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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
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Example data error before re-clustering #39

Closed Statesanalytical closed 1 year ago

Statesanalytical commented 2 years ago

Hi Saskia,

I've been trying to run your example datasets with a virtual machine and your new v1.3 with the following command:

decona -f -l 1800 -m 2500 -q 10 -c 0.80 -n 25 -M -r

However, it completes the first round of polishing but then produces the below error before it starts re-clustering:

Blast Racon sequences finished awk: run time error: not enough arguments passed to sprintf("%d (%.2f%)") FILENAME="combined2.txt" FNR=1 NR=1

I'm not sure if this is related to #23? Is there any way around this? I'm fairly new to bioinformatics so don't particularly understand the script! Also thank you for creating and sharing this pipeline, it will be incredibly useful for beginners like myself

Many thanks, Luke

Robvh-git commented 2 years ago

Hi Luke,

I've experienced the same issue (with decona v1.3.1). The likely issue is your awk version.

If you run awk -W version in the decona environment it will likely state that you have awk version 1.3.3 or something like that.

To fix this, run following command in the decona environment:

sudo apt update
sudo apt install gawk

You can check if it worked by running awk -W version again. Now you see GNU awk 4.1.4 and the problem is fixed.

Cheers, Robbert

Statesanalytical commented 2 years ago

Hi Robert,

I ran the commands you suggested and it worked perfectly after that! Thank you for your help, very much appreciated

Cheers, Luke