search

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FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries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
Other
205 stars 103 forks source link

AttributeError: 'DiGraph' object has no attribute 'node' (and a vicious networkx cycle) #711

Open goeckeritz opened 3 years ago

goeckeritz commented 3 years ago

Hi there,

I've been having trouble getting the test data set to run correctly, so I know something is wrong with the installation... At first, it appeared that I had an issue similar to https://github.com/PacificBiosciences/pbbioconda/issues/271, because I discovered that which 'package name' didn't work with samtools or pbindex. It works with gcpp. So I remade my conda environment with python 3.6 and reinstalled pb-assembly; after that, I was able to download samtools 1.9 and pbindex no problem. But now I have a new error in the .stderr file: ~/2-asm-falcon/run-Pe1d592bd8c0b56.bash.stderr

ome/goeckeri/miniconda3/bin:/mnt/home/goeckeri/miniconda3/condabin:/opt/software/powertools/bin:/opt/software/MATLAB/2018a:/opt/software/MATLAB/2018a/bin:/opt/software/Java
/1.8.0_152:/opt/software/Java/1.8.0_152/bin:/opt/software/Python/3.6.4-foss-2018a/bin:/opt/software/SQLite/3.21.0-GCCcore-6.4.0/bin:/opt/software/Tcl/8.6.8-GCCcore-6.4.0/bi
n:/opt/software/libreadline/7.0-GCCcore-6.4.0/bin:/opt/software/ncurses/6.0-GCCcore-6.4.0/bin:/opt/software/CMake/3.11.1-GCCcore-6.4.0/bin:/opt/software/bzip2/1.0.6-GCCcore
-6.4.0/bin:/opt/software/FFTW/3.3.7-gompi-2018a/bin:/opt/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/bin:/opt/software/imkl/2018.1.163-gompi-2018a/mkl/bin:/opt/software/imkl/20
18.1.163-gompi-2018a/bin:/opt/software/OpenMPI/2.1.2-GCC-6.4.0-2.28/bin:/opt/software/binutils/2.28-GCCcore-6.4.0/bin:/opt/software/GCCcore/6.4.0/bin:/usr/lib64/qt-3.3/bin:
/opt/software/core/lua/lua/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/hpcc/bin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/opt/puppetlabs/bin:/opt/dell/srvadm
in/bin:/bin
+ PATH=/mnt/home/goeckeri/miniconda3/bin:/mnt/home/goeckeri/miniconda3/bin:/mnt/home/goeckeri/miniconda3/envs/denovo_asm/bin:/mnt/home/goeckeri/miniconda3/bin:/mnt/home/goe
ckeri/miniconda3/bin:/mnt/home/goeckeri/miniconda3/condabin:/opt/software/powertools/bin:/opt/software/MATLAB/2018a:/opt/software/MATLAB/2018a/bin:/opt/software/Java/1.8.0_
152:/opt/software/Java/1.8.0_152/bin:/opt/software/Python/3.6.4-foss-2018a/bin:/opt/software/SQLite/3.21.0-GCCcore-6.4.0/bin:/opt/software/Tcl/8.6.8-GCCcore-6.4.0/bin:/opt/
software/libreadline/7.0-GCCcore-6.4.0/bin:/opt/software/ncurses/6.0-GCCcore-6.4.0/bin:/opt/software/CMake/3.11.1-GCCcore-6.4.0/bin:/opt/software/bzip2/1.0.6-GCCcore-6.4.0/
bin:/opt/software/FFTW/3.3.7-gompi-2018a/bin:/opt/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/bin:/opt/software/imkl/2018.1.163-gompi-2018a/mkl/bin:/opt/software/imkl/2018.1.16
3-gompi-2018a/bin:/opt/software/OpenMPI/2.1.2-GCC-6.4.0-2.28/bin:/opt/software/binutils/2.28-GCCcore-6.4.0/bin:/opt/software/GCCcore/6.4.0/bin:/usr/lib64/qt-3.3/bin:/opt/so
