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the-virtual-brain / tvb-recon

Tools for creating full TVB models from individual anatomical scans
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run_sequentially.py error #70

Open drsiyarb opened 3 years ago

drsiyarb commented 3 years ago

Hi, I am trying to run run_sequentially inside the docker container but getting this error.

How should I proceed?

submitter@ome/tvb-recon/:/opt/tvb-recon:/opt/tvb-recon/pegasus$ python run_sequentially.py "1" Starting to process the following subjects: %s [1] Starting to process the subject: TVB1 Configured atlas default for patient inside folder /home/submitter/data/TVB1/configs Checking currently running job ids... Currently running job ids are: [] Starting pegasus run for subject: TVB1with atlas: default main_pegasus.sh: 7: main_pegasus.sh: Bad substitution /opt/tvb-recon 2021-06-12 18:33:29,386 - tvb.recon.dax.configuration - INFO - Parsing patient configuration file /home/submitter/data/TVB1/configs/patient_flow.properties Traceback (most recent call last): File "/opt/conda/lib/python2.7/runpy.py", line 174, in _run_module_as_main "main", fname, loader, pkg_name) File "/opt/conda/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/opt/tvb-recon/tvb/recon/dax/main.py", line 55, in tracts_generation = TractsGeneration(config.props[ConfigKey.DWI_MULTI_SHELL], config.props[ConfigKey.MRTRIX_THRDS], KeyError: <ConfigKey.DWI_MULTI_SHELL: 'dwi.multi.shell'> Traceback (most recent call last): File "/usr/bin/pegasus-graphviz", line 507, in main() File "/usr/bin/pegasus-graphviz", line 497, in main dag = parse_daxfile(dagfile, options.files) File "/usr/bin/pegasus-graphviz", line 225, in parse_daxfile f = open(fname,"r") IOError: [Errno 2] No such file or directory: '/home/submitter/data/TVB1/configs/dax/main_bnm.dax' Error: dot: can't open /home/submitter/data/TVB1/configs/dax/main_bnm.dot 2021.06.12 18:33:29.784 UTC: [ERROR] Problem while determining the version of dax class java.lang.RuntimeException: java.io.FileNotFoundException: The file (/home/submitter/data/TVB1/configs/dax/main_bnm.dax ) specified does not exist 2021.06.12 18:33:29.787 UTC: [FATAL ERROR]
[1]: Instantiating DAXParser at edu.isi.pegasus.planner.parser.DAXParserFactory.loadDAXParser(DAXParserFactory.java:235) [2]: Invalid static initializer method name for DAXParser3 at edu.isi.pegasus.common.util.DynamicLoader.instantiate(DynamicLoader.java:131) ERROR while logging metrics The metrics file location is not yet initialized Checking currently running job ids... Currently running job ids are: [] Traceback (most recent call last): File "run_sequentially.py", line 185, in current_job_id = new_job_ids[0] IndexError: list index out of range