Bowtie2- --al-conc: Writting to screen and file??

[WiscoADL]

I am fairly new to mapping short read data. I have been using bowtie, but recently switched to bowtie2 mainly b/c it supports gapped alignments.

I am only interested in a portion of a chromosome in soybean, therefore the reference genome I use for mapping is only a section of one of the chromosomes. This allows me to do the mappings quickly on my old computer. The problem is all the mapping results are based on the arbitrary chromosome position resulting from my reference.

To get the correct chromosome positions, I am mapping to the small reference and outputting the reads as fastq files. I then re-run the mapping using the entire chromosome to get the correct mapping positions (this alignment only takes seconds).

Anyway, when doing the first alignment I use the --al-conc <path> output option to get the mapping results to write to a fastq file. It seems to write the hits just fine, but it is also printing them in the terminal. Bowtie did the same thing. Why does it print it to the .fastq file and the terminal? Is there a way to get it to stop. I tried --quite but still writing to terminal. Not a huge deal but if I check out my CPU usage, the terminal seems to be taking up a lot of my limited computers availability.

[WiscoADL]

This is now causing my terminal to crash. Bowtie2 keeps running and completes the mapping but I would like to get it to write the hits to the fastq file alone.

Note: using the -S option only writes the hits to the .sam file, so why does --al-con not do the same?