I am getting the following error:
one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!
My snakefile looks like the following:
#!/miniconda/bin/python
workdir: config["path_to_files"]
wildcard_constraints:
separator = config["separator"],
extension = config["file_extension"],
sample = '|' .join(config["samples"])
rule all:
input:
expand("antismash-output/{sample}/{sample}.txt", sample = config["samples"])
# merging the paired end reads (either fasta or fastq) as prodigal only takes single end reads
rule pear:
input:
forward = f"{{sample}}{config['separator']}1.{{extension}}",
reverse = f"{{sample}}{config['separator']}2.{{extension}}"
output:
"merged_reads/{sample}.{extension}"
#conda:
#"/home/lamma/env-export/antismash.yaml"
shell:
"""
set+u;source ~/miniconda3/etc/profile.d/conda.sh; set -u ;
set+u;conda activate antismash; set -u ;
pear -f {input.forward} -r {input.reverse} -o {output} -t 21
"""
# If single end then move them to merged_reads directory
rule move:
input:
"{sample}.{extension}"
output:
"merged_reads/{sample}.{extension}"
shell:
"cp {path}/{sample}.{extension} {path}/merged_reads/"
# Setting the rule order on the 3 above rules which should be treated equally and only one run.
ruleorder: pear > move
# annotating the metagenome with prodigal#. Can be done inside antiSMASH but prefer to do it out
rule prodigal:
input:
f"merged_reads/{{sample}}.{config['file_extension']}"
output:
gbk_files = "annotated_reads/{sample}.gbk",
protein_files = "protein_reads/{sample}.faa"
#conda:
#"/home/lamma/env-export/antismash.yaml"
shell:
"""
set+u;source ~/miniconda3/etc/profile.d/conda.sh; set -u ;
set+u;conda activate antismash; set -u ;
prodigal -i {input} -o {output.gbk_files} -a {output.protein_files} -p meta
"""
# running antiSMASH on the annotated metagenome
rule antiSMASH:
input:
"annotated_reads/{sample}.gbk"
output:
touch("antismash-output/{sample}/{sample}.txt")
#conda:
#"/home/lamma/env-export/antismash.yaml"
shell:
"""
set+u;source ~/miniconda3/etc/profile.d/conda.sh; set -u ;
set+u;conda activate antismash; set -u ;
antismash --knownclusterblast --subclusterblast --full-hmmer --smcog --outputfolder antismash-output/{wildcards.sample}/ {input}
"""
Any help as to why I am getting this error would be appriciated. I think it is something to do with how I am activating the conda environments, using the conda: path/to/yaml has not worked for me as I get version errors, where it seems snakemake can't satisfy the version requierments set out by the yaml file.
Edit:
The full error message is as follows:
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 16
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 pear
1
[Thu Dec 5 16:05:37 2019]
rule pear:
input: Unmap_41_1.fastq, Unmap_41_2.fastq
output: merged_reads/Unmap_41.fastq
jobid: 0
wildcards: sample=Unmap_41, extension=fastq
/usr/bin/bash: set+u: command not found
[Thu Dec 5 16:05:37 2019]
Error in rule pear:
jobid: 0
output: merged_reads/Unmap_41.fastq
shell:
set+u;source ~/miniconda3/etc/profile.d/conda.sh; set -u ;
set+u;conda activate antismash; set -u ;
pear -f Unmap_41_1.fastq -r Unmap_41_2.fastq -o merged_reads/Unmap_41.fastq -t 21
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
It also seems set+u; is an unknow command but to my understanding it is a snakemake command.
