Error at the 4-quiver step of pb-assembly using example dataset #254
Comments
|
I have the same error info with the running of the greg200k-sv2 example data set ,and there were not "cns-output" directory in "4-polish/". Thanks in advance and best regards |
|
@armintoepfer Thanks for adding the "assembly" label. Can you give any suggestion for how to overcome this error and make the falcon-unzip go through? |
|
Have you figured out how to overcome the error? I pasted this a week ago and still no answer at all. |
|
Developers address issues as time allows them. Please keep in mind that support here is not part of any service contract and thus there are no response guarantees. |
|
|
Many thanks for the information. Just wondering have you got the updated version of the test data that can work? |
|
I am having this same problem on both this test data set and my own on dataset. |
|
Hello, I think this is the same error with example dataset. Below is the error message from the screen and the error report attached. /home/mvandam/pacbio-p_sulf/data2/pb/r64044_20191116_023108/1_A01/test-data/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F_001 this seems similar to a previous issue: gconcepcion/pb-assembly#1 run-P7390d906844bee.bash.stderr.txt We are using falcon-unzip 1.3.7 falcon-kit 1.8.1 cd /home/me/pacbio-p_sulf/data2/pb/r64044_20191116_023108/1_A01/test-data/FALCON-examples/run/greg200k-sv2 fc_unzip.py fc_unzip.cfg [INFO]Popen: 'bash -C /home/me/.conda/envs/pb-assembly/lib/python3.7/site-packages/pwatcher/mains/job_start.sh >| /home/me/pacbio-p_sulf/data2/pb/r64044_20191116_023108/1_A01/test-data/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F/run-P6b579be4a29125.bash.stdout 2>| /home/me/pacbio-p_sulf/data2/pb/r64044_20191116_023108/1_A01/test-data/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F/run-P6b579be4a29125.bash.stderr' Traceback (most recent call last): |
|
I have run into this same issue - so close to the end. I have installed the latest version of miniconda3 and the lastest pb-assembly on bioconda. Python 3.7.6 Is there anyway to bypass the haplotig/phasing work to get a nice polished version of the assembly? |
|
I am also having this same issue on my own data set, any updates on a fix for this? |
|
I haven't tried this for my own data but I am not managing to get it to work for the same test dataset. Just adding a comment here in hopes that this will get more notice. |
|
To me this looks like this issue: #271 I ran into the same issue (both own dataset and test dataset). I think this is If you go to EDIT: exit code of the command is 1 |
|
Closing due to lack of activity. |
|
Hi, |
|
Pretty sure that this error is due to an older chemistry incompatibility (RS II) with the newer versions of FALCON.
|
Operating system
Linux hpc212 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Package name
I installed the last version of pb-assembly with conda and I have used the command: conda update --all.
Conda environment
$ conda list
packages in environment at /home/jiwu2573/.conda/envs/denovo_asm:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
bedtools 2.29.2 hc088bd4_0 bioconda
blasr 5.3.3 h018d624_1 bioconda
blasr_libcpp 5.3.3 h018d624_1 bioconda
bwa 0.7.17 hed695b0_7 bioconda
bzip2 1.0.8 h516909a_2 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
certifi 2019.11.28 py37_0 conda-forge
curl 7.68.0 hf8cf82a_0 conda-forge
decorator 4.4.1 py_0 conda-forge
future 0.18.2 py37_0 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge
htslib 1.9 h4da6232_3 bioconda
krb5 1.16.4 h2fd8d38_0 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_8 conda-forge
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libcurl 7.68.0 hda55be3_0 conda-forge
libdeflate 1.5 h516909a_0 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
minimap2 2.17 h8b12597_1 bioconda
mummer4 4.0.0beta2 pl526he1b5a44_5 bioconda
ncurses 6.1 hf484d3e_1002 conda-forge
networkx 2.4 py_0 conda-forge
nim-falcon 1.1.0 h2f8a211_0 bioconda
numpy 1.18.1 py37h95a1406_0 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
pb-assembly 0.0.8 0 bioconda
pb-dazzler 0.0.1 h516909a_0 bioconda
pb-falcon 2.2.4 py37hed50d52_0 bioconda
pb-falcon-phase 0.1.0 h3889886_0 bioconda
pbbam 1.0.6 hc16d5b3_1 bioconda
pbcopper 1.3.0 h3e4de3e_0 bioconda
pbgcpp 1.9.0 0 bioconda
pbmm2 1.1.0 hfb76ee0_0 bioconda
pcre 8.43 he1b5a44_0 conda-forge
perl 5.26.2 h516909a_1006 conda-forge
pip 20.0.2 py_2 conda-forge
pysam 0.15.4 py37hbcae180_0 bioconda
python 3.7.6 h357f687_2 conda-forge
python-edlib 1.3.8.post1 py37hc9558a2_0 bioconda
python-intervaltree 3.0.2 py_0 bioconda
python-msgpack 0.6.1 py37hc9558a2_1 bioconda
python-sortedcontainers 2.1.0 py_0 bioconda
racon 1.4.10 he513fc3_0 bioconda
readline 8.0 hf8c457e_0 conda-forge
samtools 1.9 h10a08f8_12 bioconda
setuptools 45.2.0 py37_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
wheel 0.34.2 py_1 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
(denovo_asm)
Describe the bug
I used the following command as this website suggested: https://github.com/PacificBiosciences/pb-assembly#example-data-set
cd run/greg200k-sv2
fc_run fc_run.cfg
fc_unzip.py fc_unzip.cfg
I have a bug with the command: fc_unzip.py fc_unzip.cfg.