ftware/core/lua/lua/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/hpcc/bin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin:
/bin
cd /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon
+ cd /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon
/bin/bash task.sh
+ /bin/bash task.sh
pypeflow 2.3.0
2020-12-28 20:25:43,192 - root - DEBUG - Running "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/do_task.py /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon/task.json"
2020-12-28 20:25:43,193 - root - DEBUG - Checking existence of '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-fa
lcon/task.json' with timeout=30
2020-12-28 20:25:43,193 - root - DEBUG - Loading JSON from '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon/task.json'
2020-12-28 20:25:43,193 - root - DEBUG - {'bash_template_fn': 'template.sh',
 'inputs': {'config': '../General_config.json',
            'db2falcon_done': '../1-preads_ovl/db2falcon/db2falcon_done',
            'db_file': '../1-preads_ovl/build/preads.db',
            'las_fofn': '../1-preads_ovl/las-merge-combine/las_fofn.json',
            'preads4falcon_fasta': '../1-preads_ovl/db2falcon/preads4falcon.fasta'},
 'outputs': {'falcon_asm_done': 'falcon_asm_done'},
 'parameters': {'fc_ovlp_to_graph_option': ' --min-len 1',
                'length_cutoff_pr': '1',
                'overlap_filtering_setting': '--max-diff 120 --max-cov 120 '
                                             '--min-cov 2 --n-core 8',
                'pypeflow_mb': 4000,
                'pypeflow_nproc': '32',
                'topdir': '..'}}
2020-12-28 20:25:43,193 - root - INFO - CD: '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon' <- '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon'
2020-12-28 20:25:43,193 - root - DEBUG - Checking existence of '../General_config.json' with timeout=30
2020-12-28 20:25:43,193 - root - DEBUG - Checking existence of '../1-preads_ovl/db2falcon/db2falcon_done' with timeout=30
2020-12-28 20:25:43,193 - root - DEBUG - Checking existence of '../1-preads_ovl/build/preads.db' with timeout=30
2020-12-28 20:25:43,194 - root - DEBUG - Checking existence of '../1-preads_ovl/las-merge-combine/las_fofn.json' with timeout=30
2020-12-28 20:25:43,194 - root - DEBUG - Checking existence of '../1-preads_ovl/db2falcon/preads4falcon.fasta' with timeout=30
2020-12-28 20:25:43,194 - root - DEBUG - Checking existence of 'template.sh' with timeout=30
2020-12-28 20:25:43,194 - root - INFO - CD: '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon' <- '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon'
2020-12-28 20:25:43,194 - root - INFO - $('/bin/bash user_script.sh')
hostname
+ hostname
pwd
+ pwd
date
+ date
# Substitution will be similar to snakemake "shell".
# Given, las_fofn.json,
# write preads.ovl:
# mobs uses binwrappers, so it does not see our "entry-points".
# So, after dropping "src/py_scripts/*.py", we can call these via python3 -m:

