Dear all, I am a little stuck with running classify-sklearn on ITS sequences, any help is appreciated.
Below I have indicated the scripts and the error message.
mpirun -np 4 qiime feature-classifier classify-sklearn --i-classifier "$class_path"
--i-reads "$path_to_data/output/rep-seqs.qza"
--o-classification "$path_to_data/output/taxonomy.qza" --verbose
--p-reads-per-batch 0 --p-n-jobs 4 --p-pre-di spatch 3*n_jobs
I put a link to the error message msg_err.txt (14.1 KB)
It might also help, I get kind of similar error message when trying to summarize rep-seqs.qza to rep-seqs.qzv.
I am using q2cli version 2018.2.0.
Many thanks.
zipfile.BadZipFile: Bad magic number for central directory
This error message indicates that something is wrong with your repseqs file itself. The fact that summarize calls the same error confirms this issue: it is a problem with the file, not with q2-feature-classifier.
The file must have become corrupted at some point. Your best bet is most likely to try recreating or re-downloading that file (however you obtained it), since the error probably occurred while that file was being created.
You are also using an old version of QIIME 2 (2018.2 is a year old). You should install the latest version (2019.1 will be released tomorrow). I doubt the old version is related to the issue with your rep seqs file, but it is always good to be up-to-date.
@Nicholas_Bokulich,
Thank you for the hint, I have used before the latestest version of q2 and indeed it did resolve the issue, though got a different one.