Because we emit the log path and the job ID together, setting cluster cancel to bkill fails with
Terminating processes on user request, this might take some time.
Traceback (most recent call last):
File "/homes/mbhall88/.config/snakemake/lsf/lsf_status.py", line 232, in <module>
print(lsf_status_checker.get_status())
File "/homes/mbhall88/.config/snakemake/lsf/lsf_status.py", line 156, in get_status
status = self._query_status_using_bjobs()
File "/homes/mbhall88/.config/snakemake/lsf/lsf_status.py", line 99, in _query_status_using_bjobs
output_stream, error_stream = OSLayer.run_process(self.bjobs_query_cmd)
File "/homes/mbhall88/.config/snakemake/lsf/OSLayer.py", line 40, in run_process
completed_process = subprocess.run(
File "/hps/software/users/iqbal/mbhall/miniconda3/envs/who-correspondence/lib/python3.10/subprocess.py", line 503, in run
stdout, stderr = process.communicate(input, timeout=timeout)
File "/hps/software/users/iqbal/mbhall/miniconda3/envs/who-correspondence/lib/python3.10/subprocess.py", line 1149, in communicate
stdout, stderr = self._communicate(input, endtime, timeout)
File "/hps/software/users/iqbal/mbhall/miniconda3/envs/who-correspondence/lib/python3.10/subprocess.py", line 2000, in _communicate
ready = selector.select(timeout)
File "/hps/software/users/iqbal/mbhall/miniconda3/envs/who-correspondence/lib/python3.10/selectors.py", line 416, in select
fd_event_list = self._selector.poll(timeout)
KeyboardInterrupt
3399781 logs/cluster/download_data/proj=PRJNA650381.sample=SAMN27765622.run=SRR18914164/jobid258_ff07f69d-f434-4b59-99f1-3f65c066bf08.out: Illegal job ID.
1 out of 1 calls to --cluster-cancel failed. This is safe to ignore in most cases.
I guess we just can't emit the log path with the job ID.
@leoisl maybe we could emit the log path to stderr?
Because we emit the log path and the job ID together, setting cluster cancel to
bkillfails withI guess we just can't emit the log path with the job ID.
@leoisl maybe we could emit the log path to stderr?