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maxwellsh / DIGDriver

Flexible and efficient tests for evidence of positive selection anywhere in the cancer genome.
BSD 3-Clause "New" or "Revised" License
23 stars 4 forks source link

Error when using Dig to annotate the mutation bed file #7

Open virdzek-g opened 7 months ago

virdzek-g commented 7 months ago

Hello,

I am getting an error when using Dig to annotate the mutation bed file created in step 1. Could you please help me find out what's wrong, please?

Best regards, Gabriela

DigPreprocess.py annotMutationFile ./input.bed ./reference_hg19_Homo_sapiens_assembly19.fasta output

Adding mutation function dyld[49721]: Library not loaded: @rpath/libgfortran.3.dylib Referenced from: <34EA1D6C-7BD3-38A2-9869-5FCB9627BA35> /Users/gv9/opt/anaconda3/envs/digdriver/lib/R/lib/libRblas.dylib Reason: tried: '/Users/gv9/opt/anaconda3/envs/digdriver/lib/R/lib/libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/R/lib/../../libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/R/lib/../../libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/opt/conda/conda-bld/r-base_1536076838216/work/lib/libgfortran.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/conda/conda-bld/r-base_1536076838216/work/lib/libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/R/bin/exec/../../../libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/opt/conda/conda-bld/r-base_1536076838216/work/lib/libgfortran.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/conda/conda-bld/r-base_1536076838216/work/lib/libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/R/bin/exec/../../../libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/R/lib/libgfortran.3.dylib' (no such file), '/Users/gv9/opt/anaconda3/envs/digdriver/lib/libgfortran.3.dylib' (no such file) Adding mutation context Reading in mutation file Traceback (most recent call last): File "/Users/gv9/opt/anaconda3/envs/digdriver/bin/DigPreprocess.py", line 366, in args.func(args) File "/Users/gv9/opt/anaconda3/envs/digdriver/bin/DigPreprocess.py", line 117, in annotMutationFile addMutationContext(args) File "/Users/gv9/opt/anaconda3/envs/digdriver/bin/DigPreprocess.py", line 82, in addMutationContext df_mut = mutation_tools.read_mutation_file(args.fmut, drop_duplicates=False) File "/Users/gv9/opt/anaconda3/envs/digdriver/lib/python3.7/site-packages/DIGDriver/data_tools/mutation_tools.py", line 48, in read_mutation_file with open(path) as f: FileNotFoundError: [Errno 2] No such file or directory: 'output.h5'

Gengchao-WANG commented 2 months ago

Have you solved the problem? I had no problem the first time I ran this program. However, when I re-installed conda and digdriver, I got this error and couldn't fix it.