Sickle is giving empty trimmed file

Question

[salmon]

Hello,

I am using RNA sequence data (forward and reverse fastq sequence) for my pure culture bacteria. I used the following sickle code and I am getting empty trimmed file. I am not sure where I am going wrong

sickle pe -f Data/K1_R1.fastq -r Data/ K1_R2.fastq -t sanger -o K1_trimmed.fastq -p K2_trimmed.fastq -s qtrim.unparied.fastq -q 30 -l 130
Warning: PE file 2 is shorter than PE file 1. Disregarding rest of PE file 1.

Result
FastQ paired records kept: 0 (0 pairs)
FastQ single records kept: 0 (from PE1: 0, from PE2: 0)
FastQ paired records discarded: 0 (0 pairs)
FastQ single records discarded: 0 (from PE1: 0, from PE2: 0)

I checked the Fastqc report of K1_R1 (Forward read) and K1_R2 (reverse read)as attached below for quality check.

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[jkim]

I just want to let you know that sickle seems quite outdated. I’d go for trimmomatic or some other tools.

[cfos4698]

Agreed. I'd recommend fastp or bbduk.

[GenoMax]

-t sanger

You are not likely to have sanger formatted data if this is recent data.

Warning: PE file 2 is shorter than PE file 1. Disregarding rest of PE file 1.

That message is odd. FastQC indicates that there are an equal number of reads in your files. I second jkim suggestion of trying a different program.

[salmon]

Thank you so much for your reply.