Cannot find summary message after Bowtie2 mapping

Question

[BeeWork]

Hi all, I tried to align the reads in Bowtie2 and command the a SAM file output. I also expect a summary file to be saved as output file. But I can only find the SAM file. did I miss out any command in my line ?

Here's my command line:

bowtie2 -X 1000 -x hg38 -1 R1_fastq -2 R2_fastq -S control.sam 

and the summary file I cannot find contain information like below :

10000 reads; of these:
  10000 (100.00%) were paired; of these:
    650 (6.50%) aligned concordantly 0 times
    8823 (88.23%) aligned concordantly exactly 1 time
    527 (5.27%) aligned concordantly >1 times
    ----
    650 pairs aligned concordantly 0 times; of these:
      34 (5.23%) aligned discordantly 1 time
    ----
    616 pairs aligned 0 times concordantly or discordantly; of these:
      1232 mates make up the pairs; of these:
        660 (53.57%) aligned 0 times
        571 (46.35%) aligned exactly 1 time
        1 (0.08%) aligned >1 times 96.70% overall alignment rate

Thanks

[GenoMax]

You will have to capture the standard out/error to save this information.

[BeeWork]

Thanks . I tired to re-run the command including the stderr file.

bowtie2 --very-sensitive --no-unal -X 1000 \
-x hg38 \
-1 R1_fastq -2 R2_fastq \
-S sample.sam \
2> sample.stderr

But i got another problem that there are some errors messages at the end of the stderr but do not have any stat summary. Here are the error messages:

Error, fewer reads in file specified with -2 than in file specified with -1
Error: Encountered internal Bowtie 2 exception (#1); bowtie2-align exited with value 1

I am not too sure what they are? are they major errors ? I still got the sam file after the run, so can I assume the job is done ?

Thanks

[Carlo Yague]

Yes the first one is a major error. For paired-end reads, you need to have the same number of reads in R1_fastq and in R2_fastq, because bowtie2 assume that the first read in R1_fastq is paired with the first read of R2_fastq. So you need to fix this. Where do those fastq file come from ? Could the files be corrupted ?

[BeeWork]

I figured out there's an error in my command line in the trimmomatic script. i was using a wrong R2 file that's why the alignment didn't work. Now it seem ok .

Thanks

[alejandra.pando]

Hello everyone,

I had the same problem as Beework but couldn’t solve it yet.

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

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

Does anyone know how to obtain an alignment summary instead of the above information?

Thank you in advance for your help!

Alejandra

[Carlo Yague]

You can start with removing the --quiet option in the bowtie command. The alignment summary should print. If you want to save it in a file, you can follow the above recommandation from genomax about capturing the standard output/error..