Hi, first of all apologies if this has been posted previously; I'm using SMRT Link 7.0.0.63985 and whereas I could previously use the software to generate CCS data using RSII .XML metadata files as an input (after converting RS to Bam), it doesn't seem possible using sequel .xml files? What happens is that after successfully importing the sequel .xml data file I try to do a CCS analysis which results to the following failed message just after a second:
"FAILED: Task pbcoretools.tasks.filterdataset-0 FAILED in 0.80 sec."
The full error message I get is quite long:
"Pbsmrtpipe job /home/tasos0104/smrtlink_7.0.0.63985/smrtlink/userdata/jobs_root/000/000043 failed with exit code 1. Task pbcoretools.tasks.filterdataset-0 Failed task pbcoretools.tasks.filterdataset exit code 1 in 0.78 sec (See file '/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/userdata/jobs_root/000/000043/tasks/pbcoretools.tasks.filterdataset-0/stderr'.) Extracted from stderr File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/tasks/filters.py", line 172, in <module> sys.exit(registry_runner(registry, sys.argv[1:])) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcommand/cli/quick.py", line 360, in registry_runner return_code = args.func(args) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcommand/cli/quick.py", line 279, in _w exit_code = func(rtc) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/tasks/filters.py", line 126, in run_filterDataSet rtc.task.options["pbcoretools.task_options.downsample_factor"]) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/tasks/filters.py", line 101, in run_filter_dataset dataSet = openDataSet(in_file, skipCounts=True) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 63, in openDataSet return tbrType(*files, **kwargs) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 2705, in __init__ super(SubreadSet, self).__init__(*files, **kwargs) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 1994, in __init__ super(ReadSet, self).__init__(*files, **kwargs) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 386, in __init__ self._modResources(_fileExists) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 1252, in _modResources func(item) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 255, in _fileExists raise InvalidDataSetIOError("Resource {f} not found".format(f=fname)) pbcore.io.dataset.DataSetErrors.InvalidDataSetIOError: Resource /mnt/ruby/PacBio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrtinub/current/private/pacbio/barcodes/Sequel_RSII_16_barcodes_v2/Sequel_RSII_16_barcodes_v2.barcodeset.xml not found"
Any ideas what's going on?
Cheers,
paxas
"FAILED: Task pbcoretools.tasks.filterdataset-0 FAILED in 0.80 sec."
The full error message I get is quite long:
"Pbsmrtpipe job /home/tasos0104/smrtlink_7.0.0.63985/smrtlink/userdata/jobs_root/000/000043 failed with exit code 1. Task pbcoretools.tasks.filterdataset-0 Failed task pbcoretools.tasks.filterdataset exit code 1 in 0.78 sec (See file '/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/userdata/jobs_root/000/000043/tasks/pbcoretools.tasks.filterdataset-0/stderr'.) Extracted from stderr File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/tasks/filters.py", line 172, in <module> sys.exit(registry_runner(registry, sys.argv[1:])) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcommand/cli/quick.py", line 360, in registry_runner return_code = args.func(args) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcommand/cli/quick.py", line 279, in _w exit_code = func(rtc) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/tasks/filters.py", line 126, in run_filterDataSet rtc.task.options["pbcoretools.task_options.downsample_factor"]) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/pacbio/pythonpkgs/pbcoretools/lib/python2.7/site-packages/pbcoretools/tasks/filters.py", line 101, in run_filter_dataset dataSet = openDataSet(in_file, skipCounts=True) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 63, in openDataSet return tbrType(*files, **kwargs) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 2705, in __init__ super(SubreadSet, self).__init__(*files, **kwargs) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 1994, in __init__ super(ReadSet, self).__init__(*files, **kwargs) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 386, in __init__ self._modResources(_fileExists) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 1252, in _modResources func(item) File "/home/tasos0104/smrtlink_7.0.0.63985/smrtlink/install/smrtlink-release_7.0.0.63985/bundles/smrttools/install/smrttools-release_7.0.0.63823/private/thirdparty/python/python_2.7.9/site-packages/pbcore/io/dataset/DataSetIO.py", line 255, in _fileExists raise InvalidDataSetIOError("Resource {f} not found".format(f=fname)) pbcore.io.dataset.DataSetErrors.InvalidDataSetIOError: Resource /mnt/ruby/PacBio/smrtlink/install/smrtlink-release_6.0.0.47841/bundles/smrtinub/current/private/pacbio/barcodes/Sequel_RSII_16_barcodes_v2/Sequel_RSII_16_barcodes_v2.barcodeset.xml not found"
Any ideas what's going on?
Cheers,
paxas
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