Test Data for Basecalling Not working

[vasquini]

So I have been trying to run micropipe. And I always fail in the demultiplexing step with my own data (there is always successful basecalling and guppy is definitely being located as I made appropriate changes in config file). So I decided to run with the example samplesheet and that is failing from the very start. Like there isn't successful basecalling or anything. I get the following error. I tried running this to get a better understanding of a working samplesheet but this is not helpful. [- ] process > basecallingdemultiplexing... - [- ] process > pycoqc - [- ] process > assembly:porechop - [- ] process > assembly:japsa - [- ] process > assembly:flye - [- ] process > assembly:racon_cpu - [- ] process > assembly:medaka_cpu - [- ] process > assembly:nextpolish - [- ] process > assembly:fixstart - [- ] process > assembly:quast - [barcode01, S24, 5.5m] [barcode01, /scicomp/home-pure/suj7/test_data/S24EC_1P_test.fastq.gz, /scicomp/home-pure/suj7/test_data/S24EC_2P_test.fastq.gz] No such file: /scicomp/home-pure/suj7/false

[vmurigneu]

Hi @vasquini

The test data does not include raw fast5 reads but already basecalled fastq files for one sample. Therefore it can only be used to test the assembly-only workflow.

Can you please share the samplesheet you used and the command to run nextflow

[vasquini]

But it still needs demultiplexing, right? Nevermind, it's assembly-only so it does not. So far only the assembly test has run. I will try the demultiplexing-assembly pipeline with the provided test data. The documentation on the test data is a bit confusing...

[vmurigneu]

Hi @vasquini No the test data only contains one sample so it is not for testing the demultiplexing step. Yes I realised the documentation on the test data part is confusing, I will modify, thanks for reporting