PacBio CCS interleave error

[Robvh-git]

Hello,

I'm trying to extract the ITS region from PacBio CCS reads using itsxpress by running following command:
itsxpress --fastq ITS__1.fq.gz --single_end --log logfile.txt --outfile ITS_select_ITS__1.fastq --region ALL --threads 23

this gives me the follow error message:

2024-10-24 13:53:35,899: INFO     Verifying the input sequences.
2024-10-24 13:53:35,978: ERROR    'File may be interleaved. ITSxpress will run with errors. Check BBmap reformat.sh to split interleaved files before using ITSxpress.
2024-10-24 13:53:35,978: ERROR    There appears to be an issue reading the input file ITS__1.fq.gz.
2024-10-24 13:53:35,978: ERROR    ITSxpress terminated with errors. See the log file for details.
2024-10-24 13:53:35,978: ERROR   

(the log file doesn't give additional info)

As this is PacBios CCS data, this data is not interleaved, and I'm unsure why itsxpress thinks it is. If - just to test - I use reformat.sh to 'de-interleave' this data, the interleaved files give the same error, so it is something about the format.

In QIIME2, I get the same error.

Do you have any idea how to fix this issue? I see people using ITSxpress on PacBio data, so it should be possible.

I've attached the file.

ITS__1.fq.gz

[arivers]

Sorry, I just saw this request. I was able to reproduce the error. I'll look into what might be causing it.

[arivers]

This issue is caused by the way the function _check_fastqs uses sequence headers to determine if a file is interleaved here. I disabled it and trimming worked. I will fix the validation logic and push an update. There are so many different ways to process PacBio data, this is a Pacbio header format I have not seen before.

[arivers]

I fixed this issue in v2.1.3, which I just released.