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unknown error: An empty string is not a valid JSON string
published 15 Feb 2021, 18:16

Hi, I keep on getting these two errors when submitting PDB files: (1) "unknown error: An empty string is not a valid JSON string." and (2) unknown error: Net::ReadTimeout. I had submitted several PDB files with the same formatting this morning and they were working fine, but now none of my PDB files get scored properly. Any help would be appreciated. Thanks!

Hello Jahir: I am checking at the logs. You sure that file did not fail before?

Fragment 2: [' H3 ', ' H26'] File "molfile_to_params.py", line 1610, in <module> sys.exit(main(sys.argv[1:])) File "molfile_to_params.py", line 1582, in main num_frags = fragment_ligand(m) File "/molfile_to_params.py", line 660, in fragment_ligand raise ValueError("Fragment %i has %i atoms; merge with another fragment or add virtual atoms to make 3 total" % (frag_id, num_atoms)) ValueError: Fragment 2 has 2 atoms; merge with another fragment or add virtual atoms to make 3 total

Hi @nlopezcarranza. Yeah, I am sure it did not fail before. I actually just resubmitted a file that was scored successfully this morning and it has been idle for more than 18 minutes now (whereas it took about 4 minutes to get scored before). I had experienced a similar issue in the past and I think it might have something to do with the server doing the scoring?

can you send me the file to n.lopezcarranza@instadeep.com? Fragment 2 has 2 atoms; merge with another fragment or add virtual atoms to make 3 total does not ring a bell as an error?

Hi to all,

i am facing the same problem. Lately only a few submissions got evaluated and the majority of submissions got rejected. I wrote an mail considering this issue but unfortunately did not get an answer.

Philipp

Thanks. I've emailed you the file that was scored correctly in the morning but that now returns a scoring error