time python3 -m falcon_kit.mains.ovlp_filter --db ../1-preads_ovl/build/preads.db --las-fofn ../1-preads_ovl/las-merge-combine/las_fofn.json --max-diff 120 --max-cov 120 --min-cov 2 --n-core 8 --min-len 1 --out-fn preads.ovl
+ python3 -m falcon_kit.mains.ovlp_filter --db ../1-preads_ovl/build/preads.db --las-fofn ../1-preads_ovl/las-merge-combine/las_fofn.json --max-diff 120 --max-cov 120 --min-cov 2 --n-core 8 --min-len 1 --out-fn preads.ovl
falcon-kit 1.4.4
pypeflow 2.3.0
[42896]starting ovlp_filter
[42896]fofn '../1-preads_ovl/las-merge-combine/las_fofn.json': ['/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las', '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las', '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las']
[DALIGNER Info] No mapping coordinates will be written for FALCON consensus. The consensus will have to re-map.

about to go into loop with novl = 10593 /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las
before Read_Overlap record j = 0 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 1 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 2 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 3 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 4 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 5 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 6 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 7 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 8 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 9 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
[DALIGNER Info] No mapping coordinates will be written for FALCON consensus. The consensus will have to re-map.
[DALIGNER Info] No mapping coordinates will be written for FALCON consensus. The consensus will have to re-map.
about to go into loop with novl = 11042 /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/
../las-merge-runs/m_00001/uow-00/preads.2.las
before Read_Overlap record j = 0 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 1 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 2 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 3 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 4 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 5 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 6 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 7 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 8 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020

about to go into loop with novl = 2663 /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las
before Read_Overlap record j = 9 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 0 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 1 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 2 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 3 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 4 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 5 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 6 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 7 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 8 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 9 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020

completed loop record j = 2663 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gatathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
completed loop record j = 2663 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020

completed loop record j = 10593 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020

completed loop record j = 11042 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020

[DALIGNER Info] No mapping coordinates will be written for FALCON consensus. The consensus will have to re-map.

about to go into loop with novl = 2663 /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las
before Read_Overlap record j = 0 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 1 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 2 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 3 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 4 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 5 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 6 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 7 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 8 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 9 out of 2663 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las Mon Dec 28 20:25:43 2020
[DALIGNER Info] No mapping coordinates will be written for FALCON consensus. The consensus will have to re-map.

about to go into loop with novl = 11042 /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las
before Read_Overlap record j = 0 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 1 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 2 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 3 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 4 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 5 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
[DALIGNER Info] No mapping coordinates will be written for FALCON consensus. The consensus will have to re-map.
before Read_Overlap record j = 6 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 7 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 8 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 9 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020

about to go into loop with novl = 10593 /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las
before Read_Overlap record j = 0 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 1 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 2 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 3 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 4 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 5 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 6 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 7 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 8 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020
before Read_Overlap record j = 9 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020

completed loop record j = 10593 out of 10593 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las Mon Dec 28 20:25:43 2020

completed loop record j = 11042 out of 11042 at /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las Mon Dec 28 20:25:43 2020

[42900]starting run_filter_stage1('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0)
[42900]maxrss:    17132
[42900]'LA4Falcon -mo ../1-preads_ovl/build/preads.db /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las'
[42900]maxrss:    17648
[42900]finished run_filter_stage1('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0)
[42900]starting run_filter_stage2('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0, <>, set(52 elem), 10)
[42900]maxrss:    17688
[42900]'LA4Falcon -mo ../1-preads_ovl/build/preads.db /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las'
[42900]maxrss:    20916
[42900]finished run_filter_stage2('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0, <>, set(52 elem), 10)
[42899]starting run_filter_stage1('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0)
[42899]maxrss:    17132
[42899]'LA4Falcon -mo ../1-preads_ovl/build/preads.db /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las'
[42899]maxrss:    18900
[42899]finished run_filter_stage1('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0)
[42899]starting run_filter_stage2('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0, <>, set(52 elem), 10)
[42899]maxrss:    18940
[42899]'LA4Falcon -mo ../1-preads_ovl/build/preads.db /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00002/uow-00/preads.3.las'
[42899]maxrss:    19476
[42899]finished run_filter_stage2('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0, <>, set(52 elem), 10)
[42898]starting run_filter_stage1('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0)
[42898]maxrss:    17124

[42898]'LA4Falcon -mo ../1-preads_ovl/build/preads.db /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00000/uow-00/preads.1.las'
[42898]maxrss:    18824
[42898]finished run_filter_stage1('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0)
[42898]starting run_filter_stage2('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0, <>, set(52 elem), 10)
[42898]maxrss:    18860
[42898]'LA4Falcon -mo ../1-preads_ovl/build/preads.db /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/1-preads_ovl/las-merge-gathered/../las-merge-runs/m_00001/uow-00/preads.2.las'
[42898]maxrss:    20804
[42898]finished run_filter_stage2('../1-preads_ovl/build/preads.db', /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/...(177), 'mo', 120, 120, 2, 1, 90.0, <>, set(52 elem), 10)
[42896]preparing filter_stage1
[42896]maxrss:    18052
[42896]preparing filter_stage2
[42896]maxrss:    18052
[42896]maxrss:    23064
[42896]finished ovlp_filter

real    0m0.577s
user    0m0.682s
sys     0m0.193s

ln -sf ../1-preads_ovl/db2falcon/preads4falcon.fasta ./preads4falcon.fasta
+ ln -sf ../1-preads_ovl/db2falcon/preads4falcon.fasta ./preads4falcon.fasta

