Is it possible to know when the code run will be completed??

Question

[Anisur Rahman]

I have run bowtie2 from the command line to align paired-end reads of Arabidopsis thaliana with its reference genome.

# Align with bowtie
bowtie2 \
    --fast-local \
    -p 6 \
    --phred33 \
    -x refseq/$refseq \
    -1 $read1 \
    -2 $read2 |\
    samtools sort > $mapped/mapped_all.bam

My PC has only 6 threads and I have assigned them all to run this code. I guess it will take quite a long time.

Is there any code or command that will estimate when the code run will be completed?

Answer 1

[ATpoint]

Run it on 1mio reads and then extrapolate, no there is no magical formula, depends on the machine, the harddrive speed, the read length etc.