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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
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AttributeError: 'IntervalTree' object has no attribute 'search' #141

Closed hangch123 closed 5 years ago

hangch123 commented 5 years ago

falcon-unzip 1.1.4 falcon-kit 1.2.4 pypeflow 2.1.1 Traceback (most recent call last): File "/home/zy/tools/miniconda2/lib/python2.7/runpy.py", line 162, in _run_module_as_main "main", fname, loader, pkg_name) File "/home/zy/tools/miniconda2/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/falcon_unzip/proto/main_augment_pb.py", line 627, in main() File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/falcon_unzip/proto/main_augment_pb.py", line 624, in main run(vars(args)) File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/falcon_unzip/proto/main_augment_pb.py", line 512, in run updated_rid2phase, phase_relation_graph, htig_to_phase = create_new_rid2phase(ctg_id, rid2phase, all_regions, m4, a_paths) File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/falcon_unzip/proto/main_augment_pb.py", line 91, in create_new_rid2phase found_regions = tree.search(reference_start, reference_end) AttributeError: 'IntervalTree' object has no attribute 'search' WARNING:root:Call '/bin/bash user_script.sh' returned 256. WARNING:root:CD: 'uow-00' -> '/home/zy/test3/3-unzip/0-phasing/000627F' Traceback (most recent call last): File "/home/zy/tools/miniconda2/lib/python2.7/runpy.py", line 162, in _run_module_as_main "main", fname, loader, pkg_name) File "/home/zy/tools/miniconda2/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 116, in main() File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 112, in main run(vars(args)) File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 65, in run pypeflow.do_task.run_bash(script, inputs, outputs, params) File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/do_task.py", line 187, in run_bash util.system(cmd) File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/io.py", line 29, in syscall raise Exception(msg) Exception: Call '/bin/bash user_script.sh' returned 256. 2018-12-28 13:04:52,395 - root - WARNING - Call '/bin/bash user_script.sh' returned 256. 2018-12-28 13:04:52,396 - root - WARNING - CD: '/home/zy/test3/3-unzip/0-phasing/000627F' -> '/home/zy/test3/3-unzip/0-phasing/000627F' 2018-12-28 13:04:52,396 - root - WARNING - CD: '/home/zy/test3/3-unzip/0-phasing/000627F' -> '/home/zy/test3/3-unzip/0-phasing/000627F' 2018-12-28 13:04:52,396 - root - CRITICAL - Error in /home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/do_task.py with args="{'json_fn': '/home/zy/test3/3-unzip/0-phasing/000627F/task.json',\n 'timeout': 30,\n 'tmpdir': None}" Traceback (most recent call last): File "/home/zy/tools/miniconda2/lib/python2.7/runpy.py", line 162, in _run_module_as_main "main", fname, loader, pkg_name) File "/home/zy/tools/miniconda2/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/do_task.py", line 267, in main() File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/do_task.py", line 259, in main run(**vars(parsed_args)) File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/do_task.py", line 253, in run run_cfg_in_tmpdir(cfg, tmpdir, '.') File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/do_task.py", line 228, in run_cfg_in_tmpdir run_bash(bash_template, myinputs, myoutputs, parameters) File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/do_task.py", line 187, in run_bash util.system(cmd) File "/home/zy/tools/miniconda2/lib/python2.7/site-packages/pypeflow/io.py", line 29, in syscall raise Exception(msg) Exception: Call '/bin/bash user_script.sh' returned 256. pwd +++ pwd ++ echo 'FAILURE. Running top in /home/zy/test3/3-unzip/0-phasing/000627F (If you see -terminal database is inaccessible- you are using the python bin-wrapper, so you will not get diagnostic info. No big deal. This process is crashing anyway.)' ++ rm -f top.txt ++ which python ++ which top ++ env -u LD_LIBRARY_PATH top -b -n 1 ++ env -u LD_LIBRARY_PATH top -b -n 1 ++ pstree -apl

real 4m30.479s user 4m7.588s sys 0m13.520s

What should I do?

Best regards Thanks

hangch123 commented 5 years ago

Used updated Falcon will happen this issue, please help me to solve

alejandrotorresn commented 5 years ago

Hi,

This is not a issue. The meta-package pb-assembly does not install all requirements. Basically, You need install pwntools (pip install pwntools).

fbemm commented 5 years ago

It does install intervaltree but the wrong version. You need to do the following after activating the conda environment:

conda install intervaltree=2.1.0

baozg commented 5 years ago

Thanks for @fbemm , it did work.