Error executing process > 'assignTaxonomy

[anilchauhanhp9]

Hi,

Thank you for the pipeline. I got an error while running the tool. The detailed error is as follows

ERROR ~ Error executing process > 'assignTaxonomy (1)'

Caused by: Process assignTaxonomy (1) terminated with an error exit status (1)

Command executed:

mkdir -p /home/leek/MetONTIIME/fin_libB2/assignTaxonomy

classifier_uc=$(awk '{print toupper($0)'} <<< Vsearch)

if [ "$classifier_uc" == "BLAST" ]; then
    qiime feature-classifier makeblastdb            --i-sequences /home/leek/MetONTIIME/fin_libB2/importDb/db_sequences.qza             --o-database /home/leek/MetONTIIME/fin_libB2/importDb/blastIndexedDb.qza

    qiime feature-classifier classify-consensus-blast           --i-query /home/leek/MetONTIIME/fin_libB2/derepSeq/rep-seqs.qza             --i-blastdb /home/leek/MetONTIIME/fin_libB2/importDb/blastIndexedDb.qza             --i-reference-taxonomy /home/leek/MetONTIIME/fin_libB2/importDb/db_taxonomy.qza         --p-num-threads 2           --p-perc-identity 0.9           --p-query-cov 0.8           --p-maxaccepts 3            --p-min-consensus 0.7           --o-classification /home/leek/MetONTIIME/fin_libB2/assignTaxonomy/taxonomy.qza          --o-search-results /home/leek/MetONTIIME/fin_libB2/assignTaxonomy/search_results.qza
elif [ "$classifier_uc" == "VSEARCH" ]; then
    qiime feature-classifier classify-consensus-vsearch             --i-query /home/leek/MetONTIIME/fin_libB2/derepSeq/rep-seqs.qza             --i-reference-reads /home/leek/MetONTIIME/fin_libB2/importDb/db_sequences.qza       --i-reference-taxonomy /home/leek/MetONTIIME/fin_libB2/importDb/db_taxonomy.qza         --p-perc-identity 0.9           --p-query-cov 0.8           --p-maxaccepts 100          --p-maxrejects 100          --p-maxhits 3   --p-min-consensus 0.7           --p-strand 'both'           --p-unassignable-label 'Unassigned'             --p-threads 2           --o-classification /home/leek/MetONTIIME/fin_libB2/assignTaxonomy/taxonomy.qza          --o-search-results /home/leek/MetONTIIME/fin_libB2/assignTaxonomy/search_results.qza
else
    echo "Classifier Vsearch is not supported (choose between Blast and Vsearch)"
fi

qiime metadata tabulate --m-input-file /home/leek/MetONTIIME/fin_libB2/assignTaxonomy/taxonomy.qza --o-visualization /home/leek/MetONTIIME/fin_libB2/assignTaxonomy/taxonomy.qzv

qiime taxa filter-table         --i-table /home/leek/MetONTIIME/fin_libB2/derepSeq/table.qza        --i-taxonomy /home/leek/MetONTIIME/fin_libB2/assignTaxonomy/taxonomy.qza        --p-exclude Unassigned      --o-filtered-table /home/leek/MetONTIIME/fin_libB2/derepSeq/table-no-Unassigned.qza

Command exit status: 1

Command output: (empty)

Command error: Plugin error from feature-classifier:

Command '['vsearch', '--usearch_global', '/tmp/qiime2/root/data/87298cbc-a648-4ba3-bbdb-0c01522bf074/data/dna-sequences.fasta', '--id', '0.9', '--query_cov', '0.8', '--strand', 'both', '--maxaccepts', '100', '--maxrejects', '100', '--db', '/tmp/qiime2/root/data/77410d71-511e-4d35-ae87-d8b7f2010977/data/dna-sequences.fasta', '--threads', '2', '--output_no_hits', '--maxhits', '3', '--blast6out', '/tmp/q2-BLAST6Format-seogno8w']' died with <Signals.SIGKILL: 9>.

Please help

[MaestSi]

Hi, you should try increasing the amount of RAM memory available for the assignTaxonomy process (line 133 or 229, depending on which -profile you are using), from: memory = { params.assignTaxonomy ? 10.GB + (2.GB * (task.attempt-1)) : 1.GB } to, for example (if you have 150 GB available): memory = { params.assignTaxonomy ? 150.GB + (2.GB * (task.attempt-1)) : 1.GB } Best, SM

[anilchauhanhp9]

Thank you for the quick response.

I'll try it out.

[anilchauhanhp9]

The pipeline is working fine.

Thank you.