seqkit pair no results

[lvgeng0914]

When using the command seqkit pair -1 reads_1.fq.gz -2 reads_2.fq.gz, empty files are output.

[shenwei356]

It means no shared sequence IDs are found in both files. You may need to set the value of the option --id-regexp (see the tip 1 in the help message below).

$ seqkit pair  -h
match up paired-end reads from two fastq files

Attention:
1. Orders of headers in the two files should be the same (not shuffled),
   otherwise, it consumes a huge number of memory for buffering reads in memory.
2. Unpaired reads are optional outputted with the flag -u/--save-unpaired.
3. If the flag -O/--out-dir is not given, the output will be saved in the same directory
   of input, with the suffix "paired", e.g., read_1.paired.fq.gz.
   Otherwise, names are kept untouched in the given output directory.
4. Paired gzipped files may be slightly larger than original files, because
   of using a different gzip package/library, don't worry.

Tips:
1. Support for '/1 'and '/2' tags for paired read files generated by platforms like MGI.
   You can simply specify the regular expression for extracting sequence IDs:
     --id-regexp '^(\S+)\/[12]'

Please run the command below and paste the result here.

seqkit head -n 5 read_{1,2}.fq.gz | seqkit seq -n