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PacificBiosciences / FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
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Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads/daligner-runs/j_2259)]) #679

Closed nsgarcia27 closed 5 years ago

nsgarcia27 commented 5 years ago

Hello,

I encountered this exception message while attempting an assembly. Parts of the error file is displayed bellow:

qdel: illegally formed job identifier: P3a31d2fbd37279 [INFO]CALL: qdel P11225c4a3d6a9b qdel: illegally formed job identifier: P11225c4a3d6a9b [INFO]CALL: qdel P5900f63255110a qdel: illegally formed job identifier: P5900f63255110a [INFO]CALL: qdel P41e3405a12c575 qdel: illegally formed job identifier: P41e3405a12c575 [INFO]CALL: qdel Pde4167f6a319ad qdel: illegally formed job identifier: Pde4167f6a319ad [INFO]CALL: qdel Pe4603454865751 qdel: illegally formed job identifier: Pe4603454865751 [INFO]CALL: qdel P8fcdeb374695b3 qdel: illegally formed job identifier: P8fcdeb374695b3 [INFO]CALL: qdel P096f58848e4825 qdel: illegally formed job identifier: P096f58848e4825 [INFO]CALL: qdel P22751a4590b0a2 qdel: illegally formed job identifier: P22751a4590b0a2 [INFO]CALL: qdel Pbdbf73355f4261 qdel: illegally formed job identifier: Pbdbf73355f4261 [INFO]CALL: qdel P75c2be7896c55c qdel: illegally formed job identifier: P75c2be7896c55c [INFO]CALL: qdel Pb7a97677c463ee qdel: illegally formed job identifier: Pb7a97677c463ee [INFO]CALL: qdel Pe3398703d6325e qdel: illegally formed job identifier: Pe3398703d6325e [INFO]CALL: qdel P5b7312d1059b1d qdel: illegally formed job identifier: P5b7312d1059b1d [INFO]CALL: qdel P740e2fa415c605 qdel: illegally formed job identifier: P740e2fa415c605 [INFO]CALL: qdel P99e9d849a8d0b8 qdel: illegally formed job identifier: P99e9d849a8d0b8 [INFO]CALL: qdel Pc91176ade57e01 qdel: illegally formed job identifier: Pc91176ade57e01 [INFO]CALL: qdel Pcd321d3ad9f69c qdel: illegally formed job identifier: Pcd321d3ad9f69c [INFO]CALL: qdel Pfc3fca62277b98 qdel: illegally formed job identifier: Pfc3fca62277b98 [INFO]CALL: qdel P6ee7405d4110d6 qdel: illegally formed job identifier: P6ee7405d4110d6 [INFO]CALL: qdel Pf2dc6085c79b14 qdel: illegally formed job identifier: Pf2dc6085c79b14 [INFO]CALL: qdel Pa48b0f3d8f448a qdel: illegally formed job identifier: Pa48b0f3d8f448a [INFO]CALL: qdel Pc7710fb3fe8afe qdel: illegally formed job identifier: Pc7710fb3fe8afe [INFO]CALL: qdel P5044f0d9d185cf qdel: illegally formed job identifier: P5044f0d9d185cf [INFO]CALL: qdel P3ad1e8f25a2982 qdel: illegally formed job identifier: P3ad1e8f25a2982 [INFO]CALL: qdel P600489ec1ad203 qdel: illegally formed job identifier: P600489ec1ad203 [INFO]CALL: qdel P38901eaeb58263 qdel: illegally formed job identifier: P38901eaeb58263 [INFO]CALL: qdel Pb902b4e56fd99b qdel: illegally formed job identifier: Pb902b4e56fd99b [INFO]CALL: qdel P4f68d2ee3b2492 qdel: illegally formed job identifier: P4f68d2ee3b2492 [INFO]CALL: qdel P254bcccf6e3374 qdel: illegally formed job identifier: P254bcccf6e3374 [INFO]CALL: qdel Pfc6028d01029ea qdel: illegally formed job identifier: Pfc6028d01029ea [INFO]CALL: qdel P24319770d636f1 qdel: illegally formed