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Not able to run flexbar with paired reads #36

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vgaout opened this issue Dec 16, 2021 · 0 comments
Open

Not able to run flexbar with paired reads #36

vgaout opened this issue Dec 16, 2021 · 0 comments

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@vgaout
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vgaout commented Dec 16, 2021

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...

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