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J35P312 / TIDDIT

TIDDIT - structural variant calling
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Change read/write to read-only for reading ref #8

Closed countdigi closed 6 years ago

countdigi commented 6 years ago

We are running into the following exception: 

working on seqence chrUn_JTFH01001997v1_decoy                                                                                                                           
working on seqence chrUn_JTFH01001998v1_decoy                                                                                                                           
variant calling time consumption= 14s                                                                                                                                   
Traceback (most recent call last):                                                                                                                                      
  File "/TIDDIT/TIDDIT.py", line 54, in <module>                                                                                                                        
    TIDDIT_clustering.cluster(args)                                                                                                                                     
  File "/TIDDIT/TIDDIT_clustering.py", line 668, in cluster                                                                                                             
    Ncontent,sequence_length=retrieve_N_content(args)                                                                                                                   
  File "/TIDDIT/TIDDIT_clustering.py", line 638, in retrieve_N_content                                                                                                  
    with open(args.ref, 'r+') as f:                                                                                                                                     
IOError: [Errno 13] Permission denied: '/shares/hii/bioinfo/ref/gotcloud/hs38DH-db142-v1/hs38DH.fa'

Removing the + from r+ mode allows reading files without having write permission.

J35P312 commented 6 years ago

That's great, thanks a lot!