Issue::DesignPrimers DECIPHER
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@46704a7e
Last seen 4 weeks ago
France

Hi, I have encountered an issue when running the DesignPrimers function of DECIPHER. I’m running DECIPHER v2.16.1 in R v4.0.2 and R version 4.1.0.

I have also installed the OligoArrayAux program which is accessible by the system (see below).

system("hybrid-min -V")

hybrid-min (OligoArrayAux) 3.8
By Nicholas R. Markham and Michael Zuker
Copyright (C) 2006
Rensselaer Polytechnic Institute
Troy, NY 12810-3590 USA

The DesignPrimers function produced an error with my dataset but also with the example provided in the function help :

db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
tiles <- TileSeqs(db, identifier=c("Enterobacteriales","Pseudomonadales"))
primers <- DesignPrimers(tiles, identifier="Enterobacteriales", start=280, end=420,
           minProductSize=50, numPrimerSets=1)
EnterobacterialesError: stack file is corrupt
Error in dG[start:end] <- as.numeric(system(paste("hybrid-min -n DNA -t",  :
  replacement has length zero
In addition: Warning message:
In system(paste("hybrid-min -n DNA -t", temp, "-T", temp, "-N",  :
  running command 'hybrid-min -n DNA -t 64 -T 64 -N 0.224783720074173 -E -q CTCACCTAGGCGACGAT ATCGTCGCCTAGGTGAG TCACCTAGGCGACGATC GATCGTCGCCTAGGTGA CACCTAGGCGACGATCC GGATCGTCGCCTAGGTG ACCTAGGCGACGATCCC GGGATCGTCGCCTAGGT CCTAGGCGACGATCCCT AGGGATCGTCGCCTAGG CTAGGCGACGATCCCTA TAGGGATCGTCGCCTAG TAGGCGACGATCCCTAG CTAGGGATCGTCGCCTA AGGCGACGATCCCTAGC GCTAGGGATCGTCGCCT GGCGACGATCCCTAGCT AGCTAGGGATCGTCGCC GCGACGATCCCTAGCTG CAGCTAGGGATCGTCGC CGACGATCCCTAGCTGG CCAGCTAGGGATCGTCG GACGATCCCTAGCTGGT ACCAGCTAGGGATCGTC ACGATCCCTAGCTGGTC GACCAGCTAGGGATCGT CGATCCCTAGCTGGTCT AGACCAGCTAGGGATCG GATCCCTAGCTGGTCTG CAGACCAGCTAGGGATC ATCCCTAGCTGGTCTGA TCAGACCAGCTAGGGAT TCCCTAGCTGGTCTGAG CTCAGACCAGCTAGGGA CCCTAGCTGGTCTGAGA TCTCAGACCAGCTAGGG CCTAGCTGGTCTGAGAG CTCTCAGACCAGCTAGG CTAGCTGGTCTGAGAGG CCTCTCAGACCAGCTAG TAGCTGGTCTGAGAGGA TCCTCTCAGACCAGCTA AGCTGGTCTGAGAGGAT ATCCTCTCAGACCAGCT GCTGGTCTGAGAGGATG CATCCTCTCAGACCAGC CTGGTCTGAGAGGATGA TCATCCTCTCAGACCAG TGGTCTGAGAGGATGAC GTCATCCTCTCAGACCA GGTCTGAGAGGATGACC GGTCATCC [... truncated]

I do not know if it is a problem of OligoArrayAux or of communication between DECIPHER and OligoArrayAux.

Any assistance would be very much appreciated!

Thank you!

DECIPHER DesignPrimers • 194 views
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The "stack file is corrupt" error message is output by hybrid-min when it is installed incorrectly. Often this happens when users install OligoArrayAux via Conda. Try deleting prior installations of OligoArrayAux and reinstalling from scratch.

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Hi, It worked! Thank you a lot!

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Hey, I'm having this issue too. I've tried reinstalling using Conda a few times without luck. Did you reinstall with Conda or from the tar ball? Thanks.

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