Open BCArg opened 4 years ago
Try snakemake --use-conda -p all
It solved a lot missing module problem for me.
I also tried this i.e. without creating a virtual environment though it did not work.
I downloaded the same pipeline from another location, which looks slightly different, and it now works, see this question
Hello everyone, I run snakemake --use-conda -p all, and got a error as below:
Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 1 all 1 auto_read_support 1 filter_vcf 1 index_vcf 1 reformat_vcf 1 sort_vcf 6
[Sat Nov 9 02:50:09 2019] rule reformat_vcf: input: my_sample/sv_calls/my_sample_sniffles_region_filtered.vcf, init output: my_sample/sv_calls/my_sample_sniffles.vcf jobid: 8 wildcards: sample=my_sample
sniffles-edit --ins-length --check --vcf-version -v my_sample/sv_calls/my_sample_sniffles_region_filtered.vcf -o my_sample/sv_calls/my_sample_sniffles.vcf /bin/bash: sniffles-edit: command not found [Sat Nov 9 02:50:09 2019] Error in rule reformat_vcf: jobid: 8 output: my_sample/sv_calls/my_sample_sniffles.vcf shell: sniffles-edit --ins-length --check --vcf-version -v my_sample/sv_calls/my_sample_sniffles_region_filtered.vcf -o my_sample/sv_calls/my_sample_sniffles.vcf (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Could give some suggestions? Thanks a lot! tjiang
In order to run this pipeline I have followed the instructions as in this github page. I have
miniconda3
installed and I have installedsnakemake
withconda install -c bioconda -c conda-forge snakemake=5.7.0
as the commandconda install -y snakemake
installed a version < 5.4.3 on my machine.After downloading and unzipping the files, I have created a virtual environment with
Then, after activating this environment I tried to run the pipeline with
At first, I got the following error message (which is my
.log
file):I then, made the following replacement on the
Snakefile
:The
cat_fastq
command now worked (inputting the full path to the python script). But then I got the following error message (again, which is my log file), which was quite surprising to me as the commandpip install /home/bhinckel/pipeline-structural-variation-1.2.0/lib &> init
ran OK.Like above, I inserted the full path to the python script in the rule
reformat_vcf
, as shown belowThough, after this replacement, I got the same error as the
.log
file shown above.If I do:
I get:
So I assume the module
sv_calling_glue
is missing.Do you know how can I fix this? The python version installed on my virtual environment is
3.6.7
.