failure to find temporary file when using stride()

[Emilio Xavier Esposito]

Hi
I am looping over a collection of PDB files with the stride() function and get the following message:

Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/var/folders/38/w9bn0kr52mgbmj5dt9nmxytw0000gn/T//Rtmp6FQbB9/fileeaa43a616372': No such file or directory

The message is returned after several successful completions of the command for several PDB files, so I know the temporary files are being created and read (by STRIDE and R). I have modified the stride() function to include a Sys.sleep(time=1) after the input PDB file is written and after the STRIDE program is called in an attempt to make sure there is ample time for data to be written. Through print statements it appears the problem is reading the resulting STRIDE output file. I have even tried the setting the temporary directory via the tempfile(tmpdir="/Users/emilio/tmp") option and defining a specific file names for the input PDB and STRIDE results files. None of these modifications remedy the problem. The failing PDB file has been different for each of the errors, thus it is unlikely the PDB file is the cause of the failure. Also, running STRIDE from the macOS command line on the offending PDB file returns a complete STRIDE output file.

I realize this is likely not a problem with stride(), but wonder if anyone has a similar experience and how they fixed it. I have done several Google searches about these types of errors with little useful information.

I am using the latest bio3d (v 2.3-4) in R (v 3.6.0) on macOS (v 10.14.5; iMac with an OWC Mercury EXTREME Pro 6G SSD and ~1.1 TB available).

Thank you for your help
Emilio

[Xinqiu Yao]

Hi Emilio,

‌

Have you tried to call stride directly from terminal? It will tell whether it was the failure of the stride program itself or an issue in the stride() function.

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If you don’t mind, you can also attach a pdb file that caused the problem for us to take a look.

[Emilio Xavier Esposito]

Hi Xinqiu
Thank you for the suggestion.

macOS 10.14.5
I created a shell script to loop over a directory/folder of PDB files: Same results of various PDB files failing to be evaluated. Rebooted, recompiled STRIDE, re-ran the script: Same results of various PDB files failing to be evaluated. The STRIDE script returns the command being executed when processing a directory of PDB files. For each failed PDB file I was able to successfully re-run the STRIDE analysis using provided command. The ability to successfully evaluate PDB files individually indicates, to me, that the files are okay.

Ubuntu Linux
Installed STRIDE on a Linux virtual machine, ran script: all PDB files were correctly evaluated.

I feel like there is likely a problem concerning STRIDE complied on macOS, but it is beyond my abilities. I will email the STRIDE maintainers and ask for assistance.

Thank you for everyone’s help!
Emilio

[Emilio Xavier Esposito]

Not a bio3d problem. Likely related to compiling STRIDE on macOS.

[Emilio Xavier Esposito]

Not a bio3d problem.