I installed pb-assembly suite on a cluster using conda (python2.7 and 3).
I have the following problem ;
[ERROR]Task Node(0-rawreads/build) failed with exit-code=1
[ERROR]Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])
[ERROR]ready: set([])
submitted: set([])
[ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
Traceback (most recent call last):
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/bin/fc_run", line 11, in
load_entry_point('falcon-kit==1.2.4', 'console_scripts', 'fc_run')()
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 726, in main
main1(argv[0], args.config, args.logger)
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 76, in main1
input_fofn_fn=input_fofn_fn,
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 242, in run
dist=Dist(NPROC=4, MB=4000, job_dict=config['job.step.da']),
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/pype.py", line 106, in gen_parallel_tasks
wf.refreshTargets()
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets
self._refreshTargets(updateFreq, exitOnFailure)
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 362, in _refreshTargets
raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])
0-rawreads/build/run-Pae771765a0c133.bash.stderr
executable=${PYPEFLOW_JOB_START_SCRIPT}
executable=/media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build/run-Pae771765a0c133.bash
timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default
timeout=60
Wait up to timeout seconds for the executable to become "executable",
then exec.
timeleft = int(timeout)
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
PATH=/media/vol2/home/lcornet/anaconda2/bin:/media/vol1/apps/perlbrew/bin:/media/vol1/apps/perlbrew/perls/perl-5.22.0-thread-multi/bin:/media/vol1/gridengine/bin/linux-x64:/tmp/973061.1.smallnodes.q:/media/vol2/home/lcornet/miniconda2/bin:/usr/lib64/openmpi/bin:/media/vol1/gridengine/bin/linux-x64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/opt/ibutils/bin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/bin
cd /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build
cd /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build
/bin/bash task.sh
/bin/bash task.sh
/media/vol2/home/lcornet/anaconda2/bin/python2.7: No module named pypeflow
+++ pwd
++ echo 'FAILURE. Running top in /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build (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
Hello,
I installed pb-assembly suite on a cluster using conda (python2.7 and 3).
I have the following problem ; [ERROR]Task Node(0-rawreads/build) failed with exit-code=1 [ERROR]Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)]) [ERROR]ready: set([]) submitted: set([]) [ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM. Traceback (most recent call last): File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/bin/fc_run", line 11, in
load_entry_point('falcon-kit==1.2.4', 'console_scripts', 'fc_run')()
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 726, in main
main1(argv[0], args.config, args.logger)
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 76, in main1
input_fofn_fn=input_fofn_fn,
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 242, in run
dist=Dist(NPROC=4, MB=4000, job_dict=config['job.step.da']),
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/pype.py", line 106, in gen_parallel_tasks
wf.refreshTargets()
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets
self._refreshTargets(updateFreq, exitOnFailure)
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 362, in _refreshTargets
raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])
0-rawreads/build/run-Pae771765a0c133.bash.stderr
executable=${PYPEFLOW_JOB_START_SCRIPT}
Wait up to timeout seconds for the executable to become "executable",
then exec.
timeleft = int(timeout)
while [[ ! -x "${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
/bin/bash ${executable}
real 0m0.685s user 0m0.034s sys 0m0.082s
Can you help me ?
Luc