PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
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Falcon error in tan-split stage #157

Open madhubioinfo opened 4 years ago

madhubioinfo commented 4 years ago

This is my config file [General] use_tmpdir = /home/madhu/FALCON-examples pwatcher_type = blocking job_type = local job_queue = bash -C ${CMD} job_queue = bash -C ${CMD} > ${STDOUT_FILE} 2> ${STDERR_FILE}

input_fofn = input.fofn

input_type = raw

The length cutoff used for seed reads used for initial mapping

genome_size = 160000000 length_cutoff = -1 seed_coverage=60

The length cutoff used for seed reads usef for pre-assembly

length_cutoff_pr = 1

jobqueue = production

sge_option_da = sge_option_la = sge_option_pda = sge_option_pla = sge_option_fc = sge_option_cns =

pa_concurrent_jobs = 32 ovlp_concurrent_jobs = 32 pa_concurrent_jobs = 6 ovlp_concurrent_jobs = 6

pa_HPCdaligner_option = -v -B4 -t16 -e.70 -l1000 -s1000 ovlp_HPCdaligner_option = -v -B4 -t32 -h60 -e.96 -l500 -s1000

pa_daligner_option = -e.70 -l000 -s100 -k18 ovlp_daligner_option = -e.95 -s100 -k24

pa_DBsplit_option = -x500 -s100 ovlp_DBsplit_option = -s100

falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 6

overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 3 --bestn 10 --n_core 24

This is the error i am receiving it ir': '/home/madhu/FALCON-examples', 'job_type': 'local', 'job_queue': 'bash -C $ {CMD} > ${STDOUT_FILE} 2> ${STDERR_FILE}'}, use_tmpdir='/home/madhu/FALCON-examp les', squash=False, job_name_style=0 [INFO]Setting max_jobs to 8; was None [INFO]Num unsatisfied: 1, graph: 2 [INFO]About to submit: Node(0-rawreads/tan-split) [INFO]Popen: 'bash -C /home/madhu/anaconda3/lib/python3.6/site-packages/pwatcher /mains/job_start.sh > /home/madhu/FALCON-examples/0-rawreads/tan-split/run-P1da4 877e9b6224.bash.stdout 2> /home/madhu/FALCON-examples/0-rawreads/tan-split/run-P 1da4877e9b6224.bash.stderr' [INFO](slept for another 0.0s -- another 1 loop iterations) [INFO](slept for another 0.30000000000000004s -- another 2 loop iterations) [ERROR]Task Node(0-rawreads/tan-split) failed with exit-code=1 [ERROR]Some tasks are recently_done but not satisfied: {Node(0-rawreads/tan-spli t)} [ERROR]ready: set() submitted: set() [ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on S IGTERM. Traceback (most recent call last): File "/home/madhu/anaconda3/bin/fc_run", line 11, in load_entry_point('falcon-kit==1.4.4', 'console_scripts', 'fc_run')() File "/home/madhu/anaconda3/lib/python3.6/site-packages/falcon_kit/mains/run1. py", line 706, in main main1(argv[0], args.config, args.logger) File "/home/madhu/anaconda3/lib/python3.6/site-packages/falcon_kit/mains/run1. py", line 73, in main1 input_fofn_fn=input_fofn_fn, File "/home/madhu/anaconda3/lib/python3.6/site-packages/falcon_kit/mains/run1. py", line 235, in run dist=Dist(NPROC=4, MB=4000, job_dict=config['job.step.da']), File "/home/madhu/anaconda3/lib/python3.6/site-packages/falcon_kit/pype.py", l ine 109, in gen_parallel_tasks wf.refreshTargets() File "/home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/simple_pwatch er_bridge.py", line 278, in refreshTargets self._refreshTargets(updateFreq, exitOnFailure) File "/home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/simple_pwatch er_bridge.py", line 362, in _refreshTargets raise Exception(msg) Exception: Some tasks are recently_done but not satisfied: {Node(0-rawreads/tan- split)}

when i check the std.err file in tan-split directory this is what i found [WARNING]Call 'bash -vex split.sh' returned 256. Traceback (most recent call last): File "/home/madhu/anaconda3/lib/python3.6/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/home/madhu/anaconda3/lib/python3.6/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/madhu/anaconda3/lib/python3.6/site-packages/falcon_kit/mains/dazzler.py", line 1532, in main() File "/home/madhu/anaconda3/lib/python3.6/site-packages/falcon_kit/mains/dazzler.py", line 1528, in main args.func(args) File "/home/madhu/anaconda3/lib/python3.6/site-packages/falcon_kit/mains/dazzler.py", line 1055, in cmd_tan_split tan_split(ours, args.config_fn, args.db_fn, args.split_fn, args.bash_template_fn) File "/home/madhu/anaconda3/lib/python3.6/site-packages/falcon_kit/mains/dazzler.py", line 310, in tan_split io.syscall('bash -vex {}'.format(script_fn)) File "/home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/io.py", line 27, in syscall raise Exception(msg) Exception: Call 'bash -vex split.sh' returned 256. 2019-12-11 19:03:55,273 - root - WARNING - Call '/bin/bash user_script.sh' returned 256. 2019-12-11 19:03:55,274 - root - INFO - CD: '/home/madhu/FALCON-examples/madhu/pypetmp//home/madhu/FALCON-examples/0-rawreads/tan-split' -> '/home/madhu/FALCON-examples/0-rawreads/tan-split' 2019-12-11 19:03:55,275 - root - INFO - CD: '/home/madhu/FALCON-examples/0-rawreads/tan-split' -> '/home/madhu/FALCON-examples/0-rawreads/tan-split' 2019-12-11 19:03:55,275 - root - CRITICAL - Error in /home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/do_task.py with args="{'json_fn': '/home/madhu/FALCON-examples/0-rawreads/tan-split/task.json',\n 'timeout': 30,\n 'tmpdir': '/home/madhu/FALCON-examples'}" Traceback (most recent call last): File "/home/madhu/anaconda3/lib/python3.6/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/home/madhu/anaconda3/lib/python3.6/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 280, in main() File "/home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 272, in main run(**vars(parsed_args)) File "/home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 266, in run run_cfg_in_tmpdir(cfg, tmpdir, '.') File "/home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 241, in run_cfg_in_tmpdir run_bash(bash_template, myinputs, myoutputs, parameters) File "/home/madhu/anaconda3/lib/python3.6/site-packages/pypeflow/do_task.py", line 200, in run_bash util.system(cmd) File "/home/madhu/anaconda3/lib/python3.6/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/madhu/FALCON-examples/0-rawreads/tan-split (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 0m0.975s user 0m0.619s sys 0m0.289s

Can you help me in resolving this?