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Peregrine: Fast Genome Assembler Using SHIMMER Index
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error in 3-asm #20

Open zhenzhenyang-psu opened 4 years ago

zhenzhenyang-psu commented 4 years ago

Hi Jason, I had an error in the 3-asm assembly stage of Peregrine. The simple error message was below:

""" 2019-11-19 13:22:08,022 - root - CRITICAL - Error in /share/home/yangzz/anaconda3/envs/peregrine/lib/python3.7/site-packages/pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg/pypeflow/do_task.py with args="{'json_fn': '/share/home/yangzz/projects/1_assembly/1_peregrine_test_run/2_assembly/wd/3-asm/task.json',\n 'timeout': 30,\n 'tmpdir': None}" """

And pasting another important message which is found in the 'asm.log' file:

""" Traceback (most recent call last): File "/share/home/yangzz/anaconda3/envs/peregrine/bin/ovlp_to_graph.py", line 4, in import('pkg_resources').run_script('peregrine-pypy==0.1', 'ovlp_to_graph.py') File "/share/home/yangzz/anaconda3/envs/peregrine/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/share/home/yangzz/anaconda3/envs/peregrine/site-packages/pkg_resources/init.py", line 1469, in run_script exec(script_code, namespace, namespace) File "/share/home/yangzz/anaconda3/envs/peregrine/site-packages/peregrine_pypy-0.1-py3.6.egg/EGG-INFO/scripts/ovlp_to_graph.py", line 1584, in File "/share/home/yangzz/anaconda3/envs/peregrine/site-packages/peregrine_pypy-0.1-py3.6.egg/EGG-INFO/scripts/ovlp_to_graph.py", line 1580, in main File "/share/home/yangzz/anaconda3/envs/peregrine/site-packages/peregrine_pypy-0.1-py3.6.egg/EGG-INFO/scripts/ovlp_to_graph.py", line 1365, in ovlp_to_graph File "/share/home/yangzz/anaconda3/envs/peregrine/site-packages/peregrine_pypy-0.1-py3.6.egg/EGG-INFO/scripts/ovlp_to_graph.py", line 891, in generate_string_graph AttributeError: 'DiGraph' object has no attribute 'node' 1552.13user 74.37system 27:10.76elapsed 99%CPU (0avgtext+0avgdata 93077216maxresident)k 0inputs+0outputs (0major+54551879minor)pagefaults 0swaps """

My command is simple as follows: printf 'yes' | pg_run.py asm reads.list 28 28 28 28 28 28 28 28 28 --with-consensus --shimmer-r 4 --best_n_ovlp 8

And I was just testing with the CHM13 dataset accessible from the Peregrine bioRxv paper. Looking forward to your reply. Zhenzhen

cschin commented 4 years ago

See issue #19. The latest docker build (cschin/peregrine:0.1.5.5) and the code in the master branch should have addressed this. Or, you can down-grade you networkx to an earlier versions.

zhenzhenyang-psu commented 4 years ago

thank you!

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From: Jason Chin notifications@github.com Sent: Friday, December 13, 2019 2:17:32 PM To: cschin/Peregrine Peregrine@noreply.github.com Cc: zhenzhenyang-psu yangzhenzhen1988@gmail.com; Author author@noreply.github.com Subject: Re: [cschin/Peregrine] error in 3-asm (#20)

See issue #19https://github.com/cschin/Peregrine/issues/19. The latest docker build (cschin/peregrine:0.1.5.5) and the code in the master branch should have addressed this. Or, you can down-grade you networkx to an earlier versions.

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