lpantano
An error occurred when running the program
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
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
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?
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
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