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- [INFO 2018-12-02 11:32:46] Extracting the associate haplotigs for p_ctg_id = 000412F
- [ERROR 2018-12-02 11:32:46] Failure in generate_haplotigs_for_ctg((u'000412F', u'../../0-phasing/000412F/uow-00/proto', './uow-000412F', u'../../..', False))
- Traceback (most recent call last):
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 74, in run_generate_haplotigs_for_ctg
- return generate_haplotigs_for_ctg(ctg_id, allow_multiple_primaries, out_dir, unzip_dir, proto_dir, logger)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 256, in generate_haplotigs_for_ctg
- extract_and_write_all_ctg(ctg_id, haplotig_graph, all_haplotig_dict, phase_alias_map, out_dir, allow_multiple_primaries, fp_proto_log)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 959, in extract_and_write_all_ctg
- raise Exception(msg)
- Exception: Skipping additional subgraphs of the primary contig: 000412F. The graph has multiple primary components.
- Traceback (most recent call last):
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/runpy.py", line 174, in _run_module_as_main
- "__main__", fname, loader, pkg_name)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/runpy.py", line 72, in _run_code
- exec code in run_globals
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 1495, in <module>
- main()
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 1491, in main
- args.func(args)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 1253, in cmd_apply
- result = run_generate_haplotigs_for_ctg(exe)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 74, in run_generate_haplotigs_for_ctg
- return generate_haplotigs_for_ctg(ctg_id, allow_multiple_primaries, out_dir, unzip_dir, proto_dir, logger)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 256, in generate_haplotigs_for_ctg
- extract_and_write_all_ctg(ctg_id, haplotig_graph, all_haplotig_dict, phase_alias_map, out_dir, allow_multiple_primaries, fp_proto_log)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 959, in extract_and_write_all_ctg
- raise Exception(msg)
- Exception: Skipping additional subgraphs of the primary contig: 000412F. The graph has multiple primary components.
- 2018-12-02 11:32:46,914 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.
- 2018-12-02 11:32:46,915 - root - WARNING - CD: '/rufous/anag/pacbio/FALCON-examples/run/eric_data/3-unzip/2-htigs/chunk_000412F' -> '/rufous/anag/pacbio/FALCON-examples/run/eric_data/3-unzip/2-htigs/chunk_000412F'
- 2018-12-02 11:32:46,915 - root - WARNING - CD: '/rufous/anag/pacbio/FALCON-examples/run/eric_data/3-unzip/2-htigs/chunk_000412F' -> '/rufous/anag/pacbio/FALCON-examples/run/eric_data/3-unzip/2-htigs/chunk_000412F'
- 2018-12-02 11:32:46,916 - root - CRITICAL - Error in /rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py with args="{'json_fn': '/rufous/anag/pacbio/FALCON-examples/run/eric_data/3-unzip/2-htigs/chunk_000412F/task.json',\n 'timeout': 30,\n 'tmpdir': None}"
- Traceback (most recent call last):
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/runpy.py", line 174, in _run_module_as_main
- "__main__", fname, loader, pkg_name)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/runpy.py", line 72, in _run_code
- exec code in run_globals
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 267, in <module>
- main()
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 259, in main
- run(**vars(parsed_args))
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 253, in run
- run_cfg_in_tmpdir(cfg, tmpdir, '.')
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 228, in run_cfg_in_tmpdir
- run_bash(bash_template, myinputs, myoutputs, parameters)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 187, in run_bash
- util.system(cmd)
- File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/io.py", line 29, in syscall
- raise Exception(msg)
- Exception: Call '/bin/bash user_script.sh' returned 256.
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