I cannot obtain summary alignment with Bowtie2

Question

[alejandra.pando]

Hello everyone,

I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following:

       ## Time loading reference: 00:00:00
       ## Time loading forward index: 00:00:00
       ## Time loading mirror index: 00:00:00
       ## Multiseed full-index search: 00:00:00
       ## Time searching: 00:00:00
       ## Overall time: 00:00:00
       ## Time loading reference: 00:00:00
       ## Time loading forward index: 00:00:00
       ## Time loading mirror index: 00:00:00
       ## Multiseed full-index search: 00:00:01
       ## Time searching: 00:00:01
       ## Overall time: 00:00:01
       ## Time loading reference: 00:00:00
       ## Time loading forward index: 00:00:00
       ## Time loading mirror index: 00:00:00
       ## Multiseed full-index search: 00:00:00
       ## Time searching: 00:00:00
       ## Overall time: 00:00:00
       ## Time loading reference: 00:00:00
       ## Time loading forward index: 00:00:00
       ## Time loading mirror index: 00:00:00
       ## Multiseed full-index search: 00:00:00
       ## Time searching: 00:00:00
       ## Overall time: 00:00:00
       ## Time loading reference: 00:00:00
       ## Time loading forward index: 00:00:00
       ## Time loading mirror index: 00:00:00
       ## Multiseed full-index search: 00:00:00
       ## Time searching: 00:00:00
       ## Overall time: 00:00:00
       ## Time loading reference: 00:00:00
       ## Time loading forward index: 00:00:00
       ## Time loading mirror index: 00:00:00
       ## Multiseed full-index search: 00:00:00
       ## Time searching: 00:00:00
       ## Overall time: 00:00:00

This is my command line to build the index:

bowtie2-build -o 3 -t 5 Nuevofastaorina human_mirs

And this is my command line to do the alignment:

bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals –-quiet > sr1prueba.sam

Does anyone know how to obtain an alignment summary instead of the above information? What I mean by alignment summary is the following:

20000 reads; of these:
  20000 (100.00%) were unpaired; of these:
    1247 (6.24%) aligned 0 times
    18739 (93.69%) aligned exactly 1 time
    14 (0.07%) aligned >1 times
93.77% overall alignment rate

Thank you in advance for your help!

Alejandra

[swbarnes2]

I confess I don't know bowtie well, but what happens if you remove --quiet?

[GenoMax]

Logically we should see the alignment stats. Though I am not sure why it is printing those 00:00:00's.

--quiet            Print nothing besides alignments and serious errors.

Nice catch.

Answer 1

[Barry Digby]

I know the below works for bowtie, you need to capture the stderr. Let me know if it works!

(bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals –-quiet > sr1prueba.sam) 2> output.err

[GenoMax]

If they are not capturing stderr then where are those 00:00:00 messages coming from I wonder?

[Barry Digby]

They must have carried over the parameter -t/--ftabchars <int> # of chars consumed in initial lookup (default: 10) in the bowtie2-build command to the alignment command.

For bowtie2 it corresponds to: -t/--time print wall-clock time taken by search phases.

Doesn't explain why it was printed 6/7 times though ;) perhaps a for loop we are not privy to