Some wrong with the flag “-l” for score_jd2.linuxgccrelease

Member Site Forums Rosetta 3 Rosetta 3 – Applications Some wrong with the flag “-l” for score_jd2.linuxgccrelease

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    • #2011

        Dear friends,
        I am not sure what is wrong with the flag “-l” for score_jd2.linuxgccrelease. When I use:

        ~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -l /mnt/hgfs/Downloads/PDBLIST.txt

        I got prompt:

        basic.options.util: Use either -s or -l to designate one or more start_files
        ERROR:: Exit from: src/basic/options/ line: 157
        Error: ERROR: Exception caught by JobDistributor while trying to fill the input jobs with JobInputter of type type ‘PdbFile’
        [ERROR] EXCN_utility_exit has been thrown from: src/basic/options/ line: 157
        ERROR:: Exit from: src/protocols/jd2/ line: 218
        caught exception
        [ERROR] EXCN_utility_exit has been thrown from: src/protocols/jd2/ line: 218

        But it is okay if I use the flag “-s”:

        ~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -s /mnt/hgfs/Downloads/clean.pdb

        Can I ask how to solve this?

        Thank you very much.

        Yours sincerely

      • #10355

          I would expect that you would get that error if the file /mnt/hgfs/Downloads/PDBLIST.txt is empty, or if there is something else wrong with it. What does the contents of the file look like?

        • #10366

            Hi R Moretti,
            So strange! I delete the file and create a new file and it is working now. :)

            Thank you.

            Yours sincerely

            I think I know the answer now. It seems that in the PDBLIST.txt file
            1) the error will occur if there is only one line for the PDB directory
            2) the last line of PDB directory will not be executed when more than one line PDB directories are given

            So I think it might be a bug.

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