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AbinitioRelax usage (3.4)

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AbinitioRelax usage (3.4)

I'm trying to run AbinitioRelax on a cluster (remotely), but I keep getting the error that there is no such file or directory when the executable tries to release. My command is as follows:

../../rosetta_source/src/apps/public/AbinitioRelax.linuxgccrelease -database ../../rosetta_database -in:file:fasta ./"Rosetta files"/pin.fasta in:file:frag3 ../"Rosetta files"/aat000_03_05.200_v1_3 -in:file:frag9 ../"Rosetta files"/aat000_09_05.200_v1_3 -abinitio:relax -relax:fast -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5 -user_filters true -psipred_ss2 ../"Rosetta files"/t000_.psipred_ss2 -kill_hairpins ./input_files/1elwA.psipred_ss2 -out:pdb pin.pdb -nstruct 10

I adapted the paths to the input files as necessary and changed the output to pdb instead of silent. Otherwise, this is pretty much verbatim the set of "optimal performance" commands as given in the documentation on the AbinitioRelax page. I ran both the /../../bin/AbinitioRelax.linuxgccrelease (as presented in the documentation) and what is shown above, since that was what was given as the path to the executable in the documentation's text. I'm executing from the Rosetta home directory (if you ls you see all the main directories, as well as the directory to my input files). What's wrong with my picture? I'm fairly new at linux, and even newer at using suites like these, so if the error is trivial and obvious, apologies.

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Fri, 2012-10-12 13:38

Make your path for the executable be rosetta_source/bin/AbinitioRelax.linuxgccrelease. You will need to fix the start of the path to make it proper relative to your run directory; for example if home is ~ and you're in ~/my_project and rosetta is in ~/rosetta, then you'd use ~/rosetta/rosetta_source/bin/AbinitioRelax.linuxgccrelease, or /home/atruong/rosetta/rosetta_source/bin/AbinitioRelax.linuxgccrelease if you prefer an absolute path).

My second guess is that it's choking on the use of a directory name with double quotes and a space. Your life will be MUCH easier if you change the directory name "Rosetta files" to rosetta_files or something similar (no quotes, no punctuation except underscore). This is a general rule for all file and directory names in command-line-mediated systems (Linux, unix, Macs where you use terminal).

You should spend some time reading about how paths work in a command line environment. For example, ./ does nothing - it just means "in the current directory", which can be omitted in most cases.

Fri, 2012-10-12 14:03

I made the change, and I got a ">" to show up before the cursor, which I guess means the app is executing? I also renamed the directory with my input files just in case that would contribute, and so far it's working well..or it's hanging. I can't really tell, since there's no output so far. As for my initial problem, I believe it's fixed. Thanks!

Fri, 2012-10-12 14:18

I have no idea what you mean by "> before the cursor".

If there's no output, it's either not running, or you've redirected the output. > is indeed the character for redirecting output in most shell environments (I assume you are using bash) so it may be redirecting to whatever file is after >. For example, if you do something like "rosetta.linuxgccrelease -some_options -more_options -etc > logfile", then all the output will end up in logfile.

You can use top to see if Rosetta is running or not. (Read up on top if you don't know how to use it, first).

Fri, 2012-10-12 14:27

Well I did designate "-out:pdb pin.pdb"...but I didn't specify an explicit redirection, since there's no > in my command. I am indeed using bash, but the full prompt (i.e. [user@location ~]$[cursor])has not shown up (just the > followed by unblinking cursor). I googled top, but I'm not sure which flag I should use with it. typing just "top" didn't output anything. In fact, nothing I've typed is outputting anything, since the full prompt hasn't shown up yet. I'm forced to conclude that it is either midprocess, or it's hanging.

Fri, 2012-10-12 14:47

You need to run top in a separate terminal. top requires no commands to be useful. It takes q to quit, or Ctrl-C.

Fri, 2012-10-12 14:57

I actually did that before I saw this. I ran top, and found that nothing resembling this executable was running. I tried running the full AbinitioRelax command again but with a syntax error(i.e. spelling the database path incorrectly), but I got the same result: a >. Something is wrong with the command I passed, but the terminal isn't showing me an error. Additionally, sifting around the directories in a different terminal show very small dump logs, meaning the job must have started, but something happened. I couldn't find my output pdb file either.

Fri, 2012-10-12 15:23

Well, post the new command (in its entirety, including your shell prompt so I know that that isn't >) and maybe I'll see something. I assume you've changed it significantly by now from that first one...

Fri, 2012-10-12 20:44

The command actually hasn't changed much...the command line basically looked like this: (sorry, I had to log out, and I don't get access again for another few hours, so I'll get back with the verbatim paste, but it looked basically like this)

[altruong@###.###.###.###]$ rosetta_source/bin/AbinitioRelax.linuxgccrelease -database ../../rosetta_database -in:file:fasta ./rosetta_files/pin.fasta in:file:frag3 ../rosetta_files/aat000_03_05.200_v1_3 -in:file:frag9 ../rosetta_files/aat000_09_05.200_v1_3 -abinitio:relax -relax:fast -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5 -user_filters true -psipred_ss2 ../rosetta_file"/t000_.psipred_ss2 -kill_hairpins ./input_files/1elwA.psipred_ss2 -out:pdb pin.pdb -nstruct 10

Note the carat at the end. That showed up only after I pressed enter, and would not accept further input.

Mon, 2012-10-15 09:20

You've still got a stray " mark in your -psipred_ss2 argument. My testing shows that (with bash at least) unterminated " gives the > behavior you experience. (This is a shell thing, not a Rosetta thing).

Mon, 2012-10-15 09:43

Indeed, I caught it, but for some reason now it says that there's no such file or directory when I try to execute. I didn't have this problem last time I accessed the cluster...

Mon, 2012-10-15 14:17

Well, since I can't see your file system, I don't know which file doesn't exist (presumably the executable path is bad, because if the arguments to rosetta are bad, then rosetta will crash rather than your shell complaining). Please post complete commands as we go so I have enough data to debug with.

Run "ls rosetta_source/bin/AbinitioRelax.linuxgccrelease"; this will almost certainly fail since the file doesn't exist. If his doesn't fail then something else is weird.

Then run "ls rosetta_source/bin/". If that directory exists, but there are no files in it, then Rosetta hasn't been compiled. If that directory does not exist, then rosetta_source is not a subdirectory where you currently are, and you need to fix the path to point at where rosetta is.

Mon, 2012-10-15 14:36

I'll keep that in mind, but since I'm still waiting for the cluster I was working on to be restructured, I won't be able to try it until it (and Rosetta) is back up and running. I'll be back with news when I'm able to access the cluster again.

Fri, 2012-10-26 13:16