Hi, thanks for developing fastp, its a great tool and a lot better then others. When I run parallel.py on my paired samples with the below code, I noticed that fastp was unable to recognise them as paired.
python parallel.py -i "$INPUT_DIR" -o fastp_output/trimmed -r fastp_output/reports -p 6 -1 _1.fastq.gz -2 _2.fastq.gz
This can be seen in my log file output below.
Running command: fastp -i ../samples/SRR5564273_1.fastq.gz -o fastp_output/trimmed/SRR5564273_1.clean.fastq.gz --html=fastp_output/reports/SRR5564273pe.html --json=fastp_output/reports/SRR5564273pe.json
Running command: fastp -i ../samples/SRR5564274_2.fastq.gz -o fastp_output/trimmed/SRR5564274_2.clean.fastq.gz --html=fastp_output/reports/SRR5564274_2.fastq.gz.html --json=fastp_output/reports/SRR5564274_2.fastq.gz.json
...
However, when I change to code slightly, to not contain the full suffix, it works.
python parallel.py -i "$INPUT_DIR" -o fastp_output/trimmed -r fastp_output/reports -p 6 -1 _1.fastq -2 _2.fastq
The above code can be seen to work, from my log file output below.
Running command: fastp -i ../samples/SRR5564273_1.fastq.gz -I ../samples/SRR5564273_2.fastq.gz -o fastp_output/trimmed/SRR5564273_1.clean.fastq.gz -O fastp_output/trimmed/SRR5564273_2.clean.fastq.gz --html=fastp_output/reports/SRR5564273pe.gz.html --json=fastp_output/reports/SRR5564273pe.gz.json
Running command: fastp -i ../samples/SRR5564276_1.fastq.gz -I ../samples/SRR5564276_2.fastq.gz -o fastp_output/trimmed/SRR5564276_1.clean.fastq.gz -O fastp_output/trimmed/SRR5564276_2.clean.fastq.gz --html=fastp_output/reports/SRR5564276pe.gz.html --json=fastp_output/reports/SRR5564276pe.gz.json
Hence there seems to be a bug in either parallel.py or fastp, whereby the file extension of _1.fastq.gz and _2.fastq.gz are not recognised.