Writing into logs in multiple shell commands in snakemake produces error

Question

[H.Hasani]

Hello all,

I'm trying to use samtools within snakemke and I split them into multiple commands as follows:

shell:
    """
       samtools sort {input.mppd} | samtools view -b -S > {output.srtd} &> {log}
       samtools index -bc {output.srtd} {output.srtd}.bai &>> {log}
    """

if i write each command alone it works smoothly; I found that it only works if I remove the first log as follows:

shell:
    """
       samtools sort {input.mppd} | samtools view -b -S > {output.srtd}
       samtools index -bc {output.srtd} {output.srtd}.bai &> {log}
     """

I still need to have the log of the first command saved but I'm not sure why it is throwing this err? any ideas?

thank you