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  • Contig Integrator for Sequence Assembly (CISA) error

    Hi,

    I am trying CISA program to integrate a set of contigs obtained with different assemblers and it seems pretty easy to run. Just 2 python scritps, one to merge the contigs and the second to perform the integration but so far I am getting this error:

    python CISA.py cisa.config
    CISA1....
    Contigs: 887
    Whole_Genome: 0
    Ref0.fa and Query0.fa start to run NUCmer!
    Done!
    Traceback (most recent call last):
    File "CISA.py", line 34, in <module>
    my_work.Start(g_l,infile,nucmer,CISA_S,current_p)
    File "/home/Documents/Software/CISA1.2/src/CISA1/Controllor_R1.py", line 43, in Start
    mywork.Start(genome_l,infile,nucmer)
    File "/home/Documents/Software/CISA1.2/src/CISA1/Auto_Run.py", line 172, in Start
    self.make_new_coords()
    File "/home/Documents/Software/CISA1.2/src/CISA1/Auto_Run.py", line 87, in make_new_coords
    f=open('CISA1/result'+str(count)+'.coords')
    IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords'


    Anyone knows what's wrong? There isn't any prework specifying anything about that result0.coords file.

    Thanks

  • #2
    I just tried this program in Centos and I got a different error:

    python CISA.py cisa.config
    Traceback (most recent call last):
    File "CISA.py", line 31, in <module>
    from Controllor_R1 import R1
    ImportError: No module named Controllor_R1

    Comment


    • #3
      Originally posted by illinu View Post
      I just tried this program in Centos and I got a different error:

      python CISA.py cisa.config
      Traceback (most recent call last):
      File "CISA.py", line 31, in <module>
      from Controllor_R1 import R1
      ImportError: No module named Controllor_R1
      Hi, illinu, I have met the same as your. Do you sovle it?

      yours sicerely,
      Yue Xu

      Comment


      • #4
        Hi Yue Xu,
        Yes! I contacted the owners and they explained that the only reason CISA can go wrong is due to not specifying the correct paths in the config file. I searched all the programs (nucmer, ncbi, etc) with 'which' command and copied the path. Then it worked.

        Hope it helps
        Illinu

        Comment


        • #5
          Hi illinu,
          Thank your reply. I also can run it.

          Best wishes,
          Yue Xu

          Comment


          • #6
            CISA answer

            Hi,

            I am trying CISA program to integrate a set of contigs obtained with different assemblers and it seems pretty easy to run. Just 2 python scritps, one to merge the contigs and the second to perform the integration but so far I am getting this error:

            python CISA.py cisa.config
            CISA1....
            Contigs: 887
            Whole_Genome: 0
            Ref0.fa and Query0.fa start to run NUCmer!
            Done!
            Traceback (most recent call last):
            File "CISA.py", line 34, in <module>
            my_work.Start(g_l,infile,nucmer,CISA_S,current_p)
            File "/home/Documents/Software/CISA1.2/src/CISA1/Controllor_R1.py", line 43, in Start
            mywork.Start(genome_l,infile,nucmer)
            File "/home/Documents/Software/CISA1.2/src/CISA1/Auto_Run.py", line 172, in Start
            self.make_new_coords()
            File "/home/Documents/Software/CISA1.2/src/CISA1/Auto_Run.py", line 87, in make_new_coords
            f=open('CISA1/result'+str(count)+'.coords')
            IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords'


            Anyone knows what's wrong? There isn't any prework specifying anything about that result0.coords file.

            Thanks

            Hello, I am just wondering if you were able to solve the problem. I ran into the same problem as above with CISA and I am yet to find a solution. Will appreciate your answer. Thank you
            eyeziko
            Last edited by eyeziko; 06-04-2014, 02:39 PM. Reason: forgot to include original question

            Comment


            • #7
              Originally posted by eyeziko View Post
              Hi,
              Hello, I am just wondering if you were able to solve the problem. I ran into the same problem as above with CISA and I am yet to find a solution. Will appreciate your answer. Thank you
              eyeziko
              Hello eyeziko, My answer above to Yue Xu explains how I got it working:

              Hi Yue Xu,
              Yes! I contacted the owners and they explained that the only reason CISA can go wrong is due to not specifying the correct paths in the config file. I searched all the programs (nucmer, ncbi, etc) with 'which' command and copied the path. Then it worked.