It looks like the step "3-unzip" of pb-assembly works well, with the files "all_p_ctg.fa" and "all_h_ctg.fa" generated, but quiver step doesn't work.
Error message
/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/all.log
2020-02-11 06:03:55,892 - pwatcher.blocking:462 - DEBUG - query(which='list', jobids=<2>)
2020-02-11 06:03:56,225 - pwatcher.blocking:234 - DEBUG - rc: 1
2020-02-11 06:03:56,225 - pwatcher.blocking:86 - DEBUG - Thread notify_exited(P76ee7211f466de->1).
2020-02-11 06:03:56,416 - pwatcher.blocking:234 - DEBUG - rc: 1
2020-02-11 06:03:56,416 - pwatcher.blocking:86 - DEBUG - Thread notify_exited(Pb0247862895112->1).
2020-02-11 06:03:56,793 - pypeflow.simple_pwatcher_bridge:325 - DEBUG - N in queue: 2 (max_jobs=2)
2020-02-11 06:03:56,793 - pwatcher.blocking:462 - DEBUG - query(which='list', jobids=<2>)
2020-02-11 06:03:56,793 - pypeflow.simple_pwatcher_bridge:94 - ERROR - Task Node(4-polish/quiver-run/000000F_001) failed with exit-code=1
2020-02-11 06:03:56,793 - pypeflow.simple_pwatcher_bridge:94 - ERROR - Task Node(4-polish/quiver-run/000000F) failed with exit-code=1
2020-02-11 06:03:56,793 - pypeflow.simple_pwatcher_bridge:343 - DEBUG - recently_done: [(Node(4-polish/quiver-run/000000F), False), (Node(4-polish/quiver-run/000000F_001), False)]
2020-02-11 06:03:56,794 - pypeflow.simple_pwatcher_bridge:344 - DEBUG - Num done in this iteration: 2
2020-02-11 06:03:56,794 - pypeflow.simple_pwatcher_bridge:358 - ERROR - Some tasks are recently_done but not satisfied: {Node(4-polish/quiver-run/000000F), Node(4-polish/quiver-run/000000F_001)}
2020-02-11 06:03:56,794 - pypeflow.simple_pwatcher_bridge:359 - ERROR - ready: set()
submitted: set()
2020-02-11 06:03:56,794 - pwatcher.blocking:466 - DEBUG - delete(which='known', jobids=<0>)
2020-02-11 06:03:56,794 - pwatcher.blocking:430 - ERROR - Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
2020-02-11 06:03:56,794 - pypeflow.simple_pwatcher_bridge:189 - DEBUG - In notifyTerminate(), result of delete:None
2020-02-11 06:03:56,794 - fc_run:199 - ERROR - Error for run(target=clr, config_fn=fc_unzip.cfg, logging_config_fn=None)
Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 195, in run
run_logged(target, config_fn)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 184, in run_logged
unzip_all(config, unzip_config_fn)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 27, in unzip_all
tasks_unzip.run_workflow(wf, config, unzip_config_fn)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_unzip/tasks/unzip.py", line 739, in run_workflow
job_dict=config['job.step.unzip.quiver'],
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/pype.py", line 195, in gen_parallel_tasks
wf.refreshTargets()
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets
self._refreshTargets(updateFreq, exitOnFailure)
File "/home/jiwu2573/.conda/envs/denovo_asm/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(4-polish/quiver-run/000000F), Node(4-polish/quiver-run/000000F_001)}
/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F/run-P76ee7211f466de.bash.stderr
executable=${PYPEFLOW_JOB_START_SCRIPT}
timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default
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 ${executable}
++ /bin/bash run.sh
export PATH=$PATH:/bin
cd /home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F
/bin/bash task.sh
pypeflow 2.3.0
2020-02-11 17:03:52,678 - root - DEBUG - Running "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py /home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F/task.json"
2020-02-11 17:03:52,679 - root - DEBUG - Checking existence of '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F/task.json' with timeout=30
