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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
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[ERROR]Task Node(3-unzip/reads/dump_rawread_ids) failed with exit-code=1 #152

Closed crkmary closed 5 years ago

crkmary commented 5 years ago

Hello All,

I am having an error while using falcon_unzip (be installed the pb-assembly), the error is as follows. My genome size is about 3.43Mb.

Thanks a lot for your help.

[INFO](slept_ for another 2.9999999999999996s -- another 4 loop iterations)
[INFO](slept for another 10.500000000000002s -- another 6 loop iterations)
[ERROR]Task Node(3-unzip/reads/dump_rawread_ids) failed with exit-code=1
[ERROR]Some tasks are recently_done but not satisfied: {Node(3-unzip/reads/dump_rawread_ids)}
[ERROR]ready: set()
                      submitted: set()
[ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
[ERROR]Error for run(target=clr, config_fn=fc_unzip.cfg, logging_config_fn=None)
Traceback (most recent call last):
 File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 195, in run
   run_logged(target, config_fn)
 File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 184, in run_logged
  unzip_all(config, unzip_config_fn)
 File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 27, in unzip_all
   tasks_unzip.run_workflow(wf, config, unzip_config_fn)
 File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/falcon_unzip/tasks/unzip.py", line 467, in run_workflow
   dist=Dist(NPROC=24, job_dict=config['job.step.unzip.blasr_aln']),
 File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/falcon_kit/pype.py", line 109, in gen_parallel_tasks
   wf.refreshTargets()
 File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets
  self._refreshTargets(updateFreq, exitOnFailure)
 File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 362, in _refreshTargets
 raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: {Node(3-unzip/reads/dump_rawread_ids)}

My Confif file is as follows:

fc_unzip.cfg

[General]
max_n_open_files = 1000
[Unzip]
input_fofn=` input.fofn
input_bam_fofn= input_bam.fofn
#sge_phasing= -pe smp 12 -q bigmem
#sge_quiver= -pe smp 12 -q sequel-farm
#sge_track_reads= -pe smp 12 -q default
#sge_blasr_aln=  -pe smp 24 -q bigmem
#sge_hasm=  -pe smp 48 -q bigmem
#unzip_concurrent_jobs = 64
#quiver_concurrent_jobs = 64

#unzip_concurrent_jobs = 12
#quiver_concurrent_jobs = 12

[job.defaults]
NPROC=6
njobs=32
#job_type = SGE
job_type = local

#use_tmpdir = /scratch
pwatcher_type = blocking
#job_type = string
submit = bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}

#njobs=120
#njobs=8
#NPROC=4
#submit = qsub -S /bin/bash -sync y -V  \

[job.step.unzip.track_reads]
njobs=1
NPROC=48
[job.step.unzip.blasr_aln]
njobs=2
NPROC=16
[job.step.unzip.phasing]
njobs=16
NPROC=2
[job.step.unzip.hasm]
njobs=1
NPROC=48
[job.step.unzip.quiver]
njobs=2
NPROC=12
### run-P8053c4ab3cf5d1.bash.stderr
executable=${PYPEFLOW_JOB_START_SCRIPT}
+ executable=/public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids/run-P8053c4ab3cf5d1.bash
timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default
+ timeout=60

while [[ ! -x "${executable}" ]]; do
    if [[ "${timeout}" == "0" ]]; then
        echo "timed out waiting for (${executable})"
        exit 77
    fi
    echo "not executable: '${executable}', waiting ${timeout}s"
    sleep 1
    timeout=$((timeout-1))
done
+ [[ ! -x /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids/run-P8053c4ab3cf5d1.bash ]]

/bin/bash ${executable}
+ /bin/bash /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids/run-P8053c4ab3cf5d1.bash
+ '[' '!' -d /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids ']'
+ cd /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids
+ eval '/bin/bash run.sh'
++ /bin/bash run.sh
export PATH=$PATH:/bin
+ export PATH=/root/miniconda3/envs/dna/bin:/root/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/miniconda3/bin:/root/bin:/bin
+ PATH=/root/miniconda3/envs/dna/bin:/root/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/miniconda3/bin:/root/bin:/bin
cd /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids
+ cd /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids
/bin/bash task.sh
+ /bin/bash task.sh
pypeflow 2.3.0
2019-10-12 10:16:58,020 - root - DEBUG - Running "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids/task.json"
2019-10-12 10:16:58,021 - root - DEBUG - Checking existence of '/public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids/task.json' with timeout=30
2019-10-12 10:16:58,021 - root - DEBUG - Loading JSON from '/public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids/task.json'
2019-10-12 10:16:58,022 - root - DEBUG - {'bash_template_fn': 'template.sh',
 'inputs': {'falcon_asm_done': '../../../2-asm-falcon/falcon_asm_done',
            'rawread_db': '../../../0-rawreads/build/raw_reads.db'},
 'outputs': {'rawread_id_file': 'rawread_ids'},
 'parameters': {'pypeflow_mb': 4000, 'pypeflow_nproc': 1, 'topdir': '../../..'}}
2019-10-12 10:16:58,023 - root - INFO - CD: '/public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids' <- '/public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids'
2019-10-12 10:16:58,023 - root - DEBUG - Checking existence of '../../../2-asm-falcon/falcon_asm_done' with timeout=30
2019-10-12 10:16:58,023 - root - DEBUG - Checking existence of '../../../0-rawreads/build/raw_reads.db' with timeout=30
2019-10-12 10:17:28,058 - root - ERROR - Was waiting for '../../../0-rawreads/build/raw_reads.db'
Traceback (most recent call last):
  File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py", line 69, in wait_for
    _wait_for(fn, timeout)
  File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py", line 85, in _wait_for
    raise Exception('Timed out waiting for {!r}'.format(fn))
Exception: Timed out waiting for '../../../0-rawreads/build/raw_reads.db'
2019-10-12 10:17:28,059 - root - INFO - CD: '/public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids' -> '/public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids'
2019-10-12 10:17:28,059 - root - CRITICAL - Error in /root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py with args="{'json_fn': '/public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids/task.json',\n 'timeout': 30,\n 'tmpdir': None}"
Traceback (most recent call last):
  File "/root/miniconda3/envs/dna/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/root/miniconda3/envs/dna/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py", line 280, in <module>
    main()
  File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py", line 272, in main
    run(**vars(parsed_args))
  File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py", line 266, in run
    run_cfg_in_tmpdir(cfg, tmpdir, '.')
  File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py", line 219, in run_cfg_in_tmpdir
    wait_for(fn)
  File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py", line 69, in wait_for
    _wait_for(fn, timeout)
  File "/root/miniconda3/envs/dna/lib/python3.7/site-packages/pypeflow/do_task.py", line 85, in _wait_for
    raise Exception('Timed out waiting for {!r}'.format(fn))
Exception: Timed out waiting for '../../../0-rawreads/build/raw_reads.db'
+++ pwd
++ echo 'FAILURE. Running top in /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids (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  0m30.740s
user  0m0.320s
sys   0m0.275s
+ finish
+ echo 'finish code: 1'
pb-cdunn commented 5 years ago 
Exception: Timed out waiting for '../../../0-rawreads/build/raw_reads.db'

You are missing that file (w.r.t. /public/home/FALCON/DBM/3-unzip/reads/dump_rawread_ids/)