snakemake: MissingOutputException within docker - docker

Question

I am trying to run a pipeline within a docker using snakemake. I am having problem using the sortmerna tool to produce {sample}_merged_sorted_mRNA and {sample}_merged_sorted output from control_merged.fq and treated_merged.fq input files.
Here my Snakefile:
SAMPLES = ["control","treated"]
for smp in SAMPLES:
print("Sample " + smp + " will be processed")
rule final:
input:
expand('/output/{sample}_merged.fq', sample=SAMPLES),
expand('/output/{sample}_merged_sorted', sample=SAMPLES),
expand('/output/{sample}_merged_sorted_mRNA', sample=SAMPLES),
rule sortmerna:
input: '/output/{sample}_merged.fq',
output: merged_file='/output/{sample}_merged_sorted_mRNA', merged_sorted='/output/{sample}_merged_sorted',
message: """---SORTING---"""
shell:
'''
sortmerna --ref /usr/share/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/ usr/share/sortmerna/rRNA_databases/index/silva-bac-23s-id98: --reads {input} --paired_in -a 16 --log --fastx --aligned {output.merged_file} --other {output.merged_sorted} -v
'''
When runnig this I get:
Waiting at most 5 seconds for missing files.
MissingOutputException in line 57 of /input/Snakefile:
Missing files after 5 seconds:
/output/control_merged_sorted_mRNA
/output/control_merged_sorted
This might be due to filesystem latency. If that is the case, consider to increase the wait $ime with --latency-wait.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /input/.snakemake/log/2018-11-05T091643.911334.snakemake.log
I tried to increase the latency with --latency-wait but I get the same result. Funny thing is that two output files control_merged_sorted_mRNA.fq and control_merged_sorted.fq are produced but the program fails and exits. The version of snakemake is 5.3.0. Any help?

Answer 1

snakemake fails because the outputs described by the rule sortmerna are not produced. This is not a latency problem, it is a problem with your outputs.
Your rule sortmerna expects as output:
/output/control_merged_sorted_mRNA
and
/output/control_merged_sorted
but the program you are using (I know nothing about sortmerna) is apparently producing
/output/control_merged_sorted_mRNA.fq
and
/output/control_merged_sorted.fq
Make sure that when you specify the options --aligned and --other on the command line of your program, it should be the real names of the files produced or if it is only the basename and the program will add a suffix .fq. If you are in the latter case, I suggest you use:
rule final:
input:
expand('/output/{sample}_merged.fq', sample=SAMPLES),
expand('/output/{sample}_merged_sorted', sample=SAMPLES),
expand('/output/{sample}_merged_sorted_mRNA', sample=SAMPLES),
rule sortmerna:
input:
'/output/{sample}_merged.fq',
output:
merged_file='/output/{sample}_merged_sorted_mRNA.fq',
merged_sorted='/output/{sample}_merged_sorted.fq'
params:
merged_file_basename='/output/{sample}_merged_sorted_mRNA',
merged_sorted_basename='/output/{sample}_merged_sorted'
message: """---SORTING---"""
shell:
"""
sortmerna --ref /usr/share/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-bac-23s-id98: --reads {input} --paired_in -a 16 --log --fastx --aligned {params.merged_file_basename} --other {params.merged_sorted_basename} -v
"""