How to input unpaired data after error correction?

[1996xjm]

Description of bug

I have a paired-end data of bacteria. After error correction using trimmomatic, I got four files: QD34_12_paired_1.fq.gz, QD34_12_paired_2.fq.gz, QD34_12_unpaired_1.fq.gz, QD34_12_unpaired_2.fq.gz. For unpaired fastq files, I don't know how to edit my YAML file. Is it right as the follow code show? Can spades recognize whether the unpaired file is forward or reverse?

YAML File

[{
	"orientation": "fr",
	"type": "paired-end",
	"left reads": ["/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_paired_1.fq.gz"],
	"right reads": ["/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_paired_2.fq.gz"]
},
{
	"type": "single",
	"single reads": ["/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_unpaired_1.fq.gz", "/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_unpaired_2.fq.gz"]
}]

spades.log

no

params.txt

Command line: /home/xjm/miniconda3/envs/spades/SPAdes-3.15.3-Linux/bin/spades.py --isolate --dataset /userData/xjm/genome_seq_Po/patch2/spades_output/QD34_12/QD34_12.yaml -t 28 -m 128 -o /userData/xjm/genome_seq_Po/patch2/spades_output/QD34_12

System information:
SPAdes version: 3.15.3
Python version: 3.7.8
OS: Linux-4.15.0-161-generic-x86_64-with-debian-buster-sid

Output dir: /userData/xjm/genome_seq_Po/patch2/spades_output/QD34_12
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
Isolate mode
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_paired_1.fq.gz']
right reads: ['/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_paired_2.fq.gz']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Library number: 2, library type: single
left reads: not specified
right reads: not specified
interlaced reads: not specified
single reads: ['/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_unpaired_1.fq.gz', '/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_unpaired_2.fq.gz']
merged reads: not specified
Assembly parameters:
k: automatic selection based on read length
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /userData/xjm/genome_seq_Po/patch2/spades_output/QD34_12/tmp
Threads: 28
Memory limit (in Gb): 128

SPAdes version

3.15.3

Operating System

Linux-4.15.0-161-generic-x86_64-with-debian-buster-sid

Python Version

3.7.8

Method of SPAdes installation

manual

No errors reported in spades.log

• Yes

[asl]

You can simply add your single reads as "single reads" portion of your paired-end library. Orientation of single reads does not make any sense, as it's single read

[1996xjm]

Can I write YAML file like this?

[{
	"orientation": "fr",
	"type": "paired-end",
	"left reads": ["/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_paired_1.fq.gz"],
	"right reads": ["/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_paired_2.fq.gz"],
"single reads": ["/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_unpaired_1.fq.gz", "/userData/xjm/genome_seq_Po/patch2/trimmomatic_output-1/QD34_12/QD34_12_unpaired_2.fq.gz"]
}]

[asl]

Yes