unexpected bowtie2 unpaired alignment behavior

[Mark]

Hello

Seemingly according to the manual, bowtie2 will attempt to align paired-end reads first as pairs but then as unpaired reads if necessary. If this is so, can someone explain the following. (Note, I expect one unpaired alignment)

Thanks

Mark

[rosema1@demeter bowtie2]$ bowtie2 -x 12274_pmi.fa --local -N 0 -L 25 -p 1 -1 s_2_1_25_PMI.fq -2 s_2_2_25_PMI.fq -S s_2_1and2_25_PMI.fq-vs-12274_pmi.fa.sam -I 0 -X 750 --score-min G,5,0 -i S,1,0
278 reads; of these:
278 (100.00%) were paired; of these:
278 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
278 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
278 pairs aligned 0 times concordantly or discordantly; of these:
556 mates make up the pairs; of these:
556 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate


[rosema1@demeter bowtie2]$ bowtie2 -x 12274_pmi.fa --local -N 0 -L 25 -p 1 -U s_2_1_25_PMI.fq,s_2_2_25_PMI.fq -S s_2_1_25_PMI.fq-and-s_2_2_25_PMI.fq-vs-12274_pmi.fa.sam -I 0 -X 750 --score-min G,5,0 -i S,1,0
556 reads; of these:
556 (100.00%) were unpaired; of these:
555 (99.82%) aligned 0 times
0 (0.00%) aligned exactly 1 time
1 (0.18%) aligned >1 times
0.18% overall alignment rate

[dpryan]

Please don't cross-post.