cbg-ethz/ngs-pipe

NGS-pipe: next-generation sequencing pipelines for precision oncology

ngs-pipe's Issues

No example for WGS data

Thanks for developing this nice pipeline. I'm trying to use it for WGS data.
In the wiki page (https://github.com/cbg-ethz/NGS-pipe/wiki/Installation-&-Testing), I saw the the command lines for WGS data. But I didn't find the corresponding files in the example folder: examples/dna.
Could you please add it? Thanks again.

memory

Hello and thank you very much for sharing your work!
I was wondering how much memory is needed for running the pipeline for DNA analysis, in order to know in advance if I have the availability in my device.
In addition, how much time would the process take, approximately?
Thank you in advance.
Lucia

No example for DNA available

The example pipeline for DNA data seems to be empty.

module 'logging' has no attribute 'StreamHandler'

When running the program on desktop or linux using the command:
python3 /path/to/snakemake/bin/snakemake -s prepare_data.snake

The following error appears:

Traceback (most recent call last):
File "/home/masih/miniconda3/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/home/masih/miniconda3/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "~/snakemake_install/snakemake/snakemake/main.py", line 2, in
from snakemake import main
File "/home/masih/miniconda3/lib/python3.6/site-packages/snakemake/init.py", line 11, in
import logging as _logging
File "/lustre4/home/masih/projects/pipeline_design_tutorial/snakemake_install/snakemake/snakemake/logging.py", line 20, in
class ColorizingStreamHandler(_logging.StreamHandler):
AttributeError: module 'logging' has no attribute 'StreamHandler'

In Example -> Provided cores: 1

Hey,

Thank you for developing that pipeline and providing it to the community.
I wanted to test your pipeline for my projects.

When running the example data (RNA & WES) , the pipeline seems to be limited to one core:

$ ./run_analysis_locally.sh
Provided cores: 1
Rules claiming more threads will be scaled down.

I try to modify the the config.json file, but it seems that the configuration here would allow more cores.
Where should I adjust the config?

The machine I am working on has 12 cores 64 GB of memory. - so this should not be the bottleneck.

Thanks!
Sincerely
Julius

Error in "Qualimap" when running the file "**run_analysis_locally.sh**"

I am getting the following error when i try to run the "run_analysis_locally.sh".
I am attaching the screen shot of the error.

Warning : "Unable to set utime on symlink {}. Your Python build does not support it"

When I run the file "run_prepare_data_locally.sh", it gives a warning "Unable to set utime on symlink {}. Your Python build does not support it" for the rule "Fastqs".

config json file

hello,

where to download and config these fields ?

"general":{
"sequencingAdapter": "/path/to/adapters.fa",
"jsvmBetaBinParams": "/path/to/jsvm_beta_bin_params.cfg",
"jsvmBetaBinPriors": "/path/to/jsvm_beta_bin_priors.cfg",
"jsvm_0.7.5_jointPriors": "/path/to/joint_priors.cfg",
"jsvm_0.7.5_jointParams": "/path/to/joint_params.cfg",
"adaclassifier_snp": "/path/to/IS3A.MVJSD.sSNV.tsv.Classifier.RData",
"adaclassifier_indel": "/path/to/IS3A.MVJSD.sINDEL.tsv.Classifier.RData"
}

thanks !

RuleException in wes example

I've just downloaded this pipeline and am trying it out in a conda environment. I downloaded the resources and when trying to run the wes example locally (./run_analysis_locally.sh) I am getting the error below. However, if I copy and paste the command to my console it works just fine. It looks like maybe the command is not working when called as a subprocess using threads.py. Is there a python version compatibility issue?

RuleException:
CalledProcessError in line 59 of /my/path/tools/NGS-pipe/snake/common/clip_trim/clip_trim_snake.py:
Command 'trimmomatic -Xmx12G  PE -phred33 -threads 4 -trimlog out/cliptrim/PCL-016/PAIREDEND/SRR1713449_clipTrim.log sra/PCL-016/PAIREDEND/SRR1713449_R1.fastq.gz sra/PCL-016/PAIREDEND/SRR1713449_R2.fastq.gz out/cliptrim/PCL-016/PAIREDEND/SRR1713449_R1.fastq.gz out/cliptrim/PCL-016/PAIREDEND/ORPHAN/SRR1713449_R1.fastq.gz out/cliptrim/PCL-016/PAIREDEND/SRR1713449_R2.fastq.gz out/cliptrim/PCL-016/PAIREDEND/ORPHAN/SRR1713449_R2.fastq.gz ILLUMINACLIP:../resources/TruSeq2-PE.fa:1:30:7:1:true SLIDINGWINDOW:4:2 LEADING:2 TRAILING:2 MINLEN:50 2> out/cliptrim/PCL-016/PAIREDEND/SRR1713449.fastq.gz.stdout.log && gzip out/cliptrim/PCL-016/PAIREDEND/SRR1713449_clipTrim.log' returned non-zero exit status 1.

File "/my/path/tools/NGS-pipe/snake/common/clip_trim/clip_trim_snake.py", line 59, in __rule_trimmomatic_paired`

File "/my/path/miniconda3/envs/ngs-pipe-dna/lib/python3.6/concurrent/futures/thread.py", line 56, in run