Running DBGWAS on docker example fails at Rscript stage
Hello I've attempted to run the example docker analysis. However it fails at the Rscript stage possibly due to memory issues. I'm running it on a mac with 16G so that slightly surprises me. any idea what might be going on here? thanks phil
docker run --rm -v /Users/klmf372/dbgwas/pseudomonas_aeruginosa_full_dataset/:/pseudomonas_aeruginosa_full_dataset leandroishilima/dbgwas:0.5.4 -strains /pseudomonas_aeruginosa_full_dataset/strains -newick /pseudomonas_aeruginosa_full_dataset/strains.newick -nc-db /pseudomonas_aeruginosa_full_dataset/Resistance_DB_for_DBGWAS.fasta -pt-db /pseudomonas_aeruginosa_full_dataset/uniprot_sprot_bacteria_for_DBGWAS.fasta -output /pseudomonas_aeruginosa_full_dataset/output -nb-cores 7 Step 1. Building DBG and mapping strains on the DBG... [WARNING] Skipping strain WH-SGI-V-07286 because its phenotype is NA and -keepNA is not set. [WARNING] Skipping strain WH-SGI-V-07290 because its phenotype is NA and -keepNA is not set. [DSK: nb solid kmers found : 54397312 ] 100 % elapsed: 4 min 46 sec remaining: 0 min 0 sec cpu: 248.1 % mem: [ 124, 3710, 3711] MB [Building BooPHF] 100 % elapsed: 0 min 25 sec remaining: 0 min 0 sec [MPHF: populate ] 100 % elapsed: 0 min 19 sec remaining: 0 min 0 sec cpu: 95.1 % mem: [ 177, 177, 3711] MB [Bloom: read solid kmers ] 100 % elapsed: 0 min 5 sec remaining: 0 min 0 sec cpu: 340.0 % mem: [ 261, 261, 3711] MB [Debloom: build extension ] 100 % elapsed: 0 min 16 sec remaining: 0 min 0 sec cpu: 491.3 % mem: [ 300, 300, 3711] MB [Debloom: finalization ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 461.3 % mem: [ 353, 353, 3711] MB [Debloom: cascading ] 100 % elapsed: 0 min 3 sec remaining: 0 min 0 sec cpu: 384.2 % mem: [ 353, 353, 3711] MB [Graph: nb branching found : 1625144 ] 100 % elapsed: 0 min 24 sec remaining: 0 min 0 sec cpu: 627.3 % mem: [ 392, 392, 3711] MB [Graph: building unitigs ] 100 % elapsed: 5 min 44 sec remaining: 0 min 0 sec cpu: 93.4 % mem: [1507, 1507, 3711] MB [Loading endpoints of unitigs ] 1.59e+03% elapsed: 0 min 11 sec remaining: 0 min 0 sec cpu: 84.8 % mem: [1969, 1969, 3711] MB [Building .nodes and .edges files ] 1.59e+03% elapsed: 0 min 58 sec remaining: 0 min 0 sec cpu: 53.9 % mem: [1970, 1970, 3711] MB ################################################################################ Stats: Number of kmers: 54397312 Number of unitigs: 2356052 ################################################################################ build_dbg [Starting mapping process... ] Using 7 cores to map 280 read files. 31570 reads processed.
[Generating bugwas and gemma input]... [Generating bugwas and gemma input] - Done! [Generating unitigs2PhenoCounter...] [Generating unitigs2PhenoCounter...] - Done!
[Mapping process finished!] Done! Step 2. Running statistical test (bugwas + gemma)... map_reads Executing Rscript --vanilla /dbgwas/bin/DBGWAS_lib//DBGWAS.R /dbgwas/bin/DBGWAS_lib/ /pseudomonas_aeruginosa_full_dataset/output/step1 /pseudomonas_aeruginosa_full_dataset/output/step1/bugwas_input.id_phenotype bugwas_out /dbgwas/bin/DBGWAS_lib//gemma.0.93b 0.01 /pseudomonas_aeruginosa_full_dataset/strains.newick 2>&1... [DBGWAS] Reading unitigs from /pseudomonas_aeruginosa_full_dataset/output/step1/bugwas_input.unique_rows.binary [DBGWAS] Reading phenotypes from /pseudomonas_aeruginosa_full_dataset/output/step1/bugwas_input.id_phenotype [DBGWAS] Preparing tree for lineage effect analysis from /pseudomonas_aeruginosa_full_dataset/strains.newick
[FATAL ERROR] Error executing Rscript --vanilla /dbgwas/bin/DBGWAS_lib//DBGWAS.R /dbgwas/bin/DBGWAS_lib/ /pseudomonas_aeruginosa_full_dataset/output/step1 /pseudomonas_aeruginosa_full_dataset/output/step1/bugwas_input.id_phenotype bugwas_out /dbgwas/bin/DBGWAS_lib//gemma.0.93b 0.01 /pseudomonas_aeruginosa_full_dataset/strains.newick 2>&1. Exit status: 35072
Killed