# Given preads.ovl,
# write sg_edges_list, c_path, utg_data, ctg_paths.
time python3 -m falcon_kit.mains.ovlp_to_graph  --min-len 1 --overlap-file preads.ovl >| fc_ovlp_to_graph.log
+ python3 -m falcon_kit.mains.ovlp_to_graph --min-len 1 --overlap-file preads.ovl
falcon-kit 1.4.4
Traceback (most recent call last):
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/ovlp_to_graph.py", line 1618, in <module>
    main(sys.argv)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/ovlp_to_graph.py", line 1614, in main
    ovlp_to_graph(args)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/ovlp_to_graph.py", line 1440, in ovlp_to_graph
    sg, sg_r, edge_data = generate_string_graph(args)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/ovlp_to_graph.py", line 898, in generate_string_graph
    nxsg.node[w]["best_in"] = v
**AttributeError: 'DiGraph' object has no attribute 'node'**
2020-12-28 20:25:44,603 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.
2020-12-28 20:25:44,604 - root - INFO - CD: '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon' -> '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon'
2020-12-28 20:25:44,604 - root - INFO - CD: '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon' -> '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon'
2020-12-28 20:25:44,605 - root - CRITICAL - Error in /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/do_task.py with args="{'json_fn': '/mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon/task.json',\n 'timeout': 30,\n 'tmpdir': None}"
Traceback (most recent call last):
 File "/mnt/home/goeckeri/miniconda3/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 280, in <module>
    main()
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 272, in main
    run(**vars(parsed_args))
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 266, in run
    run_cfg_in_tmpdir(cfg, tmpdir, '.')
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 241, in run_cfg_in_tmpdir
    run_bash(bash_template, myinputs, myoutputs, parameters)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 200, in run_bash
    util.system(cmd)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/io.py", line 27, in syscall
    raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
+++ pwd
++ echo 'FAILURE. Running top in /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-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    0m2.072s
user    0m1.667s
sys     0m5.634s
+ finish
+ echo 'finish code: 1

And here's the run0.log I made too, if that helps... 

