Counts all read zero after alignment?

Hi everyone,

I’m looking for some help because I just ran my alignment code last night for 12 RNAseq samples. After taking a look at the counts that were generated this morning, all of them are reading 0 for every gene. Oddly, here are the results in the terminal…

95887304 reads; of these:
  95887304 (100.00%) were unpaired; of these:
    2313614 (2.41%) aligned 0 times
    76638154 (79.93%) aligned exactly 1 time
    16935536 (17.66%) aligned >1 times
97.59% overall alignment rate
[bam_sort_core] merging from 32 files and 16 in-memory blocks...

Seems like the code is working for alignment but giving odd counts. Anyone have any ideas where to look?