[ERROR]Task Node(2-asm-falcon) failed with exit-code=1

[liufeibio]

Hi, I run Falcon to assemble the genome for fungi, but got error as follows: [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 "/home/sujitmaiti/miniconda3/bin/fc_run", line 11, in <module> load_entry_point('falcon-kit==1.4.1', 'console_scripts', 'fc_run')() File "/home/sujitmaiti/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/run1.py", line 706, in main main1(argv[0], args.config, args.logger) File "/home/sujitmaiti/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/run1.py", line 73, in main1 input_fofn_fn=input_fofn_fn, File "/home/sujitmaiti/miniconda3/lib/python3.6/site-packages/falcon_kit/mains/run1.py", line 460, in run wf.refreshTargets() File "/home/sujitmaiti/miniconda3/lib/python3.6/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets self._refreshTargets(updateFreq, exitOnFailure) File "/home/sujitmaiti/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)}

And this is my config for the running:

#### Input
[General]
input_fofn=input.fofn
input_type=raw
pa_DBdust_option=
pa_fasta_filter_option=pass
target=assembly
skip_checks=False
LA4Falcon_preload=false

#### Data Partitioning
pa_DBsplit_option=-x500 -s50
ovlp_DBsplit_option=-x500 -s50

#### Repeat Masking
pa_HPCTANmask_option=
pa_REPmask_code=1,100;2,80;3,60

####Pre-assembly
genome_size=73000000
seed_coverage=20
length_cutoff= -1   
pa_HPCdaligner_option=-v -B128 -t16 -e0.75 -M24 -l3200 -k18 -h480 -w8 -s100
pa_daligner_option=-v -B128 -M24 -k24 -h1024 -e.96 -l2500 -s100
falcon_sense_option=--output-multi --min-idt 0.70 --min-cov 2 --max-n-read 800
falcon_sense_greedy=False

####Pread overlapping
ovlp_daligner_option=-e.96 -l2000 -k24 -h1024 -w6 -s100
ovlp_HPCdaligner_option=-v -B128 -M24

####Final Assembly
overlap_filtering_setting=--max-diff 100 --max-cov 300 --min-cov 2
fc_ovlp_to_graph_option=
length_cutoff_pr=2000

[job.defaults]
job_type=local
pwatcher_type=blocking
JOB_QUEUE=default
MB=32768
NPROC=6
njobs=32
submit = /bin/bash -c "${JOB_SCRIPT}" > "${JOB_STDOUT}" 2> "${JOB_STDERR}"

[job.step.da]
NPROC=4
MB=32768
njobs=16
[job.step.la]
NPROC=4
MB=32768
njobs=16
[job.step.cns]
NPROC=8
MB=65536
njobs=5
[job.step.pla]
NPROC=4
MB=32768
njobs=4
[job.step.asm]
NPROC=12
MB=196608
njobs=1

Could you help with it? Thanks! Fei

[pb-cdunn]

Look for a "stderr" file under 2-asm-falcon/. That might answer your question immediately.

Note that our Issue queue is actually https://github.com/PacificBiosciences/pbbioconda

Also, conda update --all to get our most recent updates.

[B10inform]

Hi,

I am also having exactly similar error. The stderr in 2-asm-falcon/. has following message.

# write sg_edges_list, c_path, utg_data, ctg_paths.
falconc m4filt-contained --in preads.m4 --out preads.filtered.m4 --min-len 1
+ falconc m4filt-contained --in preads.m4 --out preads.filtered.m4 --min-len 1
fatal.nim(49)            sysFatal
Error: unhandled exception: overlapParser.nim(75, 20) `iSpace != -1` Bad input line '---'.
(Be sure to delete the .idx file if written!) [AssertionError]
2020-06-04 16:04:51,029 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.
2020-06-04 16:04:51,030 - root - INFO - CD: '/home/FALCON/Exam/2-asm-falcon' -> '/home/FALCON/Exam/2-asm-falcon'
2020-06-04 16:04:51,030 - root - INFO - CD: '/home/FALCON/Exam/2-asm-falcon' -> '/home/FALCON/Exam/2-asm-falcon'
2020-06-04 16:04:51,031 - root - CRITICAL - Error in /home/.conda/envs/denovo_FALCON/lib/python3.7/site-packages/pypeflow/do_task.py with argv="{'json_fn': '/home/FALCON/Exam/2-asm-falcon/task.json',\n 'timeout': 30,\n 'tmpdir': None}"
Traceback (most recent call last):
  File "/home/.conda/envs/denovo_FALCON/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/.conda/envs/denovo_FALCON/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/.conda/envs/denovo_FALCON/lib/python3.7/site-packages/pypeflow/do_task.py", line 280, in <module>
    main()
  File "/home/.conda/envs/denovo_FALCON/lib/python3.7/site-packages/pypeflow/do_task.py", line 272, in main
    run(**vars(parsed_args))
  File "/home/.conda/envs/denovo_FALCON/lib/python3.7/site-packages/pypeflow/do_task.py", line 266, in run
    run_cfg_in_tmpdir(cfg, tmpdir, '.')
  File "/home/.conda/envs/denovo_FALCON/lib/python3.7/site-packages/pypeflow/do_task.py", line 241, in run_cfg_in_tmpdir
    run_bash(bash_template, myinputs, myoutputs, parameters)
  File "/home/.conda/envs/denovo_FALCON/lib/python3.7/site-packages/pypeflow/do_task.py", line 200, in run_bash
    util.system(cmd)
  File "/home/.conda/envs/denovo_FALCON/lib/python3.7/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 /home/FALCON/Exam/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    0m1.339s
user    0m0.984s
sys 0m0.285s
+ finish
+ echo 'finish code: 1'

[pb-cdunn]

We pushed a new falconc (in Bioconda module nim-falcon), so updating that should fix this.