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valueerror samtools GRCh37 #151
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Thanks for trying out bcbio and sorry about the problem. How did you install bcbio? It looks like it's having a problem finding the reference data for GRCh37. Did you include this genome during your install? http://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#automated Happy to provide more specific advice if it is present in your installation and it's not finding it for some reason. Hope this helps. |
Hi again, Installation
would typing " --tooldir=/usr/local |
Thanks much for the details. You will need to install the biological data locally if you want to run analyses on your current. bcbio-vm is a bit more complex since it can also drive remote runs. In this case, you'd need to have Docker installed locally and also install biological data by following the rest of the installation instructions in the readme. Practically, the bcbio-vm Docker setup is still under development so if you want the easiest install and run path your best bet is to use standard bcbio with the automated installer (and include the genomes and aligners you want as above): http://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#automated Hope one of these paths gets things figured out for you. |
Hi again, the reason why I used the alternative pathway for installation was because of having errors all the time. as I tried the http://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#automated website for installation, here is the error I get; $ python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \
Cannot write to ‘requirements-conda.txt’ (Success). It recommends not to use sudo in the text. what should I do? Thanks. |
It looks like you don't have write permission to |
Hi,
I installed bcbio and its working. I built my code as bcbio_nextgen.py -w template gatk-variant /home/firat/Documents/myfile1.csv /home/firat/Downloads/resources/exampleBAM.bam
This worked. and I was told;
Configuration file created at: /home/firat/myfile1/config/myfile1.yaml
Edit to finalize and run with:
cd /home/firat/myfile1/work
bcbio_nextgen.py ../config/myfile1.yaml
And so i did;
firat@firat-X550CL:
$ cd /home/firat/myfile1/work/myfile1/work$ bcbio_nextgen.py ../config/myfile1.yamlfirat@firat-X550CL:
And here is what happened.
[2016-07-04T16:36Z] System YAML configuration: /usr/local/share/bcbio/galaxy/bcbio_system.yaml
[2016-07-04T16:36Z] Resource requests: bwa, sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16, 16
[2016-07-04T16:36Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job
[2016-07-04T16:36Z] Timing: organize samples
[2016-07-04T16:36Z] multiprocessing: organize_samples
[2016-07-04T16:36Z] Using input YAML configuration: /home/firat/myfile1/config/myfile1.yaml
[2016-07-04T16:36Z] Checking sample YAML configuration: /home/firat/myfile1/config/myfile1.yaml
[2016-07-04T16:36Z] Downloading GRCh37 samtools from AWS
Traceback (most recent call last):
File "/usr/local/bin/bcbio_nextgen.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.8', 'bcbio_nextgen.py')
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.8-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in
main(**kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.8-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
run_main(**kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 120, in variant2pipeline
[x[0]["description"] for x in samples]]])
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(_args, *_kwargs) for func, args, kwargs in self.items]
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, _args, *_kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 287, in organize_samples
return run_info.organize(*args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py", line 67, in organize
item = add_reference_resources(item, remote_retriever)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py", line 158, in add_reference_resources
data["reference"] = genome.get_refs(data["genome_build"], aligner, data["dirs"]["galaxy"], data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/genome.py", line 207, in get_refs
galaxy_config, data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/genome.py", line 159, in _get_ref_from_galaxy_loc
cur_ref = download_prepped_genome(genome_build, data, name, need_remap)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/genome.py", line 278, in download_prepped_genome
raise ValueError("Could not find reference genome file %s %s" % (genome_build, name))
ValueError: Could not find reference genome file GRCh37 samtools
Whats the reason of having such error?
Thanks already
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