extended.mtf not found

[TaufiqIslamProtick]

Dear Professor Adhikari

This is not an issue. It is just an error I am facing. The README part section 5.2 runs a script with parameters that takes input a sequence, contacts and secondary structure data and other related parameters to run the program. Everything up to this point runs without any errors. When this line is run in the terminal, 1.error.png (bold yellow box) happens. When I checked the output folder I saw in 2.extended.mtf.png(bold green box) that the extended.mtf file is created. (Although the timestamp in the two images are different, extended.mtf is created every time I run the shell script written at README Section 5.2).
Did I miss something, or does it need a special fix to run it properly in my local computer? It would be so kind of you if you shared your insights. I am attaching the snapshots for your convenience.

Best Regards
Taufiq Islam Protick

[badriadhikari]

Hi,

I accept that this is some kind of a bug (when CNS is installed in some OSs) that I myself don't understand fully. I remember installing CNS in a local Ubuntu system in our lab and we had encountered an issue similar to this. For some reason, the mtf files are not fully written to the disk, and the program continues looking for the files. I got around the issue by adding a wait()/sleep() after the mtf generation so that we wait until the mtf files are written. Waiting for 1 minute for a protein of length 100, and 2 minutes for a protein of length 200 (and so on) may be a good choice. Let us know the cause of this issue if you happen to find.

Thank you,
Badri Adhikari

[TaufiqIslamProtick]

Dear Professor Adhikari
Thank you so much for your reply. I will try the sleep() command in the confold.pl file.
Best Regards
Taufiq Islam Protick

[grandrea]

Hello,
Just to follow up on this. The issue seems to be a typo in the line:

system_cmd("./job.sh", "job.log");

This has the effect of sending job sh to background in my case, so the program continues before job.sh is done. If this is replaced with

system_cmd("./job.sh > job.log");

The program will wait for job.sh to finish.

I am also on Ubuntu

[badriadhikari]

Thank you.