I got this error when I run snakemake.
snakemake.exceptions.MissingOutputException: Job 160 completed
successfully, but some output files are missing. Missing files after 60
seconds. This might be due to filesystem latency. If that is the case,
consider to increase the wait time with --latency-wait:
TL_UB60.sam
I use snakefile like this
configfile:
"samples.json"
samples = config["samples"]
rule all:
input:
expand("{sample}.sam", sample=samples),
expand("{sample}.bam", sample=samples),
expand("{sample}.bam.bai", sample=samples)
rule make_bam:
input:
ref="reference.c1.c2.fasta",
r1="{sample}.r1.fq.gz",
r2="{sample}.r2.fq.gz"
output:
sam="{sample}.sam",
bam="{sample}.bam",
bai="{sample}.bam.bai"
shell:
"""
bbmap.sh sam=1.3 in1={input.r1} in2={input.r2} out={output.sam} ref={input.ref} nodisk
&& samtools view -Sb -q 4 {output.sam} > {output.bam}
&& samtools sort {output.bam} -o {output.bam}
&& rm {output.sam}
samtools index {output.bam} > {output.bai}
"""
And run command line
snakemake -s snakefile --cores 24 --latency-wait 60
But its doesn t work. I do not know ưhy. Anyone can help me !
I have tried changed time wait but its also not work.
I am newbie so it is tough for to solve the issue like this.