ERROR - Exit code 1

[laurichi13]

Hi! I'm trying to run Megahit for the first time, and I have an error saying that Number of sequences are not the same in paired files. Do I have to set a different parameter if the length of my PE reads are not the same?
Thank you in advance.

MEGAHIT v1.1.3
--- [Tue Oct 13 10:59:10 2020] Start assembly. Number of CPU threads 6 ---
--- [Tue Oct 13 10:59:10 2020] Available memory: 67288412160, used: 63923991552
--- [Tue Oct 13 10:59:10 2020] Converting reads to binaries ---
/home/laura/miniconda3/envs/metawrap-env/bin/megahit_asm_core buildlib megahit_result/tmp/reads.lib megahit_result/tmp/reads.lib
[ERROR] [sequence_manager.cpp : 151]: File(s) CLEAN_READS/ALL_READS_1.fastq,CLEAN_READS/ALL_READS_2.fastq: Number of sequences not the same in paired files. Abort.
Error occurs when running "megahit_asm_core buildlib"; please refer to megahit_result/log for detail
[Exit code 1]

[LizzieFrench]

I know this issue is old - but I had this same issue when using the metawrap pipeline. When I installed megahit via conda and ran it directly on the ALL_READS files from metawrap, it worked fine, so it must be an issue with metawrap.