I recently started working with qiime2. I use the qiime2-2022.8 version on a conda environment on my computer that has the following specification: 64GB RAM, HD SSD 4TB.
In the past few days, I tried to analyze a set of data composed by the combination of two set of raw sequences that have been sequenced separately (in two different times).
After the step of denoise with dada2, I had a problem with the taxonomy assignment using feature-classifier classify-consensus-vsearch and silva 138.
Here is the command:
qiime feature-classifier classify-consensus-vsearch --i-query denoised_sequences.qza --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-threads 18 --o-classification taxonomy.qza --o-search-results tophits.qza --verbose
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: vsearch --usearch_global /tmp/qiime2/adminlinux/data/aeb7935e-88a0-4436-998d-80bf2b1c78c6/data/dna-sequences.fasta --id 0.8 --query_cov 0.8 --strand both --maxaccepts 10 --maxrejects 0 --db /tmp/qiime2/adminlinux/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta --threads 18 --output_no_hits --blast6out /tmp/q2-BLAST6Format-qgbkc739
vsearch v2.21.1_linux_x86_64, 62.6GB RAM, 24 cores
I tried several time to submit this command but I had always the same results:
636194718 nt in 436680 seqs, min 900, max 3983, avg 1457
Counting k-mers 100%
Creating k-mer index 100%
Matching unique query sequences: 28760 of 28837 (99.73%)
Someone can help me to understand what is the problem of this command e why of the "killed"session?
Is there any error message that could help me to understand?