  "General": {
    "LA4Falcon_preload": false,
    "avoid_text_file_busy": true,
    "bestn": 12,
    "dazcon": false,
    "falcon_sense_greedy": false,
    "falcon_sense_option": "--output-multi --min-cov-aln 4 --min-idt 0.70 --min-cov 4 --max-n-read 200 --n-core 8",
    "falcon_sense_skip_contained": false,
    "fc_ovlp_to_graph_option": " --min-len 1",
    "genome_size": "200000",
    "input_fofn": "input.fofn",
    "input_type": "raw",
    "length_cutoff": "1000",
    "length_cutoff_pr": "1",
    "overlap_filtering_setting": "--max-diff 120 --max-cov 120 --min-cov 2 --n-core 8",
    "ovlp_DBdust_option": "",
    "ovlp_DBsplit_option": "-s5",
    "ovlp_HPCdaligner_option": "-v -B128 -M24",
    "ovlp_daligner_option": "-e.9 -l2500 -k24 -h1024 -w6 -s100",
    "pa_DBdust_option": "",
    "pa_DBsplit_option": "-a -x500 -s4",
    "pa_HPCTANmask_option": "-l500",
    "pa_HPCdaligner_option": "-v -B128 -M24",
    "pa_REPmask_code": "0,300/0,300/0,300",
    "pa_daligner_option": "-e.8 -l3200 -k18 -h480  -w8 -s100",
    "pa_dazcon_option": "-j 4 -x -l 500",
    "pa_fasta_filter_option": "streamed-internal-median",
    "pa_subsample_coverage": 0,
    "pa_subsample_random_seed": 12345,
    "pa_subsample_strategy": "random",
    "seed_coverage": 20,
    "skip_checks": false,
    "target": "assembly"
  },
  "job.defaults": {
    "NPROC": "4",
    "job_type": "string",
    "njobs": 8,
    "pwatcher_type": "blocking",
    "submit": "bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}",
"use_tmpdir": false
  },
  "job.step.asm": {
    "NPROC": "32"
  },
  "job.step.cns": {
    "NPROC": "8"
  },
  "job.step.da": {},
  "job.step.dust": {},
  "job.step.la": {},
  "job.step.pda": {},
  "job.step.pla": {}
}
[INFO]In simple_pwatcher_bridge, pwatcher_impl=<module 'pwatcher.blocking' from '/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/blocking.py'>
[INFO]job_type='string', (default)job_defaults={'job_type': 'string', 'pwatcher_type': 'blocking', 'submit': 'bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}', 'NPROC': '4', 'njobs': 8, 'use_tmpdir': False}, use_tmpdir=False, squash=True, job_name_style=0
[INFO]Setting max_jobs to 8; was None
[INFO]Num unsatisfied: 2, graph: 2
[INFO]About to submit: Node(0-rawreads/build)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/build/run-P494e97ccfac8ce.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/build/run-P494e97ccfac8ce.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.30000000000000004s -- another 2 loop iterations)
[INFO](slept for another 1.2000000000000002s -- another 3 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/build)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 1
[INFO]About to submit: Node(0-rawreads/tan-split)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-split/run-P56002e7fa62582.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-split/run-P56002e7fa62582.bash.stderr'
[INFO](slept for another 0.8999999999999999s -- another 4 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/tan-split)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 0
[INFO]Num unsatisfied: 3, graph: 5
[INFO]About to submit: Node(0-rawreads/tan-chunks/tan_000)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-chunks/tan_000/run-P2f897ded72ee47.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-chunks/tan_000/run-P2f897ded72ee47.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.30000000000000004s -- another 2 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/tan-chunks/tan_000)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 2
[INFO]About to submit: Node(0-rawreads/tan-runs/tan_000)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-runs/tan_000/run-P90aacc1ab1f604.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-runs/tan_000/run-P90aacc1ab1f604.bash.stderr'
[INFO](slept for another 0.7000000000000001s -- another 3 loop iterations)
[INFO](slept for another 1.0s -- another 4 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/tan-runs/tan_000)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 1
[INFO]About to submit: Node(0-rawreads/tan-gathered)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-gathered/run-P856990ab2ae328.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-gathered/run-P856990ab2ae328.bash.stderr'
[INFO](slept for another 1.4000000000000001s -- another 5 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/tan-gathered)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 0
[INFO]Parsed pa_REPmask_code (repa,repb,repc): [(0, 300), (0, 300), (0, 300)]
[INFO]Num unsatisfied: 2, graph: 7
[INFO]About to submit: Node(0-rawreads/tan-combine)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-combine/run-P117999f7c024f9.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/tan-combine/run-P117999f7c024f9.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.30000000000000004s -- another 2 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/tan-combine)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 1
[INFO]About to submit: Node(0-rawreads/repa/daligner-split)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-split/run-P29eae5286fd3ba.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-split/run-P29eae5286fd3ba.bash.stderr'
[INFO](slept for another 0.7000000000000001s -- another 3 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/daligner-split)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 0
[INFO]Num unsatisfied: 3, graph: 10
