lpantano / lpantano/seqcluster

An error occurred when running the program

Open
#56 4 comments 0 reactions 0 assignees View on GitHub
Dominant language
HTML
Stars
39
Forks
19
PR merge metrics
No merged PRs in 30d

Description

Hello, I want to use this tool for miRNA analysis. It has been installed, but the following error was reported when running the demo data. What should I do to solve this problem?

`[2023-11-08T02:44Z] System YAML configuration: /home/wayenbio/bcbio/galaxy/bcbio_system.yaml.
[2023-11-08T02:44Z] Locale set to C.UTF-8.
[2023-11-08T02:44Z] Resource requests: atropos, picard; memory: 4.00, 4.00; cores: 16, 16
[2023-11-08T02:44Z] Configuring 1 jobs to run, using 1 cores each with 4.00g of memory reserved for each job
[2023-11-08T02:44Z] Timing: organize samples
[2023-11-08T02:44Z] multiprocessing: organize_samples
[2023-11-08T02:44Z] Using input YAML configuration: /home/wayenbio/rnaseq-seqc/mirqc_bcbio/config/mirqc_bcbio.yaml
[2023-11-08T02:44Z] Checking sample YAML configuration: /home/wayenbio/rnaseq-seqc/mirqc_bcbio/config/mirqc_bcbio.yaml
Traceback (most recent call last):
File "/home/wayenbio/bcbio/anaconda/bin/bcbio_nextgen.py", line 245, in
main(**kwargs)
File "/home/wayenbio/bcbio/anaconda/bin/bcbio_nextgen.py", line 46, in main
run_main(**kwargs)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/main.py", line 50, in run_main
fc_dir, run_info_yaml)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/main.py", line 332, in smallrnaseqpipeline
samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/main.py", line 467, in rnaseq_prep_samples
[x[0]["description"] for x in samples]]])
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 1048, in __call__
if self.dispatch_one_batch(iterator):
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 866, in dispatch_one_batch
self._dispatch(tasks)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 784, in _dispatch
job = self._backend.apply_async(batch, callback=cb)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/joblib/_parallel_backends.py", line 208, in apply_async
result = ImmediateResult(func)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/joblib/_parallel_backends.py", line 572, in __init__
self.results = batch()
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 263, in __call__
for func, args, kwargs in self.items]
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/joblib/parallel.py", line 263, in
for func, args, kwargs in self.items]
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/utils.py", line 59, in wrapper
return f(*args, **kwargs)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/distributed/multitasks.py", line 459, in organize_samples
return run_info.organize(*args)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/run_info.py", line 81, in organize
item = add_reference_resources(item, remote_retriever)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/run_info.py", line 177, in add_reference_resources
data["dirs"]["galaxy"], data)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/genome.py", line 233, in get_refs
galaxy_config, data)
File "/home/wayenbio/bcbio/anaconda/lib/python3.7/site-packages/bcbio/pipeline/genome.py", line 180, in _get_ref_from_galaxy_loc
(genome_build, os.path.normpath(loc_file)))
ValueError: Did not find genome build hg19 in bcbio installation: /home/wayenbio/bcbio/galaxy/tool-data/sam_fa_indices.loc
`

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with bcbio_nextgen.py and the pipeline/genome.py traceback entries, then inspect the referenced tool-data/sam_fa_indices.loc file and the hg19 lookup. Reproduce the demo-data run and trace the reference setup failure; done means the run proceeds beyond genome reference initialization.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.