Running Example

[hdesale2408]

Hello,

I am trying to run the example data and I keep receiving an error during the "Run demultiplex by marker and truncate primer sequence" step.  

dePlexMarker <- demultiplexByMarker(dePlexSample, markerTab, outDeplexMarker)
Processing marker csp
Processing file R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz and R-100_Rep2_BC_Fwd_01-Rev_10_R2.fastq.gz
Processing file R-500_Rep2_BC_Fwd_02-Rev_10_R1.fastq.gz and R-500_Rep2_BC_Fwd_02-Rev_10_R2.fastq.gz
Processing file R-1000_Rep2_BC_Fwd_03-Rev_10_R1.fastq.gz and R-1000_Rep2_BC_Fwd_03-Rev_10_R2.fastq.gz
Processing file R-1500_Rep2_BC_Fwd_04-Rev_10_R1.fastq.gz and R-1500_Rep2_BC_Fwd_04-Rev_10_R2.fastq.gz
Processing file R-3000_Rep2_BC_Fwd_05-Rev_10_R1.fastq.gz and R-3000_Rep2_BC_Fwd_05-Rev_10_R2.fastq.gz
Processing file R-1_Rep2_BC_Fwd_06-Rev_09_R1.fastq.gz and R-1_Rep2_BC_Fwd_06-Rev_09_R2.fastq.gz
Processing file R-10_Rep2_BC_Fwd_07-Rev_09_R1.fastq.gz and R-10_Rep2_BC_Fwd_07-Rev_09_R2.fastq.gz
Processing file R-50_Rep2_BC_Fwd_08-Rev_09_R1.fastq.gz and R-50_Rep2_BC_Fwd_08-Rev_09_R2.fastq.gz
Processing file R-1_Rep1_BC_Fwd_13-Rev_22_R1.fastq.gz and R-1_Rep1_BC_Fwd_13-Rev_22_R2.fastq.gz
Processing file R-10_Rep1_BC_Fwd_14-Rev_22_R1.fastq.gz and R-10_Rep1_BC_Fwd_14-Rev_22_R2.fastq.gz
Processing file R-50_Rep1_BC_Fwd_15-Rev_22_R1.fastq.gz and R-50_Rep1_BC_Fwd_15-Rev_22_R2.fastq.gz
Processing file R-100_Rep1_BC_Fwd_16-Rev_22_R1.fastq.gz and R-100_Rep1_BC_Fwd_16-Rev_22_R2.fastq.gz
Processing file R-500_Rep1_BC_Fwd_17-Rev_22_R1.fastq.gz and R-500_Rep1_BC_Fwd_17-Rev_22_R2.fastq.gz
Processing file R-1000_Rep1_BC_Fwd_18-Rev_22_R1.fastq.gz and R-1000_Rep1_BC_Fwd_18-Rev_22_R2.fastq.gz
Processing file R-1500_Rep1_BC_Fwd_19-Rev_22_R1.fastq.gz and R-1500_Rep1_BC_Fwd_19-Rev_22_R2.fastq.gz
Processing file R-3000_Rep1_BC_Fwd_20-Rev_22_R1.fastq.gz and R-3000_Rep1_BC_Fwd_20-Rev_22_R2.fastq.gz
Processing marker cpmp
Processing file R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz and R-100_Rep2_BC_Fwd_01-Rev_10_R2.fastq.gz
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'args' in selecting a method for function 'do.call': error in evaluating the argument 'args' in selecting a method for function 'do.call': UserArgumentMismatch
file 'exampleHaplotypR/dePlexMarker/R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz_F.fastq.gz' exists, but mode is not 'a'

[lerch-a]

Hi

Error in h(simpleError(msg, call)) : error in evaluating the argument 'args' in selecting a method for function 'do.call': error in evaluating the argument 'args' in selecting a method for function 'do.call': UserArgumentMismatch file 'exampleHaplotypR/dePlexMarker/R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz_F.fastq.gz' exists, but mode is not 'a'

The error message tells you that a file with this name “exampleHaplotypR/dePlexMarker/R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz_F.fastq.gz'” exists already. I assume you did run the "demultiplex by marker” already before. Delete the files in the "exampleHaplotypR/dePlexMarker” folder. Best, Anita

[hdesale2408]

