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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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IOError #98

Closed panxiaoguang closed 3 years ago

panxiaoguang commented 3 years ago

When I run AA in docker, I use the commond 

/dellfsqd2/ST_LBI/USER/panxiaoguang/app/AmpliconArchitect/docker/run_aa_docker.sh --bam test.cs.rmdup.bam --bed test_AA_CNV_SEEDS.bed --out test --ref GRCh38

but I got some error 

Traceback (most recent call last):
  File "programs/AmpliconArchitect-master/src/AmpliconArchitect.py", line 96, in <module>
    logging.basicConfig(filename=args.outName[0] + '.log',level=logging.DEBUG)
  File "/usr/lib/python2.7/logging/__init__.py", line 1554, in basicConfig
    hdlr = FileHandler(filename, mode)
  File "/usr/lib/python2.7/logging/__init__.py", line 920, in __init__
    StreamHandler.__init__(self, self._open())
  File "/usr/lib/python2.7/logging/__init__.py", line 950, in _open
    stream = open(self.baseFilename, self.mode)
IOError: [Errno 13] Permission denied: '/home/output/test.log'

I don't know why? can you give me some instructions?

jluebeck commented 3 years ago

This is very likely an issue with read & write permissions for the directory - which is not something controlled by AA. More information about 'Permission denied' errors can be found in various Docker discussion threads on StackOverflow, etc. Please make sure that the real directory you are attempting to output to has global read/write permissions enabled.

Best, Jens

panxiaoguang commented 3 years ago

Thank you very much !