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dvitsios / mirnovo

Genome free discovery and classification of miRNAs from small RNA-Seq with random forests
MIT License
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Exception in thread #2

Open lurens opened 6 years ago

lurens commented 6 years ago

Hi I am trying to run mirnovo on the test dataset, but i get the following error:

Exception in thread Thread-34: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "get_genomic_features.py", line 31, in run getFeaturesForCluster(self.threadID, self.q) File "get_genomic_features.py", line 48, in getFeaturesForCluster ret_list = get_genomic_features(cluster_number) File "get_genomic_features.py", line 216, in get_genomic_features out = subprocess.check_output(cmd, shell = True) File "/usr/lib/python2.7/subprocess.py", line 574, in check_output raise CalledProcessError(retcode, cmd, output=output) CalledProcessError: Command 'echo ACCTGGCGCtaaaccattcgtagacgacctgctTCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGCTCCCTCGCTGCGATCTATTGAAAG | util/RNAfold --noPS 2>/dev/null' returned non-zero exit status 127

I am running Ubuntu 16.04.3 LTS 64-bit Have you an idea on how to solve it? Thank you in advance lorenzo

dvitsios commented 6 years ago

Hi, have you tried analysing your sample through the web-app? Does it finish successfully or do you get similar exception errors? D

lurens commented 6 years ago

Yes, it works. Unfortunately I am working on a genome which is still not available on the web-app and the only solution is at the moment to run it on my PC

dvitsios commented 6 years ago

I assume you have followed the instructions below for installing your custom genome, right? http://wwwdev.ebi.ac.uk/enright-dev/mirnovo-standalone-pkg/Genome-Annotation-1.0/README

Alternatively, if the genome you are interested in is publicly available I could add it to mirnovo's web-app.

godkin1211 commented 6 years ago

Hi, when I run the basic example ./mirnovo.pl -i ../example_file.tallied.gz -g hsa -t hsa -o example_run after downloading hsa genome and training model, I also got the same error.

The python version I use is 2.7.12.

How do I solve this problem? Thank you very much!