problem with snakemake submitting jobs with multiple wildcard on SGE - cluster-computing

Question

I used snakemake on LSF cluster before and everything worked just fine. However, recently I migrated to SGE cluster and I am getting a very strange error when I try to run a job with more than one wildcard.
When I try to submit a job based on this rule
rule download_reads :
threads : 1
output : "data/{sp}/raw_reads/{accesion}_1.fastq.gz"
shell : "scripts/download_reads.sh {wildcards.sp} {wildcards.accesion} data/{wildcards.sp}/raw_reads/{wildcards.accesion}"
I get a following error (snakemake_clust.sh details bellow)
./snakemake_clust.sh data/Ecol1/raw_reads/SRA123456_1.fastq.gz
Building DAG of jobs...
Using shell: /bin/bash
Provided cluster nodes: 10
Job counts:
count jobs
1 download_reads
1
[Thu Jul 30 12:08:57 2020]
rule download_reads:
output: data/Ecol1/raw_reads/SRA123456_1.fastq.gz
jobid: 0
wildcards: sp=Ecol1, accesion=SRA123456
scripts/download_reads.sh Ecol1 SRA123456 data/Ecol1/raw_reads/SRA123456
Unable to run job: ERROR! two files are specified for the same host
ERROR! two files are specified for the same host
Exiting.
Error submitting jobscript (exit code 1):
Shutting down, this might take some time.
When I replace the sp wildcard with a constant, it works as expected:
rule download_reads :
threads : 1
output : "data/Ecol1/raw_reads/{accesion}_1.fastq.gz"
shell : "scripts/download_reads.sh Ecol1 {wildcards.accesion} data/Ecol1/raw_reads/{wildcards.accesion}"
I.e. I get
Submitted job 1 with external jobid 'Your job 50731 ("download_reads") has been submitted'.
I wonder why I might have this problem, I am sure I used exactly the same rule on the LSF-based cluster before without any problem.
some details
The snakemake submitting script looks like this
#!/usr/bin/env bash
mkdir -p logs
snakemake $# -p --jobs 10 --latency-wait 120 --cluster "qsub \
-N {rule} \
-pe smp64 \
{threads} \
-cwd \
-b y \
-o \"logs/{rule}.{wildcards}.out\" \
-e \"logs/{rule}.{wildcards}.err\""
-b y makes the command executed as it is, -cwd changes the working directory on the computing node the the working directory from where the job was submitted. Other flags / specifications are clear I hope.
Also, I am aware of --drmaa flag, but I think out cluster is not well configured for that. --cluster was till now a more robust solution.
-- edit 1 --
When I execute exactly the same snakefile locally (on the fronend, without the --cluster flag), the script gets executed as expected. It seems to be a problem of interaction of snakemake and the scheduler.

Answer 1

-o \"logs/{rule}.{wildcards}.out\" \
-e \"logs/{rule}.{wildcards}.err\""
This is a random guess... More than one wildcards are concatenated by space before replacing them into logs/{rule}.{wildcards}.err. So despite you use double quotes, SGE treats the resulting string as two files and throws the error. What if you use single quotes instead? Like:
-o 'logs/{rule}.{wildcards}.out' \
-e 'logs/{rule}.{wildcards}.err'
Alternatively, you could concatenate the wildcards in the rule and use the result on the command line. E.g.:
rule one:
params:
wc= lambda wc: '_'.join(wc)
output: ...
Then use:
-o 'logs/{rule}.{params.wc}.out' \
-e 'logs/{rule}.{params.wc}.err'
(This second solution, if it works, kind of sucks though)