When I give two gzipped reads to fastq_pair, it seems to function normally. The output files are named with the .fq extension, but they're not a text file, nor a gzipped file.
$ fastq_pair SAMPLE_1.fq.gz SAMPLE_2.fq.gz
Writing the paired reads to SAMPLE_1.fq.gz.paired.fq and SAMPLE_2.fq.gz.paired.fq.
Writing the single reads to SAMPLE_1.fq.gz.single.fq and SAMPLE_2.fq.gz.single.fq
Left paired: 11619 Right paired: 11619
Left single: 381534 Right single: 418985
$ file -i SAMPLE_1.fq.gz.paired.fq
SAMPLE_1.fq.gz.paired.fq: application/octet-stream; charset=binary
$ gzip -t SAMPLE_1.fq.gz.paired.fq
gzip: SAMPLE_1.fq.gz.paired.fq: not in gzip format
When I give two gzipped reads to fastq_pair, it seems to function normally. The output files are named with the .fq extension, but they're not a text file, nor a gzipped file.