PermissionError in circos

[qukunjing]

Dear rengang,
When I run centomics in slurm, there is an unexpected error happened. The log as follows

23-11-27 20:38:34 [INFO] Command: /data/00/user/user225/mambaforge/envs/RepCent/bin/centromics -l hifi.fq.gz -g csa.t2t.fa -p 40
23-11-27 20:38:34 [INFO] Version: 0.3                                         
23-11-27 20:38:34 [INFO] Arguments: {'genome': 'csa.t2t.fa', 'long': ['hifi.fq.gz'], 'hic': None, 'chip': None, 'prefix': 'centomics', 'outdir': 'cent-output', 'tmpdir': 'tmp', 'subsample_x
': 5, 'subsample_n': 100000, 'trf_opts': '1 1 2 80 5 200 2000 -d -h', 'min_cov': 0.9, 'min_len': 100, 'min_monomer_len': 1, 'clust_opts': '-m jaccard -k 15 -c 0.2 -x 2 -I 2', 'min_ratio': 0
.1, 'window_size': 200000, 'chr_prefix': 'chr[\\dXYZW]+', 'ncpu': 40, 'cleanup': False, 'overwrite': False}                                                                                 
23-11-27 20:38:34 [INFO] ##Step: Processing long reads data     
23-11-27 20:38:48 [INFO] Check point file: `/data/01/user178/04.Csa.v2/13.t2t/tmp/centomics.centomics.trf.count.ok` exists; skip this step
23-11-27 20:38:48 [INFO] Copy `/data/00/user/user225/mambaforge/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/circos` to `/data/01/user178/04.Csa.v2/13.t2t/ce
nt-output`                                        
23-11-27 20:39:15 [INFO] run CMD: `cd /data/01/user178/04.Csa.v2/13.t2t/cent-output/centomics.circos && circos -conf ./circos.conf`
Traceback (most recent call last):                              
  File "/data/00/user/user225/mambaforge/envs/RepCent/bin/centromics", line 33, in <module>
    sys.exit(load_entry_point('Centromics==0.3', 'console_scripts', 'centromics')())
  File "/data/00/user/user225/mambaforge/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/pipe.py", line 272, in main
    pipeline.run()                               
  File "/data/00/user/user225/mambaforge/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/pipe.py", line 133, in run
    self.run_circos(tr_bed=tr_bed, tr_labels=tr_labels,     
  File "/data/00/user/user225/mambaforge/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/pipe.py", line 153, in run_circos
    Circos.centomics_plot(self.genome, wkdir, *args, **kargs)
  File "/data/00/user/user225/mambaforge/envs/RepCent/lib/python3.8/site-packages/Centromics-0.3-py3.8.egg/Centromics/Circos.py", line 399, in centomics_plot                               
    os.link(figfile, dstfig)                                                                                                                                                                
PermissionError: [Errno 1] Operation not permitted: '/data/01/user178/04.Csa.v2/13.t2t/cent-output/centomics.circos/circos.png' -> '/data/01/user178/04.Csa.v2/13.t2t/cent-output/centomics.c
ircos.png'

best,
kunjing

[zhangrengang]

I may have fixed the bug. You may try again.