Barcode kits

[ObRICa]

Hi Simone, Thanks for sharing us with the useful software!

My question is, is it necessary to make changes in 'config_MinION_mobile_lab_R' when using "SQK-16S024" as indicated below?

BC_int <- c("BC01", "BC02", "BC03", "BC04", "BC05", "BC06", "BC07", "BC08", "BC09", "BC10", "BC11", "BC12", "BC13", "BC14", "BC15", "BC16", "BC17", "BC18", "BC19", "BC20", "BC21", "BC22", "BC23", "BC24")

barcode_kits <- c("SQK-16S024")

kit <- "SQK-16S024"

Please let me know if there is anything else that we have to change.

[MaestSi]

Hi, yes, the kit and barcode_kits variables should be set in the config_MinION_mobile_lab.R as you suggested. Please let me know if you encounter any issues. Best, Simone

[ObRICa]

I have made the changes and ran ./Launch_MinION_mobile_lab.sh. I got following error and the barcoding_summary.txt file in the preprocessing directory was empty. I'm afraid that the changes in the barcode variables were not correctly processed by the program.

arrangement files: barcode_arrs_16s.cfg lamp arr. files: barcode_arrs_ncov8.cfg barcode_arrs_ncov96.cfg barcode_arrs_multivirus1.cfg barcode_arrs_multivirus8.cfg min. score front: 60 min. score rear: 60

Found 0 input files.

0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----|

---

Done in 6 ms. Demultiplexing finished at Thu Dec 2 15:34:51 2021

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'grep': invalid 'description' argument Calls: grep -> readLines -> file -> .handleSimpleError -> h Execution halted

[MaestSi]

Hi, I guess that in the command you ran, a part from ./Launch_MinION_mobile_lab.sh, you also specified the fast5 directory, right? If yes, did at least base-calling work? You can check if there are some fastq files in the _analysis/basecalling directory. In case base-calling worked, you can erase only _analysis/analysis and *_analysis/preprocessing directories and rerun the pipeline after modifying the config file. I would suggest to try specifying: barcode_kits <- c("SQK-RAB204", "SQK-16S024") Let me know if this works. Simone

[ObRICa]

barcode_kits <- c("SQK-RAB204", "SQK-16S024") It worked! Thanks a lot!

[MaestSi]

What in particular solved the issue? Glad it worked! I am going to close the issue. Simone