33 hidden (binary) files mixed in with the profile HMMs in zenodo release
Thanks for maintaining this important resource!
I downloaded the pHMMs (https://zenodo.org/records/8303752/files/genomad_hmm_v1.4.tar.gz), unzipped, cat'ed the hmms into a single file, and ran into errors parsing the resulting file. After a bit of exploring, I discovered that there are 33 hidden (dot) files containing binary data that appears to be macOS extended attribute metadata. No surprise that this broke the parser.
Here's the list of bad files:
$ ls genomad_hmm_v1.4/.*
genomad_hmm_v1.4/._GENOMAD.010213.VV.hmm genomad_hmm_v1.4/._GENOMAD.131272.VV.hmm
genomad_hmm_v1.4/._GENOMAD.021413.VV.hmm genomad_hmm_v1.4/._GENOMAD.148443.CP.hmm
genomad_hmm_v1.4/._GENOMAD.029760.CC.hmm genomad_hmm_v1.4/._GENOMAD.152688.VP.hmm
genomad_hmm_v1.4/._GENOMAD.030674.VV.hmm genomad_hmm_v1.4/._GENOMAD.153683.CP.hmm
genomad_hmm_v1.4/._GENOMAD.038591.CC.hmm genomad_hmm_v1.4/._GENOMAD.161173.CP.hmm
genomad_hmm_v1.4/._GENOMAD.038728.VV.hmm genomad_hmm_v1.4/._GENOMAD.165501.VV.hmm
genomad_hmm_v1.4/._GENOMAD.041967.VV.hmm genomad_hmm_v1.4/._GENOMAD.178846.CP.hmm
genomad_hmm_v1.4/._GENOMAD.045173.VV.hmm genomad_hmm_v1.4/._GENOMAD.183786.PC.hmm
genomad_hmm_v1.4/._GENOMAD.046653.CC.hmm genomad_hmm_v1.4/._GENOMAD.192394.PC.hmm
genomad_hmm_v1.4/._GENOMAD.052159.VV.hmm genomad_hmm_v1.4/._GENOMAD.196542.VC.hmm
genomad_hmm_v1.4/._GENOMAD.056799.CC.hmm genomad_hmm_v1.4/._GENOMAD.201756.VV.hmm
genomad_hmm_v1.4/._GENOMAD.074512.VV.hmm genomad_hmm_v1.4/._GENOMAD.206299.CP.hmm
genomad_hmm_v1.4/._GENOMAD.081590.VV.hmm genomad_hmm_v1.4/._GENOMAD.209284.CP.hmm
genomad_hmm_v1.4/._GENOMAD.090714.VV.hmm genomad_hmm_v1.4/._GENOMAD.212530.PC.hmm
genomad_hmm_v1.4/._GENOMAD.100916.VV.hmm genomad_hmm_v1.4/._GENOMAD.216678.VV.hmm
genomad_hmm_v1.4/._GENOMAD.108446.VV.hmm genomad_hmm_v1.4/._GENOMAD.222359.VV.hmm
genomad_hmm_v1.4/._GENOMAD.109562.CP.hmm
Here's one way to see the contents of one of the files
$ cat genomad_hmm_v1.4/._GENOMAD.222359.VV.hmm
Mac OS X 2��ATTR��H�Hcom.apple.maclpZ%�A@�SO���b�
I can clean them up myself, of course, but it would be good to ensure that the hidden files are removed in the next release.
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