Unexpected behavior of generating a interleaved fastq by bamToFastq

[chtsai0105]

I was trying to get the unmapped reads from a bam file and convert it to a interleaved fastq file by bamToFastq but having a unexpected behavior. According to the --help info, I can generate a interleaved fastq by writing both -fq and -fq2 to /dev/stdout, then redirect the output to a file:

(some smatools cmd...) | bamToFastq -i - -fq /dev/stdout -fq2 /dev/stdout > test.fq

(I'm using -i - to catch the output of samtools sort -n as the input)

However, the output test.fq only contains R2.

head -n 40 sim_1_unmapped.fastq
@AP022642.1_0_1/2
AGCCGCAGCCCCACCTCCTCGCGCTCGATGGTCTGGAACGGGTTGTTGCTGTTGCCGCCGCCGTTGGTGACGTAGTTGCCGGTGACGAAGGGGATGGTCTGGCCGACGAAGATGCTCGCCACCTCG
+
BBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFBFFFFBFFBFFFFBFFFFBFFFFFFFF<FFFFFFFFFFBFFFFFFFFBFFFFFFFFFFFFFFFFFBBFFF
@AP022642.1_0_3/2
GCCGCCTACCAGGCCAGCATCCTCGGGCTGCTGAGCAACTGAGGCAAACGGAGCGAGCGCCGCGTCACAAAACCGACAAGCTGGGGCTCCAGGTGGGACAAGTGGCCATCCATGCCGGAAAGCCGA
+
BBBBBFF/FFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFBFFF<FF<FFFFFFFF/FFF<FFFFFFFFFFFFFFFFFFF<FFFFFBFBFFFFFFF/FFBFFFFB
@AP022642.1_0_4/2
GGTGCTGCCGAACCGTTACTTCGACAACCACAACTCGGGGCACCTCATCTCCCGCATCACCTTCAACGTCACCATGGTGACCGGCGCCGCTACCGACGCCATCAAGGTGGTGATCCGCGAAGGCAT
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFF/FFF/FFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFF<F/FFFFFFFFFF<FFFBFFBFBFFFFB/
@AP022642.1_0_5/2
GAGGATTAACGCAGGTTTTGCCCGCTGGCGCGGACCAACTTTCGGCGGGTCGTGATGGGCTGAGGCGTAGGGGAGGGGATGCGGAGGCGGGAAAACGGGCCGCGCGAGGACGGCCCGGAGGGCGAT
+
BBBBBFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFFFFFFFFFBFFFF<FFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFBF/FBFFFFBF<FFFFFFFFFFFF/FFFB
@AP022642.1_0_6/2
CGTCGCCAGATTCGCGGCAGGCAGCGGCAGCATGGCCTGGCTGTTGACGCTGGCGAGCTGGAGCCAAAGCTGTTCGCCTTCGACGAACTGGTCCTGGGGCAGCCACAGGCCGTGGTGCCAGCCGTT
+
BBBBBFFFFFFFFF/FFFFFFFFFBFFFFFBFFFFFFFFFBFFFFFFBFFFFFFFFBFFFFFFFBFFFFFFFFFFFFF/FFFFFF/FFFFFF/FBFFFFFFFFFFFB/7FFFFFFFFFFFFFF/FB
@AP022642.1_0_7/2
CCCAGCGAGACCACCGTGGGCGTGCTCACCCACGAGGTGCGGGGTGAGCTGGCCGAAGGCGCCGGCATTCCCCTGGGCGAGGCCTTGCCGGGCGCCAGGGTGCAGGTGCTGGACGTTGTGCTCAAC
+
BBB/B<F/F/FF/FFFF/<F/F<FFBFBF/B//FB<FF<FFFFF<//<<F<<<F/F/F/B/FFF<F/B//FBB/F//B///F/B7<<F<B/F<<F////<F77FF/<F<7/B//B/7/FBF//<7/
@AP022642.1_0_8/2
CCAGCGCCGAGGCATAGGTCGGCAGCTCATCGTCGATGAACTCGTTGACGGTGCTGACCAGCAGGGTGCGCCCTTTGACGCCCTTCAGGCCCAGGTAGCGGATCATGGCTCGGCTCGCTCTAGTTC
+
BBBBBF/FFFFFFFFFFFFFFFFFFFFFFFF/FFFFBFFFFFFFF<FFFFFFFBFFFFFFFFFFFF/FFFFFFBFFF<FF/FFFFFFFFFBFFFFFFFBFFFBFFFFFFFFFFFFFFFFFFFFFFF
@AP022642.1_0_9/2
TGTCGTCGACGCTGATGGAGGAGCGGATGCGGTCCTCGAAGCCCAGGCGGATCAGGCCGGCGGCAGCGAGGATGATGGCGTCGTACTCGCCGGCATCCAGCTTGGCCAGGCGGGTGTTGACGTTGC
+
BBBBBB<FFFFFFFFFFFFFFFFFFBFF<FFFFF<FFFFFFFF<B<FFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF/FFFFFFFFFFF
@AP022642.1_1_0/2
TGAGAATCGCGTAGTCCACGCCTATGGCCGTCACCAGCAGCAGCCCGAACAGGCTGAACAGCGTCAGCGGCTGGCCCAGCCAGCCGAGGCAGGCCAGGGACGCCAGCGCCGCCAGCAGCGGCAGCG
+
BBBBBFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFF/<FFFFFFFFFFFFFF<F<F7FFFFFFF7F<F<FFFFFFFFFFBFFFFFFFFBFFF
@AP022642.1_1_1/2
AAGCTGACCCCCACCGAGCTGCTCAACGCCCTGCTCAAGGCCCCGGTGGACCTGATCTGGAACGGCGGCATCGGCACCTACGTGAAGTCCAGCAAGGAAAGGCACGCCGACGTCGGCGACAAGGCC
+
BBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFF/B/FFFFFFF/FFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFF/FFF<FFFFFFFBFFFFFFFFFFFF