              Comment


              • #8
                Thank you. it did work.

                Comment


                • #9
                  Originally posted by Yue Xu View Post
                  Hi illinu,
                  Thank your reply. I also can run it.

                  Best wishes,
                  Yue Xu
                  I am having the same problem but after putting the way after running the command which it continues not working.

                  Thatśs my CISA config file:

                  genome=7000000
                  infile=1D14_Merged.ctg.fa
                  outfile=1D14_CISA.ctg.fa
                  nucmer=/usr/bin/nucmer
                  R2_Gap=0.95
                  CISA=/home/user/Illumina/software/CISA1.3/CISA.py
                  makeblastdb=/usr/bin/makeblastdb
                  blastn=/usr/bin/blastn

                  Any clue?

                  Thanks in advance

                  Comment


                  • #10
                    Yes, change
                    CISA=/home/user/Illumina/software/CISA1.3/CISA.py
                    for
                    CISA=/home/user/Illumina/software/CISA1.3

                    Comment


                    • #11
                      Originally posted by illinu View Post
                      Yes, change
                      CISA=/home/user/Illumina/software/CISA1.3/CISA.py
                      for
                      CISA=/home/user/Illumina/software/CISA1.3
                      Thank you very much for your comment. I did it and now I got the following error:

                      CISA.config
                      CISA1....
                      Contigs: 2013
                      Whole_Genome: 0
                      Ref0.fa and Query0.fa start to run NUCmer!
                      Done!
                      Traceback (most recent call last):
                      File "/home/user/Illumina/software/CISA1.3/CISA.py", line 34, in <module>
                      my_work.Start(g_l,infile,nucmer,CISA_S,current_p)
                      File "/home/user/Illumina/software/CISA1.3//src/CISA1/Controllor_R1.py", line 43, in Start
                      mywork.Start(genome_l,infile,nucmer)
                      File "/home/user/Illumina/software/CISA1.3//src/CISA1/Auto_Run.py", line 172, in Start
                      self.make_new_coords()
                      File "/home/user/Illumina/software/CISA1.3//src/CISA1/Auto_Run.py", line 87, in make_new_coords
                      f=open('CISA1/result'+str(count)+'.coords')
                      IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords'

                      In theory this error is due to the wrong path for nucmer as told in troubleshooting but I do not know why am I getting that error.

                      If I run nucmer (it's on the path) it runs normally so I don know what's happening

                      Thanks again

                      Comment


                      • #12
                        Did you get the paths to nucmer with
                        $ which nucmer

                        I have it in /usr/bin/nucmer but you might have it elsewhere... check that well. Check it for all.

                        Also make sure you write
                        CISA=/home/user/Illumina/software/CISA1.3
                        and not
                        CISA=/home/user/Illumina/software/CISA1.3/

                        remove the last '/'

                        Comment


                        • #13
                          Originally posted by chariko View Post
                          Thank you very much for your comment. I did it and now I got the following error:

                          CISA.config
                          CISA1....
                          Contigs: 2013
                          Whole_Genome: 0
                          Ref0.fa and Query0.fa start to run NUCmer!
                          Done!
                          Traceback (most recent call last):
                          File "/home/user/Illumina/software/CISA1.3/CISA.py", line 34, in <module>
                          my_work.Start(g_l,infile,nucmer,CISA_S,current_p)
                          File "/home/user/Illumina/software/CISA1.3//src/CISA1/Controllor_R1.py", line 43, in Start
                          mywork.Start(genome_l,infile,nucmer)
                          File "/home/user/Illumina/software/CISA1.3//src/CISA1/Auto_Run.py", line 172, in Start
                          self.make_new_coords()
                          File "/home/user/Illumina/software/CISA1.3//src/CISA1/Auto_Run.py", line 87, in make_new_coords
                          f=open('CISA1/result'+str(count)+'.coords')
                          IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords'

                          In theory this error is due to the wrong path for nucmer as told in troubleshooting but I do not know why am I getting that error.

                          If I run nucmer (it's on the path) it runs normally so I don know what's happening

                          Thanks again
                          I could finally run the program when I put all my files in the CISA1.3 folder. I still don't know why it does not work in their original folder but at least it worked.

                          Thanks a lot

                          Comment

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