Assign Taxonomy Error Unclear

[irc47]

Hi Simone, Can you help me understand this error? I'm not able to find in it any indication of what might have gone wrong. It is a failure of assignTaxonomy and occurs after a great deal of time has elapsed so seems to be something later on in the taxonomy task.

executor > local (1) [bd/84419f] importDb (1) | 1 of 1, cached: 1 ? [c3/fc5509] concatenateFastq | 1 of 1, cached: 1 ? [d5/69d73a] filterFastq | 1 of 1, cached: 1 ? [2b/01d8d1] downsampleFastq | 1 of 1, cached: 1 ? [3b/59f0b3] importFastq | 1 of 1, cached: 1 ? [f0/c9b0b4] derepSeq | 1 of 1, cached: 1 ? [06/bf1206] assignTaxonomy (1) | 1 of 1, failed: 1 ? [- ] filterTaxa - [- ] taxonomyVisualization - [- ] collapseTables - [e1/24a426] dataQC | 1 of 1, cached: 1 ? [- ] diversityAnalyses - ERROR ~ Error executing process > 'assignTaxonomy (1)'

Caused by: Process assignTaxonomy (1) terminated with an error exit status (137)

Command executed:

mkdir -p /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy

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

.commaif [ "$classifier_uc" == "BLAST" ]; then ery /home/exouqiime feature-classifier makeblastdb e_greengenes_august--i-sequences /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/importDb/2022.10.backbone.full-length.fna.qza .backbone.full-leng--o-database /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/importDb/blastIndexedDb.qza

ts 3 --p-min-cqiime feature-classifier classify-consensus-blast bel 'Unassigned' --p-t--i-query /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/derepSeq/rep-seqs.qza nTaxonomy/taxonom--i-blastdb /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/importDb/blastIndexedDb.qza search_results.--i-reference-taxonomy /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/importDb/2022.10.backbone.tax.qza --p-num-threads 6 --p-perc-identity 0.9 --p-query-cov 0.8 --p-maxaccepts 3 --p-min-consensus 0.7 --o-classification /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/taxonomy.qza --o-search-results /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/search_results.qza nd linelif [ "$classifier_uc" == "VSEARCH" ]; then qiime feature-classifier classify-consensus-vsearch --i-query /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/derepSeq/rep-seqs.qza --i-reference-reads /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/importDb/2022.10.backbone.full-length.fna.qza --i-reference-taxonomy /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/importDb/2022.10.backbone.tax.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 6 --o-classification /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/taxonomy.qza --o-search-results /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/search_results.qza else echo "Classifier Vsearch is not supported (choose between Blast and Vsearch)" fi

qiime metadata tabulate --m-input-file /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/taxonomy.qza --o-visualization /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/taxonomy.qzv

qiime taxa filter-table         --i-table /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/derepSeq/table.qza        --i-taxonomy /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/taxonomy.qza        --p-exclude Unassigned      --o-filtered-table /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/derepSeq/table-no-Unassigned.qza

Command exit status: 137

Command output: (empty)

Command error: .command.sh: line 14: 10 Killed qiime feature-classifier classify-consensus-vsearch --i-query /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/derepSeq/rep-seqs.qza --i-reference-reads /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/importDb/2022.10.backbone.full-length.fna.qza --i-reference-taxonomy /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/importDb/2022.10.backbone.tax.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 6 --o-classification /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/taxonomy.qza --o-search-results /home/exouser/MetONTIIME/NP24/results_metontiime_greengenes_august6/assignTaxonomy/search_results.qza

Work dir: /home/exouser/MetONTIIME/work/06/bf120609eaa5caa9f839a9068e2f15

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details

[MaestSi]

Hi, I think this is a RAM memory error, similar to this one. See that issue for proposed solutions. SM

[MaestSi]

Closing this one, as conversation continued in the related issue. Best, SM