2020-02-11 17:03:52,684 - root - DEBUG - Loading JSON from '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F/task.json'
2020-02-11 17:03:52,685 - root - DEBUG - {'bash_template_fn': 'template.sh',
'inputs': {'bash_template': '../../quiver-split/bash-template.sh',
'units_of_work': '../../quiver-chunks/000000F/some-units-of-work.json'},
'outputs': {'results': 'results.json'},
'parameters': {'pypeflow_mb': 4000, 'pypeflow_nproc': '12'}}
2020-02-11 17:03:52,685 - root - INFO - CD: '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F' <- '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F'
2020-02-11 17:03:52,685 - root - DEBUG - Checking existence of '../../quiver-split/bash-template.sh' with timeout=30
2020-02-11 17:03:52,685 - root - DEBUG - Checking existence of '../../quiver-chunks/000000F/some-units-of-work.json' with timeout=30
2020-02-11 17:03:52,685 - root - DEBUG - Checking existence of 'template.sh' with timeout=30
2020-02-11 17:03:52,686 - root - INFO - CD: '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F' <- '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F'
2020-02-11 17:03:52,687 - root - INFO - $('/bin/bash user_script.sh')
hostname
pwd
date
Substitution will be similar to snakemake "shell".
python3 -m falcon_kit.mains.generic_run_units_of_work --nproc=12 --units-of-work-fn=../../quiver-chunks/000000F/some-units-of-work.json --bash-template-fn=../../quiver-split/bash-template.sh --results-fn=results.json
falcon-kit 1.8.1 (pip thinks "falcon-kit 1.8.1")
pypeflow 2.3.0
INFO:root:For multiprocessing, parallel njobs=12 (cpu_count=24, nproc=12, nproc_per_uow=1)
INFO:root:Started a worker in 94660 from parent 94659
INFO:root:Started a worker in 94662 from parent 94659
INFO:root:Started a worker in 94664 from parent 94659
INFO:root:Started a worker in 94666 from parent 94659
INFO:root:Started a worker in 94669 from parent 94659
INFO:root:Started a worker in 94667 from parent 94659
INFO:root:Started a worker in 94671 from parent 94659
INFO:root:Started a worker in 94673 from parent 94659
INFO:root:Started a worker in 94675 from parent 94659
INFO:root:Started a worker in 94676 from parent 94659
INFO:root:Started a worker in 94678 from parent 94659
INFO:root:Started a worker in 94680 from parent 94659
INFO:root:running 1 units-of-work, 12 at a time...
[94660]starting run_uow('uow-00', set -vex
trap 'touch {output.job_done}.exit' EXIT
hostname
date
VC_IGNORE_ERROR='{params.vc_ignore_...(1555), <'ctg_type', 'read_bam', 'ref_fasta'>, <'cns_fasta', 'cns_fastq', 'cns_vcf', 'ctg_type_again', 'job_done'>, <'ctg_id', 'use_blasr', 'vc_ignore_error', 'pypeflow_nproc'>)
[94660]maxrss: 14572
INFO:root:$('rm -rf uow-00')
INFO:root:CD: 'uow-00' <- '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F'
INFO:root:$('/bin/bash user_script.sh')
hostname
pwd
date
set -vex
trap 'touch quiver_done.exit' EXIT
hostname
date
VC_IGNORE_ERROR='0'
echo "VC_IGNORE_ERROR='$VC_IGNORE_ERROR'"
USE_BLASR='0'
echo "USE_BLASR='$USE_BLASR'"
nproc=1
samtools faidx ../../../quiver-split/refs/000000F/ref.fasta
if [[ $USE_BLASR != 1 ]]; then
pbmm2 align --sort ../../../quiver-split/refs/000000F/ref.fasta /home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/segregate-run/segr001/segregated/000000F/000000F.bam aln-000000F.bam
pbindex aln-000000F.bam
else
pbalign --tmpDir=$(pwd)/tmp --nproc=$nproc --minAccuracy=0.75 --minLength=50 --minAnchorSize=12 --maxDivergence=30 --concordant --algorithm=blasr --algorithmOptions=--useQuality --maxHits=1 --hitPolicy=random --seed=1 /home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/segregate-run/segr001/segregated/000000F/000000F.bam ../../../quiver-split/refs/000000F/ref.fasta aln-000000F.bam
fi
#python3 -c 'import ConsensusCore2 as cc2; print cc2' # So quiver likely works.
