No such variable: pairId

[andeleconradie]

Hi,

I have been struggling to run the pipeline and keep running into the same error.
It does not seem to find the reverse read (downloaded both and both have content).

If I run:

nextflow run AlfredUg/QuasiFlow -r main --reads "$PWD/*_{1,2}.fastq" -profile conda

I get:

N E X T F L O W  ~  version 0.30.1
Launching `/home/andele/quasiflow/QuasiFlow/quasiflow.nf` [distraught_kare] - revision: 4010e047cc
============================================================
 AlfredUg/QuasiFlow   ~  version 1.0.1
============================================================
Run Name       : distraught_kare
Reads          : /home/andele/quasiflow/*_{1,2}.fastq
Output directory: /home/andele/quasiflow/QuasiFlow/results
Reporting threshold: 1
Consensus percentage: 20
Minimum read quality: 30
Length cut off : 100
Score cutoff   : 30
Minimum variant quality: 30
Minimum depth  : 100
Minimum allele count: 5
Minimum mutation frequency: 0.01
Report template: /home/andele/quasiflow/QuasiFlow/assets/hivdr.Rmd
Current home   : /home/andele
Current user   : andele
Current path   : /home/andele/quasiflow
Script dir     : /home/andele/quasiflow/QuasiFlow
Config Profile : conda
=========================================
[warm up] executor > local
ERROR ~ No such variable: pairId

 -- Check script 'quasiflow.nf' at line: 140 or see '.nextflow.log' file for more details

I would really appreciate some help!
Thanks!

[AlfredUg]

Heya @andeleconradie, this should work if you got the paired end FASTQ files in the current working directory. Do you have any FASTQ files in the same directory where you are running this command?

[andeleconradie]

Hi @AlfredUg, yes all the fastq files are in this directory - current working directory.