AdapterRemoval Tool line error

Question

[Sarah]

Hi, everyone.

I am very new to bioinformatics and struggling with AdapterRemoval. I am on a MacBook Pro and using a conda environment in the terminal. I have two documents that I am trying to trim and pair. My code is below:

adapterremoval \
  --file1 /Users/*******/Desktop/PRO_CAN_NK15018_20M_R1.fastq.gz \
  --file2 /Users/*******/Desktop/PRO_CAN_NK15018_20M_R2.fastq.gz \
  --basename /Users/*******/Desktop/PRO_CAN_PAIRED_R3.fastq.gz

The code runs, but then stops with the error:

Error reading FASTQ record at line 14821369; aborting:
    partial FASTQ record; cut off after sequence
Aborting thread due to error.

It seems there is something wrong with the fastq.gz files I am inputting, but I'm not sure how to fix the error. The files I am inputting have been checked for quality with FastQC and downsampled using Reformat.sh in bbmap.

Thanks for any help.

[barslmn]

Have you looked at the 14821369th line?

[Sarah]

Is there a way to view a specific line in the terminal? I'm not sure how to maneuver such a large file.

[barslmn]

You can do so with zcat and sed

zcat my.fastq.gz | sed -n 14821360,14821380p