I have a problem reading my bam files with samtools. Whenever I try to run the code
samtools view your_file.bam
it tells me
dyld[69540]: Library not loaded: @rpath/libdeflate.so
Referenced from: <D6D57EAF-7BCE-33F1-B9CE-57A7A42BD16D> /Users/faleevamaria/anaconda3/envs/ARTDeco/bin/samtools
Reason: tried: '/Users/faleevamaria/anaconda3/envs/ARTDeco/bin/../lib/libdeflate.so' (no such file), '/Users/faleevamaria/anaconda3/envs/ARTDeco/bin/../lib/libdeflate.so' (no such file), '/usr/local/lib/libdeflate.so' (no such file), '/usr/lib/libdeflate.so' (no such file, not in dyld cache)
Abort trap: 6
Following this back, I tried to check
samtools --version
and got the same error message (even though I see the updated package when I type in conda list)
I then tried to check the library path:
otool -L /Users/faleevamaria/anaconda3/envs/ARTDeco/bin/samtools
and got:
/Users/faleevamaria/anaconda3/envs/ARTDeco/bin/samtools:
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
@rpath/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
@rpath/libbz2.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/liblzma.5.dylib (compatibility version 8.0.0, current version 8.3.0)
@rpath/libdeflate.so (compatibility version 0.0.0, current version 0.0.0)
@rpath/libcurl.4.dylib (compatibility version 10.0.0, current version 10.0.0)
@rpath/libncursesw.5.dylib (compatibility version 5.0.0, current version 5.0.0)
@rpath/libcrypto.1.0.0.dylib (compatibility version 1.0.0, current version 1.0.0)
I think the problem is with the libdeflate.so, which says its not installed (even though I also see the updated version in my conda list).
I have tried all variations of libderflate and samtools installation/reinstallation, but nothing seems to be doing the trick. Any insight would be greatly appreciated.