An error occurred when running the program

charles-xue commented 1 year ago

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 <module> 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 <listcomp> 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

lpantano commented 1 year ago

Hi, can you let me know what was the command you were running? how did you install seqcluster? and the version you are using? Thanks

charles-xue commented 1 year ago

I installed bcbio and downloaded the miRNA data from it following the guide at https://seqcluster.readthedocs.io/ page. template.yaml `upload: dir: upload details:

analysis: smallRNA-seq algorithm: aligner: star adapters: ["TGGAATTCTCGGGTGC"] species: hsa description: miRQCa genome_build: hg19` and then run it But the error message described above appeared. I saw that the error message said that the genome-related files were not found. I guessed that this should be a problem that occurred during the installation, but I don’t know how to solve it. Can you Give some tips?

lpantano commented 1 year ago

If you are using bcbio maybe something else is missing. Here there is more information if you want to run bcbio: https://bcbio-nextgen.readthedocs.io/en/latest/contents/small_rnaseq.html. And here to install data: https://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#install-data. If you want to run only seqcluster then I can help you with that in a different way. You can use nf-core smrnaseq as well, it is a little different but it will get you seqcluster running.https://nf-co.re/smrnaseq/2.2.3

charles-xue commented 1 year ago

Yes, I found the relevant content about smallRNA analysis in the nf-core page through the information on your seqcluster page. I am trying to install this kit to perform the pipeline of miRNA analysis. I hope everything goes well. Also thanks for your answer

lpantano / seqcluster

An error occurred when running the program #56