pb-assembly fails at 2-asm-falcon stage with unclear error

[charlesfeigin]

Running pb-assembly locally using settings in cfg file in the attachment. Run went smoothly until 2-asm-falcon stage, but failed with an error that I don't really understand. End of the stderr file (also attached) says:

time python -m falcon_kit.mains.collect_pread_gfa --add-string-graph >| sg.gfa.json

python -m falcon_kit.mains.collect_pread_gfa --add-string-graph
falcon-kit 1.3.0
pypeflow 2.2.0
Traceback (most recent call last):
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/collect_pread_gfa.py", line 243, in
main()
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/collect_pread_gfa.py", line 240, in main
run(sys.stdout, **vars(args))
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/collect_pread_gfa.py", line 196, in run
add_string_graph_to_gfa(gfa_graph, sg_edges_list, utg_data, ctg_paths, preads_dict, preads_overlap_dict, sg_edges_dict)
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/collect_pread_gfa.py", line 129, in add_string_graph_to_gfa
asm_graph = AsmGraph(sg_edges_list, utg_data, ctg_paths)
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/fc_asm_graph.py", line 33, in init
self.build_node_map()
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/fc_asm_graph.py", line 169, in build_node_map
sg = self.get_sg_for_ctg(ctg_id)
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/fc_asm_graph.py", line 156, in get_sg_for_ctg
nx.add_path(sg, one_path)
AttributeError: 'module' object has no attribute 'add_path'
2019-11-21 08:21:02,683 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.
2019-11-21 08:21:02,683 - root - INFO - CD: '/home/myusername/data/genomes/my_species/2-asm-falcon' -> '/home/myusername/data/genomes/my_species/2-asm-falcon'
2019-11-21 08:21:02,683 - root - INFO - CD: '/home/myusername/data/genomes/my_species/2-asm-falcon' -> '/home/myusername/data/genomes/my_species/2-asm-falcon'
2019-11-21 08:21:02,684 - root - CRITICAL - Error in /home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py with args="{'json_fn': '/home/myusername/data/genomes/my_species/2-asm-falcon/task.json',\n 'timeout': 30,\n 'tmpdir': None}"
Traceback (most recent call last):
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 281, in
main() File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 273, in main
run(**vars(parsed_args))
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 267, in run
run_cfg_in_tmpdir(cfg, tmpdir, '.')
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 242, in run_cfg_in_tmpdir
run_bash(bash_template, myinputs, myoutputs, parameters)
File "/home/myusername/.conda/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/do_task.py", line 201, in run_bash
util.system(cmd)
File "/home/myusername/.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.
+++ pwd
++ echo 'FAILURE. Running top in /home/myusername/data/genomes/my_species/2-asm-falcon (If you see -terminal database is inaccessible- you are using the python bin-wrapper, so you will not get diagnostic info. No big deal. This process is crashing anyway.)'
++ rm -f top.txt
++ which python
++ which top
++ env -u LD_LIBRARY_PATH top -b -n 1
++ env -u LD_LIBRARY_PATH top -b -n 1
++ pstree -apl

real 25m15.321s user 51m59.876s sys 4m7.425s

finish
echo 'finish code: 1'

Is this because of a missing python module? It seems like python can't find something it should be able to but I don't really know the language. Is it possible to resume this run without starting from the beginning? Thanks so much for your help, I'm happy to provide any other information that may be helpful.

my_pb-assembly_run.zip

[pb-cdunn]

Your networkx is inconsistent with your python code. We no longer support python2.7. Please switch to python3.7 and update all.

[pb-cdunn]

Also, we generally don't look at these old repos anymore. Please see https://github.com/PacificBiosciences/pbbioconda