I then ran the bamToFastq again without redirecting the output. Now the R1 showed up:

(some smatools cmd...) | bamToFastq -i - -fq /dev/stdout -fq2 /dev/stdout | head -n 41
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
@AP022642.1_0_1/1
ACTACGCGGAGAACCTCGACCGGGTGGCGGCGATCATCGCCAACATCGACGTGCCGGGCTCGGTGGACACCGACGTGGTGCCGGTGCGCAACGGCATCGCCACCGACATCGCCGCGATGCTCGGCG
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFBFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFF/FBFF/BBFFFFFBFFBFFFFFFFF
@AP022642.1_0_1/2
AGCCGCAGCCCCACCTCCTCGCGCTCGATGGTCTGGAACGGGTTGTTGCTGTTGCCGCCGCCGTTGGTGACGTAGTTGCCGGTGACGAAGGGGATGGTCTGGCCGACGAAGATGCTCGCCACCTCG
+
BBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFBFFFFBFFBFFFFBFFFFBFFFFFFFF<FFFFFFFFFFBFFFFFFFFBFFFFFFFFFFFFFFFFFBBFFF
@AP022642.1_0_3/1
CCCAGGTCTTGCTCTTCAGCGTGGCGTAGGTGTCCCAGAGCCCGGGTTGGGCGGCCTGGGCCAGCAACGGCAGCAACAGGGGAAGGGTGAGGGCCAGACGGCCCAGACGGTGTTTCGACATGACCA
+
BBBBBFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFB<FF/FFFFFFFFFF/FFFFBFFFFFFFF<FFFFFFBFFFFFFFFFBBF<FFFFFFFFFFF<FFFFFFFFFFFBFBBFFFFFB7
@AP022642.1_0_3/2
GCCGCCTACCAGGCCAGCATCCTCGGGCTGCTGAGCAACTGAGGCAAACGGAGCGAGCGCCGCGTCACAAAACCGACAAGCTGGGGCTCCAGGTGGGACAAGTGGCCATCCATGCCGGAAAGCCGA
+
BBBBBFF/FFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFBFFF<FF<FFFFFFFF/FFF<FFFFFFFFFFFFFFFFFFF<FFFFFBFBFFFFFFF/FFBFFFFB
@AP022642.1_0_4/1
TAGCCCTGGGGCATCTTCTCGATGAACTCGGCGGCGAAGGCGGCTTCGGCGGCGGCCTTGACGTCTTCCAGCGGGGCGCCGGCGAGGTCGCCGTAGGCGATGTTGTTGGTGACCGTGTCGTTGAAC
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FF/FFFFFBFFFFFBFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFBBFFFFFF/
@AP022642.1_0_4/2
GGTGCTGCCGAACCGTTACTTCGACAACCACAACTCGGGGCACCTCATCTCCCGCATCACCTTCAACGTCACCATGGTGACCGGCGCCGCTACCGACGCCATCAAGGTGGTGATCCGCGAAGGCAT
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFF/FFF/FFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFF<F/FFFFFFFFFF<FFFBFFBFBFFFFB/
@AP022642.1_0_5/1
TCGTCGCCTACACCCTGAACAAGCCCCTGGTGCTGTTCCGCAAGCAGGGCTAGCTGCCGGCCGACGTGCTCGCCGAGGGCTACCAGACCGAATACGGCGAAGCCTTCCTCGAAGTGCACGCCGACA
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFF/FFF<FFFFFFFFBF/FFFFFFFFFBFFFFFFFFFFF<FFFFFF</<FFF/FFFFFFBFFFF<FFFFFFFFF7FFF
@AP022642.1_0_5/2
GAGGATTAACGCAGGTTTTGCCCGCTGGCGCGGACCAACTTTCGGCGGGTCGTGATGGGCTGAGGCGTAGGGGAGGGGATGCGGAGGCGGGAAAACGGGCCGCGCGAGGACGGCCCGGAGGGCGAT
+
BBBBBFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFFFFFFFFFBFFFF<FFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFBF/FBFFFFBF<FFFFFFFFFFFF/FFFB
@AP022642.1_0_6/1
ACCGCAACCCTACCTGCCACTGGACCAGCCCGCCCGCGCCCCGTCCACCCAGTTGCGCAGGCTCGAACTGGGCCCCCTGCTGGTGGCCCTGTACGAACCCGCGCCCCTGCAAAGCCCGGTCGAGCA
+
BBBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFF/FFFFFFFFFFFFFFFBFFFFF7FFFFFFFFFFFFFBFFFFFBFFFFF<FFFFFBFFFFFFFFFFFFBFFBFFFFFFFFFFFFFFFF7
@AP022642.1_0_6/2
CGTCGCCAGATTCGCGGCAGGCAGCGGCAGCATGGCCTGGCTGTTGACGCTGGCGAGCTGGAGCCAAAGCTGTTCGCCTTCGACGAACTGGTCCTGGGGCAGCCACAGGCCGTGGTGCCAGCCGTT
+
BBBBBFFFFFFFFF/FFFFFFFFFBFFFFFBFFFFFFFFFBFFFFFFBFFFFFFFFBFFFFFFFBFFFFFFFFFFFFF/FFFFFF/FFFFFF/FBFFFFFFFFFFFB/7FFFFFFFFFFFFFF/FB
@AP022642.1_0_7/1