Tried this and received the following error:

dePlexMarker <- demultiplexByMarker(dePlexSample, markerTab, outDeplexMarker)
Processing marker csp
Processing file R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz and R-100_Rep2_BC_Fwd_01-Rev_10_R2.fastq.gz
Processing file R-500_Rep2_BC_Fwd_02-Rev_10_R1.fastq.gz and R-500_Rep2_BC_Fwd_02-Rev_10_R2.fastq.gz
Processing file R-1000_Rep2_BC_Fwd_03-Rev_10_R1.fastq.gz and R-1000_Rep2_BC_Fwd_03-Rev_10_R2.fastq.gz
Processing file R-1500_Rep2_BC_Fwd_04-Rev_10_R1.fastq.gz and R-1500_Rep2_BC_Fwd_04-Rev_10_R2.fastq.gz
Processing file R-3000_Rep2_BC_Fwd_05-Rev_10_R1.fastq.gz and R-3000_Rep2_BC_Fwd_05-Rev_10_R2.fastq.gz
Processing file R-1_Rep2_BC_Fwd_06-Rev_09_R1.fastq.gz and R-1_Rep2_BC_Fwd_06-Rev_09_R2.fastq.gz
Processing file R-10_Rep2_BC_Fwd_07-Rev_09_R1.fastq.gz and R-10_Rep2_BC_Fwd_07-Rev_09_R2.fastq.gz
Processing file R-50_Rep2_BC_Fwd_08-Rev_09_R1.fastq.gz and R-50_Rep2_BC_Fwd_08-Rev_09_R2.fastq.gz
Processing file R-1_Rep1_BC_Fwd_13-Rev_22_R1.fastq.gz and R-1_Rep1_BC_Fwd_13-Rev_22_R2.fastq.gz
Processing file R-10_Rep1_BC_Fwd_14-Rev_22_R1.fastq.gz and R-10_Rep1_BC_Fwd_14-Rev_22_R2.fastq.gz
Processing file R-50_Rep1_BC_Fwd_15-Rev_22_R1.fastq.gz and R-50_Rep1_BC_Fwd_15-Rev_22_R2.fastq.gz
Processing file R-100_Rep1_BC_Fwd_16-Rev_22_R1.fastq.gz and R-100_Rep1_BC_Fwd_16-Rev_22_R2.fastq.gz
Processing file R-500_Rep1_BC_Fwd_17-Rev_22_R1.fastq.gz and R-500_Rep1_BC_Fwd_17-Rev_22_R2.fastq.gz
Processing file R-1000_Rep1_BC_Fwd_18-Rev_22_R1.fastq.gz and R-1000_Rep1_BC_Fwd_18-Rev_22_R2.fastq.gz
Processing file R-1500_Rep1_BC_Fwd_19-Rev_22_R1.fastq.gz and R-1500_Rep1_BC_Fwd_19-Rev_22_R2.fastq.gz
Processing file R-3000_Rep1_BC_Fwd_20-Rev_22_R1.fastq.gz and R-3000_Rep1_BC_Fwd_20-Rev_22_R2.fastq.gz
Processing marker cpmp
Processing file R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz and R-100_Rep2_BC_Fwd_01-Rev_10_R2.fastq.gz
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'args' in selecting a method for function 'do.call': error in evaluating the argument 'args' in selecting a method for function 'do.call': UserArgumentMismatch
file 'exampleHaplotypR/dePlexMarker/R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz_F.fastq.gz' exists, but mode is not 'a'
In addition: Warning messages:
1: In for (i in seq_along(snames)) { :
closing unused connection 4 (exampleHaplotypR/dePlexSample/R-100_Rep2_BC_Fwd_01-Rev_10_R2.fastq.gz)
2: In for (i in seq_along(snames)) { :
closing unused connection 3 (exampleHaplotypR/dePlexSample/R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz)

[lerch-a]

This is exactly the same error message as the last one. Do you have duplicated sampleID? The error message tells you that the file "exampleHaplotypR/dePlexMarker/R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz_F.fastq.gz" exists already on your file system. Also this filename "exampleHaplotypR/dePlexMarker/R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz_F.fastq.gz" is very strange. Did you follow the instruction step by step? I suggest you delete the folder “exampleHaplotypR" and start again.

[hdesale2408]

I've honestly just copy/pasted the code from this GitHub. I deleted all files, restarted R, and received the same error when I tried again the pipline. I'll read through the sample IDs to see

[lerch-a]

I would need more information to help you. The complete R script with some output after each step and the sessionInfo() output. But over the Christmas holiday, I will not be able to respond.