ambarishnag

fc_unzip error message

Dec 3rd, 2018
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  1. [INFO 2018-12-02 11:32:46] Extracting the associate haplotigs for p_ctg_id = 000412F
  2. [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))
  3. Traceback (most recent call last):
  4. 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
  5. return generate_haplotigs_for_ctg(ctg_id, allow_multiple_primaries, out_dir, unzip_dir, proto_dir, logger)
  6. 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
  7. extract_and_write_all_ctg(ctg_id, haplotig_graph, all_haplotig_dict, phase_alias_map, out_dir, allow_multiple_primaries, fp_proto_log)
  8. 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
  9. raise Exception(msg)
  10. Exception: Skipping additional subgraphs of the primary contig: 000412F. The graph has multiple primary components.
  11. Traceback (most recent call last):
  12. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/runpy.py", line 174, in _run_module_as_main
  13. "__main__", fname, loader, pkg_name)
  14. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/runpy.py", line 72, in _run_code
  15. exec code in run_globals
  16. 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>
  17. main()
  18. 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
  19. args.func(args)
  20. 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
  21. result = run_generate_haplotigs_for_ctg(exe)
  22. 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
  23. return generate_haplotigs_for_ctg(ctg_id, allow_multiple_primaries, out_dir, unzip_dir, proto_dir, logger)
  24. 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
  25. extract_and_write_all_ctg(ctg_id, haplotig_graph, all_haplotig_dict, phase_alias_map, out_dir, allow_multiple_primaries, fp_proto_log)
  26. 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
  27. raise Exception(msg)
  28. Exception: Skipping additional subgraphs of the primary contig: 000412F. The graph has multiple primary components.
  29. 2018-12-02 11:32:46,914 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.
  30. 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'
  31. 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'
  32. 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}"
  33. Traceback (most recent call last):
  34. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/runpy.py", line 174, in _run_module_as_main
  35. "__main__", fname, loader, pkg_name)
  36. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/runpy.py", line 72, in _run_code
  37. exec code in run_globals
  38. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 267, in <module>
  39. main()
  40. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 259, in main
  41. run(**vars(parsed_args))
  42. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 253, in run
  43. run_cfg_in_tmpdir(cfg, tmpdir, '.')
  44. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 228, in run_cfg_in_tmpdir
  45. run_bash(bash_template, myinputs, myoutputs, parameters)
  46. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 187, in run_bash
  47. util.system(cmd)
  48. File "/rufous/anag/.conda-envs/denovo_asm/lib/python2.7/site-packages/pypeflow/io.py", line 29, in syscall
  49. raise Exception(msg)
  50. Exception: Call '/bin/bash user_script.sh' returned 256.
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