220] [info] Normalised: overlap 500 -> 498
[2024-09-30 16:49:50.220] [info] > Creating basecall pipeline
[2024-09-30 16:50:03.757] [info] - set batch size to 672
libc++abi: terminating due to uncaught exception of type std::invalid_argument: Trim interval 102-99 is invalid for sequence TTTATTCGTTGGTTGTGAATTTGGTGGCACCCAACGAGTCTCTTGGGACCCATAGAGTTTTCAAATTATCGTGAAACGCTTTCGCGTTTTTAACTAATCTGAAGCGGCGCACAAAAACGCGAAAGCATTCACGATAAATGCGAAAACTCTATGGTCCCGAGACTG
zsh: abort
When I run the same command including the "--no-trim" argument, it all works. No biggie just thought I ll let you know.
Cheers
HI @SynBioExplorer,
This looks like a duplicate of #1020. I'll close this one and you can follow updates there.