Fail with 18S data and swarm algorithm

[cpavloud]

I wanted to run 18S data using the current version (pema v.2.1.3) and with the swarm algorithm.

I used the attached parameter setting parameters_1st_try.txt

However, the analysis went until step 4.mergingPairedEndFiles and then an error came up ` Merging step by SPAdes is completed Marker gene under study 18S. Fatal error: /home/modules/initialize.bds, line 193, pos 18. Map 'params' does not have key 'clusteringAlgoFor16S_18SrRNA'. pema_latest.bds, line 95 : buildDirectories(paramsSpadesMerging, globalVars ) initialize.bds, line 158 : string buildDirectories(string{} params, string{ } globalVars){ initialize.bds, line 162 : if ( params{'gene'} == 'gene_COI' ) { initialize.bds, line 175 : } else if ( params{'gene'} == 'gene_16S' ) { initialize.bds, line 188 : } else if ( params{'gene'} == 'gene_18S' ) { initialize.bds, line 193 : if ( params{'clusteringAlgoFor16S_18SrRNA' } == 'algo_Swarm' ) {

ProgramCounter.pop(100): Node ID does not match! PC : PC: size 10 / 0, nodes: 1422 -> 8178 -> 8179 -> 2295 -> 230 3 -> 2356 -> 2409 -> 2415 -> 2432 -> 2433 Node Id : 2434 bdsNode Id : 2433 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 9 / 0, nodes: 1422 -> 8178 -> 8179 -> 2295 -> 2303 -> 2356 -> 2409 -> 2415 -> 2432 Node Id : 2433 bdsNode Id : 2432 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 8 / 0, nodes: 1422 -> 8178 -> 8179 -> 2295 -> 2303 -> 2356 -> 2409 -> 2415 Node Id : 2432 bdsNode Id : 2415 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 7 / 0, nodes: 1422 -> 8178 -> 8179 -> 2295 -> 2303 -> 2356 -> 2409 Node Id : 2415 bdsNode Id : 2409 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 6 / 0, nodes: 1422 -> 8178 -> 8179 -> 2295 -> 2303 -> 2356 Node Id : 2409 bdsNode Id : 2356 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 5 / 0, nodes: 1422 -> 8178 -> 8179 -> 2295 -> 2303 Node Id : 2356 bdsNode Id : 2303 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 4 / 0, nodes: 1422 -> 8178 -> 8179 -> 2295 Node Id : 2303 bdsNode Id : 2295 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 3 / 0, nodes: 1422 -> 8178 -> 8179 Node Id : 2295 bdsNode Id : 8179 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 2 / 0, nodes: 1422 -> 8178 Node Id : 8179 bdsNode Id : 8178 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 1 / 0, nodes: 1422 Node Id : 8178 bdsNode Id : 1422 `

Then, I thought that maybe it needed a little tricking (like the one I did here), so I changed the gene (in the parameters) parameters_2nd_try.txt

This time, the analysis went until step 7.mainOutput and the files asvs_representatives_all_samples.fasta all.denovo.nonchimeras.fasta asvs_repr_with_singletons.fasta all_samples.fasta asvs.stats all_sequences_grouped.fa asvs.swarms amplicon_contingency_table.tsv mysilvamod132_18S_taxon_assign.xml asvs_contingency_table.tsv were created but nothing was added in the 18S_taxon_assign folder and this error came up

` Traceback (most recent call last): File "/home/tools/CREST/LCAClassifier/bin/classify", line 16, in sys.exit(LCAClassifier.classify.main()) File "/home/tools/CREST/LCAClassifier/src/LCAClassifier/classify.py", line 662, in main otuFile=open(options.otus,"r") IOError: [Errno 2] No such file or directory: 'allTab_18S_taxon_assign.tsv' Task failed: Program & line : '/home/modules/taxAssignment.bds', line 59 Task Name : '' Task ID : 'pema_latest.bds.20211019_114721_581/task.taxAssignment.line_59.id_1843' Task PID : '3380' Task hint : '/home/tools/CREST/LCAClassifier/bin/classify; -c /home/tools/CREST/LCAClassifier/parts/etc/lcaclassifier.conf; -d silva132; -t allTab_18S_taxon_assign' Task resources : 'cpus: 1 mem: -1.0 B timeout: 86400 wall-timeout: 86400' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[]' Output files : '[]' Script file : '/home1/bilbao/pema_latest.bds.20211019_114721_581/task.taxAssignment.line_59.id_1843.sh' Exit status : '1' StdErr (10 lines) : Traceback (most recent call last): File "/home/tools/CREST/LCAClassifier/bin/classify", line 16, in sys.exit(LCAClassifier.classify.main()) File "/home/tools/CREST/LCAClassifier/src/LCAClassifier/classify.py", line 662, in main otuFile=open(options.otus,"r") IOError: [Errno 2] No such file or directory: 'allTab_18S_taxon_assign.tsv'

Fatal error: /home/modules/taxAssignment.bds, line 65, pos 13. Task/s failed. pema_latest.bds, line 151 : if ( paramsForTaxAssign{'custom_ref_db'} != 'Yes'){ pema_latest.bds, line 153 : if ( paramsForTaxAssign{'gene'} == 'gene_16S' || paramsForTaxAssign{'gene'} == 'gene_18S' || paramsForTaxAssign{'gene'} == 'gene_ITS') { pema_latest.bds, line 165 : if (paramsForTaxAssign{'taxonomyAssignmentMethod'} != 'phylogeny') { pema_latest.bds, line 167 : crestAssign(paramsForTaxAssign, globalVars) taxAssignment.bds, line 4 : string crestAssign(string{} params, string{} globalVars) { taxAssignment.bds, line 6 : if ( params{'custom_ref_db'} != 'Yes') { taxAssignment.bds, line 9 : if ( (params{'gene'} == 'gene_16S' || params{'gene'} == 'gene_18S') && params{'taxonomyAssignmentMethod'} != 'phylogeny' ) { taxAssignment.bds, line 24 : if ( params{'silvaVersion'} == 'silva_128' ) { taxAssignment.bds, line 46 : } else if ( params{'silvaVersion'} == 'silva_132' ) { taxAssignment.bds, line 65 : wait `

[hariszaf]

Issue was resolved.