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hariszaf / pema

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
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Fail with 18S data and vsearch algorithm #22

Closed hariszaf closed 3 years ago

hariszaf commented 3 years ago

Christina has found a bug when using 18S data. @cpavloud Could you please describe it?

cpavloud commented 3 years ago

I wanted to run 18S data using the current version (pema v.2.1.3) and with the vsearch algorithm. So, at the "GENE - dependent parameters" I wrote

gene gene_18S

This was my parameter setting parameters.txt

However, the analysis was reaching step 4 (mergine) and an error was coming 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 -> 2303 -> 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 `

But then I tricked the parameters and instead of 18S, I wrote

gene gene_16S

And everything worked fine.

hariszaf commented 3 years ago

The issue has been resolved simultaneously with the #24 issue.

hariszaf commented 3 years ago

In addition, a sannity_check folder is now available. Input data and parameters files support cross checking each and every marker gene and software combination.