[INFO]About to submit: Node(0-rawreads/repa/daligner-chunks/rep_0000)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-chunks/rep_0000/run-Pd24f68d6b741b9.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-chunks/rep_0000/run-Pd24f68d6b741b9.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.30000000000000004s -- another 2 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/daligner-chunks/rep_0000)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 2
[INFO]About to submit: Node(0-rawreads/repa/daligner-runs/rep_0000)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-runs/rep_0000/run-P2351a7215f8ecc.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-runs/rep_0000/run-P2351a7215f8ecc.bash.stderr'
[INFO](slept for another 0.7000000000000001s -- another 3 loop iterations)
[INFO](slept for another 1.0s -- another 4 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/daligner-runs/rep_0000)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 1
[INFO]About to submit: Node(0-rawreads/repa/daligner-gathered)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-gathered/run-P489569a2bf76ee.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-gathered/run-P489569a2bf76ee.bash.stderr'
[INFO](slept for another 1.4000000000000001s -- another 5 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/daligner-gathered)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 0
[INFO]Num unsatisfied: 2, graph: 12
[INFO]About to submit: Node(0-rawreads/repa/daligner-combine)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-combine/run-P527e5c348041cb.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/daligner-combine/run-P527e5c348041cb.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.30000000000000004s -- another 2 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/daligner-combine)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 1
[INFO]About to submit: Node(0-rawreads/repa/las-merge-split)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-split/run-Pda1d5f5e49c09b.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-split/run-Pda1d5f5e49c09b.bash.stderr'
[INFO](slept for another 0.7000000000000001s -- another 3 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/las-merge-split)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 0
[INFO]Num unsatisfied: 7, graph: 19
[INFO]About to submit: Node(0-rawreads/repa/las-merge-chunks/m_00000)
[INFO]About to submit: Node(0-rawreads/repa/las-merge-chunks/m_00002)
[INFO]About to submit: Node(0-rawreads/repa/las-merge-chunks/m_00001)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-chunks/m_00000/run-P8589b843cdb63b.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-chunks/m_00000/run-P8589b843cdb63b.bash.stderr'
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-chunks/m_00002/run-P03dd221a1084d0.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-chunks/m_00002/run-P03dd221a1084d0.bash.stderr'
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-chunks/m_00001/run-Pcf97594a8f6688.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-chunks/m_00001/run-Pcf97594a8f6688.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.30000000000000004s -- another 2 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/las-merge-chunks/m_00001),
 Node(0-rawreads/repa/las-merge-chunks/m_00000),
 Node(0-rawreads/repa/las-merge-chunks/m_00002)}
[INFO]Num satisfied in this iteration: 3
[INFO]Num still unsatisfied: 4
[INFO]About to submit: Node(0-rawreads/repa/las-merge-runs/m_00000)
[INFO]About to submit: Node(0-rawreads/repa/las-merge-runs/m_00001)
[INFO]About to submit: Node(0-rawreads/repa/las-merge-runs/m_00002)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-runs/m_00001/run-P8be191897c5d7c.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-runs/m_00001/run-P8be191897c5d7c.bash.stderr'
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-runs/m_00002/run-Pded974135ae4b1.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-runs/m_00002/run-Pded974135ae4b1.bash.stderr'
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-runs/m_00000/run-P001f469d894b8b.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-runs/m_00000/run-P001f469d894b8b.bash.stderr'
[INFO](slept for another 0.4s -- another 3 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/las-merge-runs/m_00002)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 3
[INFO](slept for another 0.9s -- another 4 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/las-merge-runs/m_00000),
 Node(0-rawreads/repa/las-merge-runs/m_00001)}
[INFO]Num satisfied in this iteration: 2
[INFO]Num still unsatisfied: 1
blyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-gathered/run-P150abde26245e3.bash.stderr'
[INFO](slept for another 0.7000000000000001s -- another 5 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/las-merge-gathered)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 0
[INFO]Num unsatisfied: 2, graph: 21
[INFO]About to submit: Node(0-rawreads/repa/las-merge-combine)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-combine/run-Pbba386bb378ef1.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/las-merge-combine/run-Pbba386bb378ef1.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.30000000000000004s -- another 2 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/las-merge-combine)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 1
[INFO]About to submit: Node(0-rawreads/repa/rep-split)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-split/run-Pd3a121b084a5af.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-split/run-Pd3a121b084a5af.bash.stderr'
