After using Trinity (V 2.1.1) to assembly, I want to assess the quality of it. Then, I use bowtie2, mapping the reads back to the transcriptome assembled by Trinity. First, I use the bowtie2-build to build the reference. The order is like this :

bowtie2-build Fa_trinity_out.Trinity.fasta ./Fa_transcriptome.fasta --threads 4

Fa_trinity_out.Trinity.fasta is the result of Trinity.

Then, use bowtie2 to align, the command is like this:

bowtie2 -p 10 -q --no-unal -k 20 -x Fa_transcriptome.fasta -1 ./Fa_1.clean.fq -2 ./Fa_2.clean.fq > Fa_bowtie2_stats.txt | samtools view -Sb -o 2_F3r_bowtie2.bam

During all these process, there is no error report, I get the final .bam file successfully. However, the .bam file is too small, just 63.Then,I try to use "samtools flagstat" to view the results, there is nothing, It's like this:

 0 + 0 in total (QC-passed reads + QC-failed reads) 
 0 + 0 secondary 
 0 + 0 supplementary 
 0 + 0 duplicates 
 0 + 0 mapped (N/A : N/A) 
 0 + 0 paired in sequencing 
 0 + 0 read1 
 0 + 0 read2 
 0 + 0 properly paired (N/A : N/A) 
 0 + 0 with itself and mate mapped 
 0 + 0 singletons (N/A : N/A) 
 0 + 0 with mate mapped to a different chr 
 0 + 0 with mate mapped to a different chr (mapQ>=5)

SO,I wonder is there any mistake in my commands that result in these? OR other reasons? Thank you!!!