5 parsing failures

[valery-shap]

Hello,

I have sequencing_summary.txt file from guppy (FLO-MIN106, SQK-LSK108). I tried to use MinIONQC script and had such error:

INFO [2019-11-29 13:30:37] Loading input file: /home/valery/Documents/data/Doroshenko/sequencing_summary.txt
Warning: 5 parsing failures.
row col expected actual file
8001 -- 18 columns 1 columns '/home/valery/Documents/data/Doroshenko/sequencing_summary.txt'
8002 -- 18 columns 3 columns '/home/valery/Documents/data/Doroshenko/sequencing_summary.txt'
8003 -- 18 columns 1 columns '/home/valery/Documents/data/Doroshenko/sequencing_summary.txt'
8004 -- 18 columns 3 columns '/home/valery/Documents/data/Doroshenko/sequencing_summary.txt'
8005 -- 18 columns 3 columns '/home/valery/Documents/data/Doroshenko/sequencing_summary.txt'

Error in if (max(d$channel) <= 512) { :
missing value where TRUE/FALSE needed
Calls: single.flowcell -> load_summary
Execution halted

my command was Rscript /home/valery/Downloads/MinIONQC.R -i /home/valery/Documents/data/Doroshenko/sequencing_summary.txt -o /home/valery/Documents/Doroshenko -p 30

After basecalling i used guppy for trim barcoding(kit EXP-NBD103), but this file is before trimming.

Could you help me?

Before i used MinIONQC with other data and everything was excellent. But the data was without barcodes.

Thanks a lot.

[roblanf]

Hi @valery-shap, I see you closed this - could you let me know the issue?

If possible I'd like to do something that would at least give a more useful error message than the one that you got. If you're willing to send me a subset of your input file (e.g. a thousand lines or so) that I could use as a test case, that could also be useful.

Cheers,

Rob

[valery-shap]

Thank you for your answer. I had the error with NanoPlot tool too and wdecoster answered me that there are NaNs in my file. When I manually delete these fast5 files, everything is ok with NanoPLot and MinIONQC. When i basecalled with guppy I didn't have any errors.
I tried PycoQC tool too and it worked with NaNs in the file.
wdecoster/NanoPlot#160

I'd like to have a statistics within barcodes(not only count reads), Is it possible for MinIONQC?
sorry for the question not in the topic theme.

[roblanf]

Hi Valery, I can certainly look into supporting barcodes and NaNs. If you could send me an example file I'd be very happy to take a look. My contact details are here: http://robertlanfear.com/contact/ Cheers, Rob

…

On Mon, 2 Dec 2019 at 20:19, valery-shap ***@***.***> wrote: Thank you for your answer. I had the error with NanoPlot tool too and wdecoster answered me that there are NaNs in my file. When I manually delete these fast5 files, everything is ok with NanoPLot and MinIONQC. When i basecalled with guppy I didn't have any errors. I tried PycoQC tool too and it worked with NaNs in the file. wdecoster/NanoPlot#160 <wdecoster/NanoPlot#160> I'd like to have a statistics within barcodes(not only count reads), Is it possible for MinIONQC? sorry for the question not in the topic theme. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#48?email_source=notifications&email_token=AAG2SE234AW4AVJCYDN6SHLQWTHK5A5CNFSM4JS56DP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFSZT7I#issuecomment-560306685>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG2SEZRUDWWFXCRZX5WYSDQWTHK5ANCNFSM4JS56DPQ> .

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra www.robertlanfear.com