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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
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Task Node(3-unzip/0-phasing/000010F/blasr) failed with exit-code=256 #98

Closed yanboANU closed 6 years ago

yanboANU commented 7 years ago

When I run fc_unzip.py fc_unzip.cfg, some error happen:

ERROR]Task Node(3-unzip/0-phasing/000010F/blasr) failed with exit-code=256 [ERROR]Task Node(3-unzip/0-phasing/000004F/blasr) failed with exit-code=256 [ERROR]Task Node(3-unzip/0-phasing/000001F/blasr) failed with exit-code=256 [ERROR]Task Node(3-unzip/0-phasing/000007F/blasr) failed with exit-code=256 [ERROR]Task Node(3-unzip/0-phasing/000005F/blasr) failed with exit-code=256 [ERROR]Task Node(3-unzip/0-phasing/000008F/blasr) failed with exit-code=256 [ERROR]Task Node(3-unzip/0-phasing/000002F/blasr) failed with exit-code=256 [ERROR]Task Node(3-unzip/0-phasing/000011F/blasr) failed with exit-code=256 [INFO]recently_satisfied: set([]) [INFO]Num satisfied in this iteration: 0 [INFO]Num still unsatisfied: 13 [ERROR]Some tasks are recently_done but not satisfied: set([Node(3-unzip/0-phasing/000002F/blasr), Node(3-unzip/0-phasing/000008F/blasr), Node(3-unzip/0-phasing/000011F/blasr), Node(3-unzip/0-phasing/000007F/blasr), Node(3-unzip/0-phasing/000001F/blasr), Node(3-unzip/0-phasing/000010F/blasr), Node(3-unzip/0-phasing/000005F/blasr), Node(3-unzip/0-phasing/000004F/blasr)]) [ERROR]ready: set([Node(3-unzip/0-phasing/000012F/blasr), Node(3-unzip/0-phasing/000006F/blasr), Node(3-unzip/0-phasing/000003F/blasr), Node(3-unzip/0-phasing/000009F/blasr), Node(3-unzip/0-phasing/000000F/blasr)]) submitted: set([]) Traceback (most recent call last): File "/home/lin/liyanbo/Tools/falcon/fc_env_171026/bin/fc_unzip.py", line 11, in load_entry_point('falcon-unzip==0.4.0', 'console_scripts', 'fc_unzip.py')() File "/scratch/cdunn/fork/.git/LOCAL/lib/python2.7/site-packages/falcon_unzip/unzip.py", line 382, in main File "/scratch/cdunn/fork/.git/LOCAL/lib/python2.7/site-packages/falcon_unzip/unzip.py", line 253, in unzip_all File "/home/lin/liyanbo/Tools/falcon/fc_env_171026/local/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 226, in refreshTargets self._refreshTargets(updateFreq, exitOnFailure) File "/home/lin/liyanbo/Tools/falcon/fc_env_171026/local/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 292, in _refreshTargets raise Exception(msg) Exception: Some tasks are recently_done but not satisfied: set([Node(3-unzip/0-phasing/000002F/blasr), Node(3-unzip/0-phasing/000008F/blasr), Node(3-unzip/0-phasing/000011F/blasr), Node(3-unzip/0-phasing/000007F/blasr), Node(3-unzip/0-phasing/000001F/blasr), Node(3-unzip/0-phasing/000010F/blasr), Node(3-unzip/0-phasing/000005F/blasr), Node(3-unzip/0-phasing/000004F/blasr)])

And I have checked 3-unzip/reads/, these reads are exist.

And the file of 3-unzip/0-phasing/000010F/blasr/pwatcher.dir/stderr is here: stderr.txt

yanboANU commented 7 years ago

I used install_unzip.sh in http://pb-falcon.readthedocs.io/en/latest/quick_start.html to install falcon and falcon-unzip. Any reply is appreciate. Thanks a lot.

mroach-awri commented 7 years ago

What version of blasr are you running? blasr --version

yanboANU commented 7 years ago

blasr 5.3.9e940aa

mroach-awri commented 7 years ago

Maybe try running the failed script and see what the error is. bash /home/lin/liyanbo/Project/falcon_test2_ecoli/./3-unzip/0-phasing/000010F/blasr/aln_000010F.sh

BenjaminSchwessinger commented 7 years ago

Apologies for chipping in. In case Yanbo is actually at the Australian National University in Canberra I am happy to meet in person as I got FALCON to run on a local cluster.

If not at ANU I apologies.

On 11/7/17 11:38 AM, yanboANU wrote:

blasr 5.3.9e940aa

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yanboANU commented 7 years ago

In /home/lin/liyanbo/Project/falcon_test2_ecoli/./3-unzip/0-phasing/000010F/blasr/aln_000010F.sh, I change "time /path/to/smrtcmds/bin/blasr ...." to "time blasr ..." blasr can work.

But I don't want to change these shell one by one. Could do you please tell me what I can do?

Thanks a lot.

mroach-awri commented 7 years ago

Falcon Unzip is not very smart, you need to open up the fc_unzip.cfg file and update the smrt_bin= to match the path to blasr, which you can find like so: type -p blasr

yanboANU commented 7 years ago

Thank you very much. Unzip can work. But when I run fc_quiver.py fc_unzip.cfg, following error happen:

[ERROR]Task Node(4-quiver/reads) failed with exit-code=256 [INFO]recently_satisfied: set([]) [INFO]Num satisfied in this iteration: 0 [INFO]Num still unsatisfied: 2 [ERROR]Some tasks are recently_done but not satisfied: set([Node(4-quiver/reads)]) [ERROR]ready: set([]) submitted: set([]) Traceback (most recent call last): File "/home/lin/liyanbo/Tools/falcon/fc_env/bin/fc_quiver.py", line 11, in load_entry_point('falcon-unzip==0.4.0', 'console_scripts', 'fc_quiver.py')() File "/scratch/cdunn/fork/.git/LOCAL/lib/python2.7/site-packages/falcon_unzip/run_quiver.py", line 383, in main File "/home/lin/liyanbo/Tools/falcon/fc_env_171026/local/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 226, in refreshTargets self._refreshTargets(updateFreq, exitOnFailure) File "/home/lin/liyanbo/Tools/falcon/fc_env_171026/local/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 292, in _refreshTargets raise Exception(msg) Exception: Some tasks are recently_done but not satisfied: set([Node(4-quiver/reads)])

And quiver --version 2.2.0

mroach-awri commented 7 years ago

If you can't get the quiver step to work you can just put the assembly through a smrtanalysis resequencing run.

pb-cdunn commented 6 years ago

blasr now comes from $PATH, for convenience.