fasta_gz=cns.fasta.gz
fastq_gz=cns.fastq.gz
fasta_fn=${fasta_gz%.gz}
fastq_fn=${fastq_gz%.gz}
set +e
gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j
rc=$?
if [[ $rc != 0 ]]; then
if [[ $VC_IGNORE_ERROR != 1 ]]; then
echo ERROR gcpp failed. Maybe no reads for this block?
exit 1
else
echo WARNING gcpp failed. Maybe no reads for this block.
# We expect gcpp to write files even on error, so we do not need to "touch" them.
fi
fi
touch quiver_done.exit
WARNING:root:Call '/bin/bash user_script.sh' returned 256.
INFO:root:CD: 'uow-00' -> '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F'
ERROR:root:failed multiprocessing
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/util/io.py", line 68, in run_func
ret = func(*args)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 45, in run_uow
pypeflow.do_task.run_bash(script, inputs, outputs, params)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 200, in run_bash
util.system(cmd)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/io.py", line 27, in syscall
raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/util/io.py", line 73, in run_func
raise Exception(traceback.format_exc())
Exception: Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/util/io.py", line 68, in run_func
ret = func(*args)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 45, in run_uow
pypeflow.do_task.run_bash(script, inputs, outputs, params)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 200, in run_bash
util.system(cmd)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/io.py", line 27, in syscall
raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 103, in run
for res in exe_pool.imap(run_func, inputs):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/multiprocessing/pool.py", line 748, in next
raise value
Exception: Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/util/io.py", line 68, in run_func
ret = func(*args)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 45, in run_uow
pypeflow.do_task.run_bash(script, inputs, outputs, params)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 200, in run_bash
util.system(cmd)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/io.py", line 27, in syscall
raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/util/io.py", line 68, in run_func
ret = func(*args)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 45, in run_uow
pypeflow.do_task.run_bash(script, inputs, outputs, params)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 200, in run_bash
util.system(cmd)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/io.py", line 27, in syscall
raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/util/io.py", line 73, in run_func
raise Exception(traceback.format_exc())
Exception: Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/util/io.py", line 68, in run_func
ret = func(*args)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 45, in run_uow
pypeflow.do_task.run_bash(script, inputs, outputs, params)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 200, in run_bash
util.system(cmd)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/io.py", line 27, in syscall
raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 152, in
main()
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 148, in main
run(**vars(args))
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 103, in run
for res in exe_pool.imap(run_func, inputs):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/multiprocessing/pool.py", line 748, in next
raise value
Exception: Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/util/io.py", line 68, in run_func
ret = func(*args)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py", line 45, in run_uow
pypeflow.do_task.run_bash(script, inputs, outputs, params)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 200, in run_bash
util.system(cmd)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/io.py", line 27, in syscall
raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
2020-02-11 17:03:55,562 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.
2020-02-11 17:03:55,562 - root - INFO - CD: '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F' -> '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F'
2020-02-11 17:03:55,562 - root - INFO - CD: '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F' -> '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F'
2020-02-11 17:03:55,562 - root - CRITICAL - Error in /home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py with args="{'json_fn': '/home/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F/task.json',\n 'timeout': 30,\n 'tmpdir': None}"
Traceback (most recent call last):
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 280, in
main()
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 272, in main
run(**vars(parsed_args))
File "/home/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 266, in run
run_cfg_in_tmpdir(cfg, tmpdir, '.')
File "/home/jiwu2573/.conda/envs/denovo_asm/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/jiwu2573/.conda/envs/denovo_asm/lib/python3.7/site-packages/pypeflow/do_task.py", line 200, in run_bash
util.system(cmd)
File "/home/jiwu2573/.conda/envs/denovo_asm/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/jiwu2573/tools/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F (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 0m3.836s
user 0m2.836s
sys 0m0.618s
To Reproduce
The example dataset is here: https://github.com/PacificBiosciences/pb-assembly#example-data-set
Expected behavior
I would expect the test case will exit cleanly and I should find fasta files with a
size greater than 0 in the 4-polish/cns-output directory.
The text was updated successfully, but these errors were encountered: