TypeError: unsupported operand type(s)
ianaebutler opened this issue · comments
Describe the bug
I am trying to run some Oxford Nanopore data and I am getting the following error message.
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
Error message
[1429643 INFO] 2023-06-01 10:59:19 NextDenovo start... [1429643 INFO] 2023-06-01 10:59:19 version:2.5.2 logfile:pid1429643.log.info [1429643 WARNING] 2023-06-01 10:59:19 Re-write workdir [1429643 INFO] 2023-06-01 10:59:19 skip mkdir: /home/ianbutler/NextDenovo/./ [1429643 INFO] 2023-06-01 10:59:19 mkdir: /home/ianbutler/NextDenovo/.//01.raw_align [1429643 INFO] 2023-06-01 10:59:19 mkdir: /home/ianbutler/NextDenovo/.//02.cns_align [1429643 INFO] 2023-06-01 10:59:19 mkdir: /home/ianbutler/NextDenovo/.//03.ctg_graph
And here is the traceback that has a bit more information
Traceback (most recent call last): File "./nextDenovo", line 857, in main(args) File "./nextDenovo", line 595, in main task.set_run(max_parallel_job=1, job_type=cfg['job_type'], use_drmaa=cfg['use_drmaa'], \ File "/usr/local/lib/python3.8/dist-packages/paralleltask/task_control.py", line 175, in set_run self.run = Cluster(self.jobs, max_parallel_job, self.shell, job_type, interval_time, \ File "/usr/local/lib/python3.8/dist-packages/paralleltask/task_control.py", line 202, in __init__ self.mem = self._parse_mem(str(mem)) File "/usr/local/lib/python3.8/dist-packages/paralleltask/task_control.py", line 239, in _parse_mem unit_cfg_fpath = os.getenv('LSF_ENVDIR') + "/lsf.conf" TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
Genome characteristics
Genome is about 200Mb. Not sure about other things
Input data
Number of bases: 188433154
mean read length: 1240
median read length: 563
N50: 2629
Config file
[General] job_type = lsf job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 2 input_type = raw read_type = ont input_fofn = ./CNIN4784input.fofn workdir = ./ [correct_option] read_cutoff = 1k genome_size = 200m pa_correction = 2 sort_options = -m 1g -t 2 minimap2_options_raw = -t 8 correction_options = -p 15 [assemble_option] minimap2_options_cns = -t 8 nextgraph_options = -a 1
Operating system
Ubuntu 20.04.4 LTS
GCC
gcc version 9.4.0
Python
Python 3.8.10
NextDenovo
nextDenovo 2.5.2
you can try to set job_type = local
or see here to set the environment variable: LSF_ENVDIR
.
Setting job_type = local
solved the problem. Thanks