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.