job identifier: P24319770d636f1 [INFO]CALL: qdel P86140c88b5195e qdel: illegally formed job identifier: P86140c88b5195e [INFO]CALL: qdel P64ef3cfa445cdf qdel: illegally formed job identifier: P64ef3cfa445cdf [INFO]CALL: qdel P3e872d7d8655ee qdel: illegally formed job identifier: P3e872d7d8655ee [INFO]CALL: qdel P7d49fd392864a4 qdel: illegally formed job identifier: P7d49fd392864a4 [INFO]CALL: qdel Pe0350a22db4de7 qdel: illegally formed job identifier: Pe0350a22db4de7 [INFO]CALL: qdel Pe22c64ada20998 qdel: illegally formed job identifier: Pe22c64ada20998 [INFO]CALL: qdel P0b3ce2e0bb7aa8 qdel: illegally formed job identifier: P0b3ce2e0bb7aa8 [INFO]CALL: qdel P9f143cb415f7af qdel: illegally formed job identifier: P9f143cb415f7af [INFO]CALL: qdel Pd19fe0ea1d32d4 qdel: illegally formed job identifier: Pd19fe0ea1d32d4 [INFO]CALL: qdel Pdc953369fc9ab0 qdel: illegally formed job identifier: Pdc953369fc9ab0 [INFO]CALL: qdel P417234534de67a qdel: illegally formed job identifier: P417234534de67a [INFO]CALL: qdel P88b32adc0c5f40 qdel: illegally formed job identifier: P88b32adc0c5f40 [INFO]CALL: qdel P7b8e59dd09ae8b qdel: illegally formed job identifier: P7b8e59dd09ae8b [INFO]CALL: qdel Pc40bb84c60c563 qdel: illegally formed job identifier: Pc40bb84c60c563 [INFO]CALL: qdel P4bf4c51042aebb qdel: illegally formed job identifier: P4bf4c51042aebb [INFO]CALL: qdel P5ead79cab0b9db qdel: illegally formed job identifier: P5ead79cab0b9db [INFO]CALL: qdel P34387c501862a7 qdel: illegally formed job identifier: P34387c501862a7 [INFO]CALL: qdel Pf920719a0228a1 qdel: illegally formed job identifier: Pf920719a0228a1 [INFO]CALL: qdel P047711308f3540 qdel: illegally formed job identifier: P047711308f3540 [INFO]CALL: qdel Pffaecf10403805 qdel: illegally formed job identifier: Pffaecf10403805 [INFO]CALL: qdel Pdcef11cc17e632 qdel: illegally formed job identifier: Pdcef11cc17e632 [INFO]CALL: qdel Pc33bc246dd8877 qdel: illegally formed job identifier: Pc33bc246dd8877 [INFO]CALL: qdel Pfc4684d84306f3 qdel: illegally formed job identifier: Pfc4684d84306f3 [INFO]CALL: qdel P561bca0efd8b08 qdel: illegally formed job identifier: P561bca0efd8b08 [INFO]CALL: qdel P114e35ffee9ef3 qdel: illegally formed job identifier: P114e35ffee9ef3 [INFO]CALL: qdel Pa6dc7ad5babf05 qdel: illegally formed job identifier: Pa6dc7ad5babf05 [INFO]CALL: qdel P28a8d4477862a0 qdel: illegally formed job identifier: P28a8d4477862a0 [INFO]CALL: qdel Pa17743e0b14477 qdel: illegally formed job identifier: Pa17743e0b14477 [INFO]CALL: qdel P3f3170554c457d qdel: illegally formed job identifier: P3f3170554c457d [INFO]CALL: qdel P36d822c3043dcf qdel: illegally formed job identifier: P36d822c3043dcf [INFO]CALL: qdel Pa7783904ebdabb qdel: illegally formed job identifier: Pa7783904ebdabb [INFO]CALL: qdel P66c6400f1e1d60 qdel: illegally formed job identifier: P66c6400f1e1d60 [INFO]CALL: qdel P28bcea4f57a755 qdel: illegally formed job identifier: P28bcea4f57a755 [INFO]CALL: qdel P7a00cb34aee10c qdel: illegally formed job identifier: P7a00cb34aee10c [INFO]CALL: qdel Pa3382aa1a64510 qdel: illegally formed job identifier: Pa3382aa1a64510 [INFO]CALL: qdel P2b6d179e695c2e qdel: illegally formed job identifier: P2b6d179e695c2e [INFO]CALL: qdel Pc053975e47f010 qdel: illegally formed job identifier: Pc053975e47f010 [INFO]CALL: qdel P5cfca97d0f5b6a qdel: illegally formed job identifier: P5cfca97d0f5b6a [INFO]CALL: qdel Pc629b97b5ed22e qdel: illegally formed job identifier: Pc629b97b5ed22e [INFO]CALL: qdel Pb4b0de2850c530 qdel: illegally formed job identifier: Pb4b0de2850c530 [INFO]CALL: qdel P12a1551be5a3e1 qdel: illegally formed job identifier: P12a1551be5a3e1 [INFO]CALL: qdel Pd09984a7543a6e qdel: illegally formed job identifier: Pd09984a7543a6e [INFO]CALL: qdel P3e649ab9c85dc1 qdel: illegally formed job identifier: P3e649ab9c85dc1 [INFO]CALL: qdel P20136d59231f1d qdel: illegally formed job identifier: P20136d59231f1d [INFO]CALL: qdel P500562582f83e4 qdel: illegally formed job identifier: P500562582f83e4 [INFO]CALL: qdel Pec7352ff9470f9 qdel: illegally formed job identifier: Pec7352ff9470f9 [INFO]CALL: qdel P2ede23f06fd9c6 qdel: illegally formed job identifier: P2ede23f06fd9c6 [INFO]CALL: qdel P1aec2f2f9ca525 qdel: illegally formed job identifier: P1aec2f2f9ca525 [INFO]CALL: qdel P36a9dab0f9aecd qdel: illegally formed job identifier: P36a9dab0f9aecd [INFO]CALL: qdel P96ff74ced96a2a qdel: illegally formed job identifier: P96ff74ced96a2a [INFO]CALL: qdel P94ec8865c127c4 qdel: illegally formed job identifier: P94ec8865c127c4 [INFO]CALL: qdel P6e56a168a7151b qdel: illegally formed job identifier: P6e56a168a7151b [INFO]CALL: qdel P07d0b68ad17499 qdel: illegally formed job identifier: P07d0b68ad17499 Traceback (most recent call last): File "/home/chenc1/garci191/.conda/envs/denovo_asm_2.7/bin/fc_run", line 11, in load_entry_point('falcon-kit==1.2.4', 'console_scripts', 'fc_run')() File "/home/chenc1/garci191/.conda/envs/denovo_asm_2.7/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 726, in main main1(argv[0], args.config, args.logger) File "/home/chenc1/garci191/.conda/envs/denovo_asm_2.7/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 76, in main1 input_fofn_fn=input_fofn_fn, File "/home/chenc1/garci191/.conda/envs/denovo_asm_2.7/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 301, in run daligner_split_script=pype_tasks.TASK_DB_DALIGNER_SPLIT_SCRIPT, File "/home/chenc1/garci191/.conda/envs/denovo_asm_2.7/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 539, in add_daligner_and_merge_tasks dist=Dist(NPROC=4, MB=4000, job_dict=daligner_job_config), File "/home/chenc1/garci191/.conda/envs/denovo_asm_2.7/lib/python2.7/site-packages/falcon_kit/pype.py", line 194, in gen_parallel_tasks wf.refreshTargets() File "/home/chenc1/garci191/.conda/envs/denovo_asm_2.7/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets self._refreshTargets(updateFreq, exitOnFailure) File "/home/chenc1/garci191/.conda/envs/denovo_asm_2.7/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 362, in _refreshTargets raise Exception(msg) Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads/daligner-runs/j_2259)])

As you can see, there were many "illegally formed job identifier" prior to the exception notification. I went to the directory 0-rawreads/daligner-runs/j_2259 and found no error message. But I did find run.sh.done file which is empty.

Any advice on how to proceed? Thank you.

Nelson