search

voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
588 stars 134 forks source link

ERROR - Exit code 1 #288

Open laurichi13 opened 3 years ago

laurichi13 commented 3 years ago

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 commented 3 years ago

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.