HI, I run Falcon on pacbio reads successfully, but failed to run falcon-unzip. Here is the error report:
It seems that errors occurred at this step 3-unzip/1-hasm. The file 'preads.p_ovl' is empty. could you please help me to solve this issue? Many thanks.
The log information in file 'run-P5d87a9de2f785c.bash.stderr' under this folder '3-unzip/1-hasm'
executable=${PYPEFLOW_JOB_START_SCRIPT}
+ executable=/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falcon
unzip/3-unzip/1-hasm/run-P5d87a9de2f785c.bash
timeout=${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
+ [[ ! -x /export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunz
ip/3-unzip/1-hasm/run-P5d87a9de2f785c.bash ]]
/bin/bash ${executable}
+ /bin/bash /export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconu
nzip/3-unzip/1-hasm/run-P5d87a9de2f785c.bash
+ '[' '!' -d /export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falcon
unzip/3-unzip/1-hasm ']'
+ cd /export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-
unzip/1-hasm
+ eval '/bin/bash run.sh'
++ /bin/bash run.sh
export PATH=$PATH:/bin
cd /export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-un
zip/1-hasm
+ cd /export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-
unzip/1-hasm
/bin/bash task.sh
+ /bin/bash task.sh
pypeflow 2.2.0
2020-03-14 22:10:24,164 - root - DEBUG - Running "/export/scratch3/vincent/software/miniconda3
/envs/pacbio/lib/python2.7/site-packages/pypeflow/do_task.py /export/scratch3/vincent/project/
TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm/task.json"
2020-03-14 22:10:24,165 - root - DEBUG - Checking existence of '/export/scratch3/vincent/proje
ct/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm/task.json' with timeou
t=30
2020-03-14 22:10:24,165 - root - DEBUG - Loading JSON from '/export/scratch3/vincent/project/T
GS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm/task.json'
2020-03-14 22:10:24,165 - root - DEBUG - {u'bash_template_fn': u'template.sh',
u'inputs': {u'las_fofn': u'../../1-preads_ovl/las-merge-combine/las_fofn.json',
u'preads4falcon': u'../../1-preads_ovl/db2falcon/preads4falcon.fasta',
u'preads_db': u'../../1-preads_ovl/build/preads.db',
u'rid_to_phase_all': u'concatenated-rid-to-phase/rid_to_phase.all'},
u'outputs': {u'p_ctg': u'p_ctg.fa'},
u'parameters': {u'pypeflow_mb': 4000,
u'pypeflow_nproc': u'48',
u'topdir': u'../..'}}
2020-03-14 22:10:24,166 - root - INFO - CD: '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm' <- '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm'
2020-03-14 22:10:24,166 - root - DEBUG - Checking existence of u'concatenated-rid-to-phase/rid_to_phase.all' with timeout=30
2020-03-14 22:10:24,166 - root - DEBUG - Checking existence of u'../../1-preads_ovl/build/preads.db' with timeout=30
2020-03-14 22:10:24,166 - root - DEBUG - Checking existence of u'../../1-preads_ovl/las-merge-combine/las_fofn.json' with timeout=30
2020-03-14 22:10:24,166 - root - DEBUG - Checking existence of u'../../1-preads_ovl/db2falcon/preads4falcon.fasta' with timeout=30
2020-03-14 22:10:24,166 - root - DEBUG - Checking existence of u'template.sh' with timeout=30
2020-03-14 22:10:24,166 - root - INFO - CD: '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm' <- '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm'
2020-03-14 22:10:24,189 - root - INFO - $('/bin/bash user_script.sh')
hostname
+ hostname
pwd
+ pwd
date
+ date
# Substitution will be similar to snakemake "shell".
# TODO: Needs preads.db
rm -f ./ctg_paths
+ rm -f ./ctg_paths
python -m falcon_unzip.mains.ovlp_filter_with_phase_strict --fofn ../../1-preads_ovl/las-merge-combine/las_fofn.json --max-diff 120 --max-cov 120 --min-cov 1 --n-core 48 --min-len 2500 --db ../../1-preads_ovl/build/preads.db --rid-phase-map concatenated-rid-to-phase/rid_to_phase.all > preads.p_ovl
+ python -m falcon_unzip.mains.ovlp_filter_with_phase_strict --fofn ../../1-preads_ovl/las-merge-combine/las_fofn.json --max-diff 120 --max-cov 120 --min-cov 1 --n-core 48 --min-len 2500 --db ../../1-preads_ovl/build/preads.db --rid-phase-map concatenated-rid-to-phase/rid_to_phase.all
falcon-unzip 1.2.0 (pip thinks "falcon-unzip 1.2.0")
falcon-kit 1.3.0
pypeflow 2.2.0
Traceback (most recent call last):
File "/export/scratch1/home/vincent/software/miniconda3/envs/pacbio/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "/export/scratch1/home/vincent/software/miniconda3/envs/pacbio/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/falcon_unzip/mains/ovlp_filter_with_phase_strict.py", line 408, in <module>
main()
File "/export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/falcon_unzip/mains/ovlp_filter_with_phase_strict.py", line 404, in main
run(args)
File "/export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/falcon_unzip/mains/ovlp_filter_with_phase_strict.py", line 333, in run
arid2phase[row[0]] = (row[1], row[2], row[3]) # ctg_id, phase_blk_id, phase_id
IndexError: list index out of range
2020-03-14 22:10:24,355 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.
2020-03-14 22:10:24,355 - root - INFO - CD: '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm' -> '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm'
2020-03-14 22:10:24,355 - root - INFO - CD: '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm' -> '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm'
2020-03-14 22:10:24,356 - root - CRITICAL - Error in /export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/pypeflow/do_task.py with args="{'json_fn': '/export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm/task.json',\n 'timeout': 30,\n 'tmpdir': None}"
Traceback (most recent call last):
File "/export/scratch1/home/vincent/software/miniconda3/envs/pacbio/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "/export/scratch1/home/vincent/software/miniconda3/envs/pacbio/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/pypeflow/do_task.py", line 281, in <module>
main()
File "/export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/pypeflow/do_task.py", line 273, in main
run(**vars(parsed_args))
File "/export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/pypeflow/do_task.py", line 267, in run
run_cfg_in_tmpdir(cfg, tmpdir, '.')
File "/export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/pypeflow/do_task.py", line 242, in run_cfg_in_tmpdir
run_bash(bash_template, myinputs, myoutputs, parameters)
File "/export/scratch3/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/pypeflow/do_task.py", line 201, in run_bash
util.system(cmd)
File "/export/scratch1/home/vincent/software/miniconda3/envs/pacbio/lib/python2.7/site-packages/pypeflow/io.py", line 29, in syscall
raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
+++ pwd
++ echo 'FAILURE. Running top in /export/scratch3/vincent/project/TGS_assembly/other_assemblers/clr/mhc/25x/falconunzip/3-unzip/1-hasm (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 0m0.585s
user 0m0.296s
sys 0m0.141s
+ finish
+ echo 'finish code: 1'
HI, I run Falcon on pacbio reads successfully, but failed to run falcon-unzip. Here is the error report: It seems that errors occurred at this step 3-unzip/1-hasm. The file 'preads.p_ovl' is empty. could you please help me to solve this issue? Many thanks.
The log information in file 'run-P5d87a9de2f785c.bash.stderr' under this folder '3-unzip/1-hasm'