View Single Post
Old 09-23-2021, 03:06 PM   #692
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,131
Default

Quote:
Originally Posted by lmusgrove View Post
Hi Brian,

I'm running BBMap with the rpkm output option and would like to know how to see mapped rate for each read file. I run multiple files consecutively with nohup. Here's my code:

bbmap.sh ref=data/Assembly.fasta \
in1=data/clean/A_1.clean.fq.gz \
in2=data/clean/A_2.clean.fq.gz \
rpkm=data/fpkm/A.fpkm \
t=5 &

bbmap.sh ref=data/Assembly.fasta \
in1=data/clean/B_1.clean.fq.gz \
in2=data/clean/B_2.clean.fq.gz \
rpkm=data/fpkm/B.fpkm \
t=5

etc etc

So far it's worked really well. However, while the stdout file shows the mapped rates it doesn't tell me which read files relate to which stats. It just has a number of repeated --- Results 1 ---- records and I don't know which is which.

Is there a flag I need to add to ensure I can see which stats are for which files?

Thanks!

Lisa
You should be able to use
Code:
covstats=<file>         Per-scaffold coverage info.
for each of your commands. You can also capture the stderr/out to a file to get statistics. https://linuxize.com/post/bash-redirect-stderr-stdout/
GenoMax is offline   Reply With Quote