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Questions and answers > RNA structures (DSSR)
Turn of Auxiliary File Creation (x3dna-dssr)
saladi:
Dear DSSR Community,
Is is possible to turn of the generation of the auxiliary files by x3dna-dssr? I am interested in the output given in the command line only at this time as I analyze the frames of a MD trajectory.
Alternatively, does x3dna-dssr use these auxiliary files created in the process of calculating the parameters printed?
Thanks,
Shyam
xiangjun:
Hi Shyam,
It'd certainly be possible to turn off the various auxiliary files generatd with DSSR -- there are actually more than you see by default. However, I do not see the point of why bother of doing so. For one thing, the files have fixed file names, and thus would be overwritten each time. Second, the auxiliary files are created in parallel to the main output file, and have been proven to be of general use. Third, along the same line, the main DSSR ouput itself is likely to contain more parameters than you'd be interested in, especially with the --more option turned on. Why not simply select the portion that are relevent to your project, and ignore the rest?
If there is sufficient interest, I'd consider to add a new option so users can control whether to produce the auxiliary files. Does anyone else have such a need?
HTH,
Xiang-Jun
chemikeris:
I have a also a question related to auxiliary files created by DSSR.
In current version (I use v1.7.4-2018jan30) creation of these files may be regulated by '--prefix' option which is useful if you are interested only in the main output file. However, we have noticed that DSSR also creates a file named 'x3dna-dssr.log' in the directory from which it is run. It causes problems when running multiple instances of DSSR in parallel (for example, on a high-performance cluster), because for some processes we get an error message like this:
--- Code: ---remove_file failed: x3dna-dssr.log
--- End code ---
I do not know what is happening but probably some other DSSR process has already removed the file in the cases when this message appears?
Now I solved this problem by changing the working directory before calling DSSR in my script, but in general the problem persists, so I think that you should know it :-) Please contact me, if you need some additional information.
Regards,
Justas
xiangjun:
Hi Justas,
Thanks for reporting the issue when running DSSR in parallel. Please try the following DSSR options in your script, and report back it does the trick.
--- Code: -----auxfile=no --parallel
--- End code ---
Best regards,
Xiang-Jun
chemikeris:
Hello.
I see that using "--auxfile=no" does not create any auxiliary files. When using "--parallel" , the x3dna-dssr.log file is created but not deleted. Probably it works as the authors expected :-)
Maybe the real problem is that this behavior and the command line options are not described in the manual of the software? The options were available in the DSSR version I had in my computer, update was not necessary, but I did not find any information about that in the PDF manual.
Regards,
Justas
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
