ITS extraction error - Missing sequence for record beginning on line 17

[arwqiime (ARW)]

Hello,
I received a similar error from q2 itsxpress trim-single using q2-amplicon-2024.10

Plugin error from itsxpress:
  Command '['vsearch', '--fastx_uniques', '/tmp/qiime2/bt140047/data/853a4d2f-f6c9-44d1-81cc-7c32908d874d/data/ITSa-AW2024-009_1_L001_R1_001.fastq.gz', '--fastaout', '/tmp/itsxpress_p2sdyw0r/rep.fa', '--uc', '/tmp/itsxpress_p2sdyw0r/uc.txt', '--strand', 'both']' returned non-zero exit status 1.

I tried to update ITSxpress to 2.1.4 using
conda install -c bioconda -c conda-forge ITSxpress=2.1.4
but it is not (yet) available in these channels.

Any suggestions how to solve this issue?
Best,

EDIT: I would like to add @Adam_Rivers here; ITSxpress is working without errors in the standalone conda environment!

[Adam_Rivers]

Thaks for the heads up. I'll check with the Bioconda team on why the latest version didn't build. It has somthing to do with the way their build system handles dynamic versioning using setuptools-scm. The PR about this is here: Update itsxpress to 2.1.4 by BiocondaBot · Pull Request #53211 · bioconda/bioconda-recipes · GitHub

If you don't want to wait, you can

1. remove the older version of ITSxpress with conda from within your conda environment conda remove -n itsxpress
2. Download ITSxpress v2.1.4 it from github. git clone -b v2.1.4 git@github.com:USDA-ARS-GBRU/itsxpress.git
3. cd into the top-level direcory, and install the package with pip install . Note that Hmmer 3.4 and Vsearch 2.22 will need to be installed in your same conda environment.

[arwqiime (ARW)]

Hi @Adam_Rivers
Thank you for your suggestion. The git clone command returns this error message:

Klone nach 'itsxpress'...
git@github.com: Permission denied (publickey).

I will wait until the bioconda update will be available.
Thanks!

[Adam_Rivers]

Its something with the ssh key settings, the https access method may work better for your computerhttps://github.com/USDA-ARS-GBRU/itsxpress.git.

But anyway, I just checked and itsxpress v2.1.4 is avaialbe from bioconda now.

[arwqiime (ARW)]

I was able to install v2.1.4 and the job completed successfully!
Thank you for your support!

[Pardal_Oblackovy (Karel Švec)]

Hey Adam, I assume this post of yours is addressed to @arwqiime and is not related to my "missing sequence for record beginning on line 17 BUG", right? because I already tried Itsxpress v2.1.4 and I got the same error on my datasets (but not on tutorial ITS data mentioned in my post above).

Thx K.

[Pardal_Oblackovy (Karel Švec)]

Hi guys @gregcaporaso @salias @Adam_Rivers @colinbrislawn , have we agreed that this problem of mine is a bug that will be solved in the future with the help of the ITS express update, or the problem lies somewhere else (we don't know where) and I should "just forget about the whole thing"? Thank you very much for your time in any case I already learn lot of thinqs on my way up to here so i dont consider it as lost time <3

[gregcaporaso]

Hi @Pardal_Oblackovy, Sorry for the lack of reply here. Catching up, it seems like we're still scratching our heads over this. @Adam_Rivers is helping another user with the same problem over here now - we will get this sorted out! Are you able to share the full input file with us? I could provide you with a Google Drive folder link by private message if so.

@Adam_Rivers - let me know if I can do anything to help with debugging.

[Pardal_Oblackovy (Karel Švec)]

Dear @gregcaporaso i would be super happy to help you with the development of Qiime. What do you need? RAW data, processed artefact.qza and list of used commands?

[gregcaporaso]

Hi @Pardal_Oblackovy and @Adam_Rivers,
@Adam_Rivers, @Pardal_Oblackovy has some input data to share that might be helpful in debugging this. Can you describe what specific input you would like? I would recommend that the two of you connect by Direct Message on the forum, and share files through a service like Dropbox of Google Drive. Let me know how I can help.

[Adam_Rivers]

I will direct message him. Thanks.