MetaSPAdes shotgun paired end genome assembly

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1

Hi friends, Metagenomic paired end raw data with cut adapt
‘Maximum error rate 0.3’
Match times: 1
Minimum overlap length:3
minimum lenght: 15
Max N: 0.3
Max expected errors: 30 parameters.

Then I aligned the host genome with gallus gallus with BBmap tool. I want to Assembly unmapped read. However, MetaSPAdes gives the following error code.

Metaspades input : single end unmapped aligned ’ |K-mer size values|21,33,55,77|
|Set Phred quality offset|64 (Illumina)|’

Metaspades Output Error: Command line: /usr/local/tools/_conda/envs/mulled-v1-689e080ce12220d7a8b4d59ef6b3f5f70c4406747478ca6091b549f487382e53/bin/metaspades.py -o /data/jwd02f/main/065/497/65497189/working/output -t 16 -m 350 --pe-1 1 /data/jwd02f/main/065/497/65497189/working/

how can ı solve this error?

2

Hi @Busrak

Try this:

  1. Use one of the paired-end input settings
  2. Confirm that the read pairs are “intact” within the input files.