Quasiflow error: PairID

[vfdiamante]

Hello! Can I get an idea on how to solve the PairID error that I keep getting in. See bellow for your reference.

(base) diamantev@afrims-PowerEdge-R740:~/HIV_Quasiflow$ sudo nextflow run QuasiFlow/ --reads *_{1,2}.fastq -profile conda`
N E X T F L O W  ~  version 19.07.0
Launching `QuasiFlow/quasiflow.nf` [gloomy_brown] - revision: 4010e047cc
============================================================
AlfredUg/QuasiFlow   ~  version 1.0.1
============================================================
Run Name       : gloomy_brown
Reads          : DRR030218_1.fastq
Output directory: /home/diamantev/HIV_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/diamantev/HIV_Quasiflow/QuasiFlow/assets/hivdr.Rmd
Current home   : /root
Current user   : root
Current path   : /home/diamantev/HIV_Quasiflow
Script dir     : /home/diamantev/HIV_Quasiflow/QuasiFlow
Config Profile : conda
=========================================
No such variable: pairId
 -- Check script 'QuasiFlow/quasiflow.nf' at line: 140 or see '.nextflow.log' file for more details

Thanks,
Van

[AlfredUg]

Hi @vfdiamante

Looks like QuasiFlow can not find the reverse reads file. To fix this issue, you could add the corresponding reverse reads file by downloading it as follows wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR030/DRR030218/DRR030218_2.fastq.gz and uncompress it using gunzip DRR030218_2.fastq.gz. Then run nextflow run QuasiFlow/ --reads *_{1,2}.fastq -profile conda.

Let us know how it goes.

[vfdiamante]

Hello Alfred,

Thanks for the reply. I already got all the files needed both the forward (1) and reverse reads (2). However, same error still persist.

(base) diamantev@afrims-PowerEdge-R740:~/HIV_Quasiflow/sampledata$ ll
total 264132
drwxrwxr-x 4 diamantev diamantev      4096 Feb  6 14:24 ./
drwxrwxr-x 7 diamantev diamantev      4096 Feb  6 09:07 ../
-rwxrwxrwx 1 diamantev diamantev 135181396 Feb  3 08:33 DRR030218_1.fastq*
-rwxrwxrwx 1 diamantev diamantev 135207546 Feb  3 08:36 DRR030218_2.fastq*
drwxr-xr-x 3 root      root           4096 Feb  6 14:24 .nextflow/
-rw-r--r-- 1 root      root          15535 Feb  6 14:24 .nextflow.log
-rw-r--r-- 1 root      root           2662 Feb  6 14:22 .nextflow.log.1
-rw-r--r-- 1 root      root          15407 Feb  6 08:38 .nextflow.log.2
-rw-r--r-- 1 root      root          15502 Feb  6 08:36 .nextflow.log.3
drwxr-xr-x 2 root      root           4096 Feb  6 08:36 work/
(base) diamantev@afrims-PowerEdge-R740:~/HIV_Quasiflow/sampledata$ cd ..
(base) diamantev@afrims-PowerEdge-R740:~/HIV_Quasiflow$ sudo nextflow run /home/diamantev/HIV_Quasiflow/QuasiFlow/ --reads "/home/diamantev/HIV_Quasiflow/sampledata/*_{1,2}.fastq" --outdir /home/diamantev/HIV_Quasiflow/results -profile conda
WARN: Can't read history file: .nextflow/history
N E X T F L O W  ~  version 19.07.0
Launching `/home/diamantev/HIV_Quasiflow/QuasiFlow/quasiflow.nf` [cheesy_rosalind] - revision: 4010e047cc
============================================================
AlfredUg/QuasiFlow   ~  version 1.0.1
============================================================
Run Name       : cheesy_rosalind
Reads          : /home/diamantev/HIV_Quasiflow/sampledata/*_{1,2}.fastq
Output directory: /home/diamantev/HIV_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/diamantev/HIV_Quasiflow/QuasiFlow/assets/hivdr.Rmd
Current home   : /root
Current user   : root
Current path   : /home/diamantev/HIV_Quasiflow
Script dir     : /home/diamantev/HIV_Quasiflow/QuasiFlow
Config Profile : conda
=========================================
No such variable: pairId

 -- Check script 'QuasiFlow/quasiflow.nf' at line: 140 or see '.nextflow.log' file for more details
(base) diamantev@afrims-PowerEdge-R740:~/HIV_Quasiflow$ 

Thanks,
Van