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Not able to run flexbar with paired reads
I am trying to use flexbar at the paired-end mode but only calling reads 1/2 files and the adaptor sequence file, I obtain the following error:
Processing reads ...Error: single read in paired mode, or file reading error!
These are the options I am using:
Local time: Thu Dec 16 13:38:45 2021
Target name: flexbar
File type: fastq
Reads file: SRR3674996_1_1_trimmed.fq
Reads file 2: SRR3674996_1_2_trimmed.fq (paired run)
Adapter file: /home/vera/Desktop/BSSeq/Amort_et_al_Lusser_Genome_Biol_2017/Illumina_universal_adapter.fasta
threads: 20
max-uncalled: 0
min-read-length: 18
adapter-trim-end: RIGHT
adapter-min-overlap: 3
adapter-threshold: 3
adapter-match: 1
adapter-mismatch: -1
adapter-gap: -6
Adapter: Sequence:
adapter1 AGATCGGAAGAG
My code line is this one:
flexbar -r SRR3674996_1_1_trimmed.fq -p SRR3674996_1_2_trimmed.fq -a Illumina_universal_adapter.fasta
I also though this problem would get solved using the -ap ON
option, but when I add that option the error I obtain is:
flexbar: invalid combination of arguments -- -ap
So I do not know what can be the error with the reads...