Sequence Tolerance Failed – Rosetta Commons

This topic has 18 replies, 3 voices, and was last updated 7 years, 11 months ago by Anonymous.

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- January 3, 2017 at 3:13 pm #2557
  Anonymous
  Dear all,
  
  I submitted six jobs to Rosie (28069 through 28074) under the username dstork. They failed quickly with no error messages beyond “Failed * Tech support has been notified of this error” anywhere that I can see. After waiting a few weeks the issue hasn’t been resolved. What can I do to get this job to work?
  
  Thanks,
  
  -Devon
- January 3, 2017 at 3:45 pm #12051
  Anonymous
  I looked at the first one. The PDB has at least one flaw: the TER card inserted between chains didn’t get an endline character, so it looks like this:
  
  ATOM 4278 2HA GLY A 314 -22.943 -27.890 -53.537 1.00 0.00
  
  TERATOM 37105 CA LYS B 2 -5.906 -14.805 -49.957 1.00 0.00
  
  ATOM 37106 C LYS B 2 -6.439 -13.943 -51.110 1.00 0.00
  
  I guess that could be the problem, especially if that was a residue you were working with.
- January 3, 2017 at 3:45 pm #12572
  Anonymous
  I looked at the first one. The PDB has at least one flaw: the TER card inserted between chains didn’t get an endline character, so it looks like this:
  
  ATOM 4278 2HA GLY A 314 -22.943 -27.890 -53.537 1.00 0.00
  
  TERATOM 37105 CA LYS B 2 -5.906 -14.805 -49.957 1.00 0.00
  
  ATOM 37106 C LYS B 2 -6.439 -13.943 -51.110 1.00 0.00
  
  I guess that could be the problem, especially if that was a residue you were working with.
- January 3, 2017 at 3:45 pm #13093
  Anonymous
  I looked at the first one. The PDB has at least one flaw: the TER card inserted between chains didn’t get an endline character, so it looks like this:
  
  ATOM 4278 2HA GLY A 314 -22.943 -27.890 -53.537 1.00 0.00
  
  TERATOM 37105 CA LYS B 2 -5.906 -14.805 -49.957 1.00 0.00
  
  ATOM 37106 C LYS B 2 -6.439 -13.943 -51.110 1.00 0.00
  
  I guess that could be the problem, especially if that was a residue you were working with.
- January 6, 2017 at 4:27 pm #12059
  Anonymous
  Thank you for your fast response, that was a good catch. I fixed the TER issue, resubmitted (28417–28422) and got the same problem. Could the issue be that between Chain A & Chain B the atom number jumps from 4278 to 37105 because this was originally a much larger file?
  
  Thanks.
- January 6, 2017 at 4:27 pm #12580
  Anonymous
  Thank you for your fast response, that was a good catch. I fixed the TER issue, resubmitted (28417–28422) and got the same problem. Could the issue be that between Chain A & Chain B the atom number jumps from 4278 to 37105 because this was originally a much larger file?
  
  Thanks.
- January 6, 2017 at 4:27 pm #13101
  Anonymous
  Thank you for your fast response, that was a good catch. I fixed the TER issue, resubmitted (28417–28422) and got the same problem. Could the issue be that between Chain A & Chain B the atom number jumps from 4278 to 37105 because this was originally a much larger file?
  
  Thanks.
- January 7, 2017 at 4:36 pm #12061
  Anonymous
  Sergey showed me a log file I couldn’t find that shows there’s a bug in the script being run. No idea when it can be fixed.
- January 7, 2017 at 4:36 pm #12582
  Anonymous
  Sergey showed me a log file I couldn’t find that shows there’s a bug in the script being run. No idea when it can be fixed.
- January 7, 2017 at 4:36 pm #13103
  Anonymous
  Sergey showed me a log file I couldn’t find that shows there’s a bug in the script being run. No idea when it can be fixed.
- January 9, 2017 at 2:25 pm #12063
  Anonymous
  Thank you for the information and the help.
  
  I will pursue other ways of doing the same computation, but I still hope to run it here eventually.
- January 9, 2017 at 2:25 pm #12584
  Anonymous
  Thank you for the information and the help.
  
  I will pursue other ways of doing the same computation, but I still hope to run it here eventually.
- January 9, 2017 at 2:25 pm #13105
  Anonymous
  Thank you for the information and the help.
  
  I will pursue other ways of doing the same computation, but I still hope to run it here eventually.
- January 10, 2017 at 12:37 am #12067
  Anonymous
  Script is not fixed but only “positive” result is that app is now terminated silently. I am contacting original auhor of this app so maybe he will know what going on here…
- January 10, 2017 at 12:37 am #12588
  Anonymous
  Script is not fixed but only “positive” result is that app is now terminated silently. I am contacting original auhor of this app so maybe he will know what going on here…
- January 10, 2017 at 12:37 am #13109
  Anonymous
  Script is not fixed but only “positive” result is that app is now terminated silently. I am contacting original auhor of this app so maybe he will know what going on here…
- January 6, 2017 at 4:48 pm #12060
  Anonymous
  I expect not. Rosetta ignores atom numbers in all cases of which I am aware. It pays close attention to RESIDUES and their numbering, but not the atom numbers.
  
  There don’t seem to be log files for me to diagnose further. Maybe there’s a missing executable or something server side. I’ll bring it Sergey’s attention.
- January 6, 2017 at 4:48 pm #12581
  Anonymous
  I expect not. Rosetta ignores atom numbers in all cases of which I am aware. It pays close attention to RESIDUES and their numbering, but not the atom numbers.
  
  There don’t seem to be log files for me to diagnose further. Maybe there’s a missing executable or something server side. I’ll bring it Sergey’s attention.
- January 6, 2017 at 4:48 pm #13102
  Anonymous
  I expect not. Rosetta ignores atom numbers in all cases of which I am aware. It pays close attention to RESIDUES and their numbering, but not the atom numbers.
  
  There don’t seem to be log files for me to diagnose further. Maybe there’s a missing executable or something server side. I’ll bring it Sergey’s attention.
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