[INFO](slept for another 0.7000000000000001s -- another 3 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/rep-split)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 0
[INFO]Num unsatisfied: 7, graph: 28
[INFO]About to submit: Node(0-rawreads/repa/rep-chunks/rep_000)
[INFO]About to submit: Node(0-rawreads/repa/rep-chunks/rep_001)
[INFO]About to submit: Node(0-rawreads/repa/rep-chunks/rep_002)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-chunks/rep_000/run-P93fc1ef212b00e.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-chunks/rep_000/run-P93fc1ef212b00e.bash.stderr'
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-chunks/rep_001/run-P7dcf53ad409117.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-chunks/rep_001/run-P7dcf53ad409117.bash.stderr'
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-chunks/rep_002/run-P4c94643f0f7eab.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-chunks/rep_002/run-P4c94643f0f7eab.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.30000000000000004s -- another 2 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/rep-chunks/rep_001)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 6
[INFO]About to submit: Node(0-rawreads/repa/rep-runs/rep_001)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-runs/rep_001/run-P9e07d40b818c7d.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-runs/rep_001/run-P9e07d40b818c7d.bash.stderr'
[INFO]recently_satisfied:
{Node(0-rawreads/repa/rep-chunks/rep_000)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 5
[INFO]About to submit: Node(0-rawreads/repa/rep-runs/rep_000)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-runs/rep_000/run-Pc4d86ecf6e5a57.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-runs/rep_000/run-Pc4d86ecf6e5a57.bash.stderr'
[INFO](slept for another 0.30000000000000004s -- another 3 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/rep-chunks/rep_002)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 4
[INFO]About to submit: Node(0-rawreads/repa/rep-runs/rep_002)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-runs/rep_002/run-P28cb663c393f10.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-runs/rep_002/run-P28cb663c393f10.bash.stderr'
[INFO](slept for another 0.4s -- another 4 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/rep-runs/rep_001), Node(0-rawreads/repa/rep-runs/rep_000)}
[INFO]Num satisfied in this iteration: 2
[INFO]Num still unsatisfied: 2
[INFO]recently_satisfied:
{Node(0-rawreads/repa/rep-runs/rep_002)}
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 1
[INFO]About to submit: Node(0-rawreads/repa/rep-gathered)
[INFO]Popen: '/bin/bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-gathered/run-P5811b11102f35d.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/0-rawreads/repa/rep-gathered/run-P5811b11102f35d.bash.stderr'
[INFO](slept for another 1.0s -- another 6 loop iterations)
[INFO]recently_satisfied:
{Node(0-rawreads/repa/rep-gathered)}
blah
blah
blah
[INFO]About to submit: Node(2-asm-falcon)
[INFO]Popen: 'bash -C /mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pwatcher/mains/job_start.sh >| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon/run-Pe1d592bd8c0b56.bash.stdout 2>| /mnt/gs18/scratch/users/goeckeri/Montmorency/FALCON/assemblyA/TEST/FALCON-examples/run/greg200k-sv2/2-asm-falcon/run-Pe1d592bd8c0b56.bash.stderr'
[INFO](slept for another 0.6000000000000001s -- another 4 loop iterations)
[INFO](slept for another 1.5s -- another 5 loop iterations)
[ERROR]Task Node(2-asm-falcon) failed with exit-code=1
[ERROR]Some tasks are recently_done but not satisfied: {Node(2-asm-falcon)}
[ERROR]ready: set()
        submitted: set()
[ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
Traceback (most recent call last):
  File "/mnt/home/goeckeri/miniconda3/bin/fc_run", line 11, in <module>
    load_entry_point('falcon-kit==1.4.4', 'console_scripts', 'fc_run')()
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/run1.py", line 706, in main
    main1(argv[0], args.config, args.logger)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/run1.py", line 73, in main1
    input_fofn_fn=input_fofn_fn,
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/run1.py", line 460, in run
    wf.refreshTargets()
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets
    self._refreshTargets(updateFreq, exitOnFailure)
  File "/mnt/home/goeckeri/miniconda3/lib/python3.6/site-packages/pypeflow/simple_pwatcher_bridge.py", line 362, in _refreshTargets
    raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: {Node(2-asm-falcon)}

A couple of other github issues implied that a different version of networkx could solve the problem... (https://github.com/dgorissen/pycel/issues/80 and https://github.com/victorlei/smop/issues/153)... but I checked the version and it was 2.5, so I don't think my version is too old. I even tried downgrading it to 2.4 and 1.11, hoping that would do something, but I still get the same error. Weirdly enough, when I do 'which networkx' while in my denovo_asm environment for any of these installations, conda can't find the damn thing. Yet, when I do conda install networkx, conda says it is already installed!

Any idea what the fix for this might be? Thank you so much in advance for your help!!

Kindly, Charity

pb-cdunn commented 3 years ago

It's very difficult to main that old code. It's even difficult to update at this point, but if you find a definite fix we would try.

Switching to HiFi (CCS) is a much better solution. The source-code for dealing with those reads is so much simpler, no matter which assembler you choose.