prep.losoto_plot_RM.losot_plot - file existing error

Hi,

Running the latest master of linc (together with latest singularity) on a completely new run I can the following error:

[lotss-tshimwell@ui-01 L2005609]$ cat failed_CWLJob_prep.losoto_plot_RM.losoto_plot_kind--CWLJob-instance--kjg0k_48_v1000.log 
[2024-02-05T12:26:37+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2024-02-05T12:26:37+0100] [MainThread] [I] [toil] Running Toil version 5.9.2-54bfe0b146b76ecc6221de384c255e1be89547c6 on host wn-dc-03.spider.surfsara.nl.
[2024-02-05T12:26:37+0100] [MainThread] [I] [toil.worker] Working on job 'CWLJob' prep.losoto_plot_RM.losoto_plot kind-CWLJob/instance-kjg0k_48 v1
[2024-02-05T12:26:37+0100] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' prep.losoto_plot_RM.losoto_plot kind-CWLJob/instance-kjg0k_48 v1) from description 'CWLJob' prep.losoto_plot_RM.losoto_plot kind-CWLJob/instance-kjg0k_48 v1
[2024-02-05T12:26:37+0100] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/lotss/Software/linc-master//pull
[2024-02-05T12:26:38+0100] [MainThread] [I] [cwltool] [job prep.losoto_plot_RM.losoto_plot] /project/lotss/Software/linc-master/detailed-logs/L2005609/L2005609ns69cg87$ singularity \
    --quiet \
    exec \
    --contain \
    --ipc \
    --cleanenv \
    --userns \
    --home \
    /project/lotss/Software/linc-master/detailed-logs/L2005609/L2005609ns69cg87:/DpUURT \
    --bind \
    /project/lotss/Software/linc-master/tmpdir/L2005609/7zlb0jy9:/tmp \
    --bind \
    /project/lotss/Software/linc-master/detailed-logs/L2005609/L2005609w0xoi_cc/cal_solutions.h5:/DpUURT/cal_solutions.h5:ro \
    --pwd \
    /DpUURT \
    --net \
    --network \
    none \
    /project/lotss/Software/linc-master/pull/astronrd_linc.sif \
    bash \
    run_losoto_plot.sh > /project/lotss/Software/linc-master/detailed-logs/L2005609/L2005609ns69cg87/cal_solutions.h5-losoto.log 2> /project/lotss/Software/linc-master/detailed-logs/L2005609/L2005609ns69cg87/cal_solutions.h5-losoto_err.log
[2024-02-05T12:26:41+0100] [MainThread] [W] [cwltool] [job prep.losoto_plot_RM.losoto_plot] exited with status: 1
[2024-02-05T12:26:41+0100] [MainThread] [W] [cwltool] [job prep.losoto_plot_RM.losoto_plot] completed permanentFail
Traceback (most recent call last):
  File "/home/lotss-tshimwell/.local/lib/python3.9/site-packages/toil/worker.py", line 403, in workerScript
    job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
  File "/home/lotss-tshimwell/.local/lib/python3.9/site-packages/toil/job.py", line 2743, in _runner
    returnValues = self._run(jobGraph=None, fileStore=fileStore)
  File "/home/lotss-tshimwell/.local/lib/python3.9/site-packages/toil/job.py", line 2660, in _run
    return self.run(fileStore)
  File "/home/lotss-tshimwell/.local/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2301, in run
    raise cwl_utils.errors.WorkflowException(status)
cwl_utils.errors.WorkflowException: permanentFail
[2024-02-05T12:26:41+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-dc-03.spider.surfsara.nl

Looking at the error log that it points to I see:

[lotss-tshimwell@ui-01 L2005609]$ cat /project/lotss/Software/linc-master/detailed-logs/L2005609/L2005609ns69cg87/cal_solutions.h5-losoto_err.log
Traceback (most recent call last):
  File "/usr/local/bin/losoto", line 141, in <module>
    H = h5parm(args.h5parm, readonly=False)
  File "/usr/local/lib/python3.8/dist-packages/losoto/h5parm.py", line 80, in __init__
    self.H = tables.open_file(h5parmFile, 'r+', IO_BUFFER_SIZE=1024*1024*10, BUFFER_TIMES=500)
  File "/usr/local/lib/python3.8/dist-packages/tables/file.py", line 300, in open_file
    return File(filename, mode, title, root_uep, filters, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/tables/file.py", line 750, in __init__
    self._g_new(filename, mode, **params)
  File "tables/hdf5extension.pyx", line 366, in tables.hdf5extension.File._g_new
  File "/usr/local/lib/python3.8/dist-packages/tables/utils.py", line 173, in check_file_access
    raise PermissionError(f"file ``{path}`` exists but it can not be written")
PermissionError: file ``/DpUURT/cal_solutions.h5`` exists but it can not be written
[lotss-tshimwell@ui-01 L2005609]$