The logging file for snakemake

Question

[wangdp123]

Hi there,

I am trying to correctly understand how logging system works in snakemake.

In the original tutorial, it states like this:

 shell:
        "(bwa mem -R '{params.rg}' -t {threads} {input} | "
        "samtools view -Sb - > {output}) 2> {log}"

And in other places, I keep seeing something like this:

macs2 callpeak -t {input[0]} \
                -c {input[1]} -f BAM -g {config[macs_g]} \
                --outdir 04peak -n {wildcards.sample} -q 0.001 &> {log}

wigToBigWig -clip samples/bwig/{wildcards.smp}_min.wig {params.chr} {output.min} 2>&1 >> {output.min}.log

bam2wig.py  -i {input.min} -s {params.chr} -o samples/bwig/{wildcards.smp}_min  &> {output.min}.log

I just wonder:

1. What is the function of the symbol "&" before ">"?
2. What do the number "1" and "2" mean? especially what does this mean (2>&1 >>)?

Many thanks,

Regards,

Tom

Answer 1

[cpad0112]

http://www.tldp.org/LDP/abs/html/io-redirection.html

   &>filename
      # Redirect both stdout and stderr to file "filename."
      # This operator is now functional, as of Bash 4, final release.

   M>&N
     # "M" is a file descriptor, which defaults to 1, if not set.
     # "N" is another file descriptor.

 2>&1
      # Redirects stderr to stdout.
      # Error messages get sent to same place as standard output.
        >>filename 2>&1
            bad_command >>filename 2>&1
            # Appends both stdout and stderr to the file "filename" ...
        2>&1 | [command(s)]
            bad_command 2>&1 | awk '{print $5}'   # found
            # Sends stderr through a pipe.
            # |& was added to Bash 4 as an abbreviation for 2>&1 |.

https://unix.stackexchange.com/questions/99263/what-does-21-in-this-command-mean