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  • For those with the problem with the -x 1 "Process 'extend/format contigs' failed":
    I wrote an email yesterday to the company that distributes the program (Baseclear) and they told me:
    I understand this point, yet we do not have plans at this very moment to address this.
    So please continue to use the –x 0 option. My apologies.
    So I asked for a previous version and they send me the 2.0.

    Good luck.

    PS: the 2.0 needs Perl 4 ¬¬'
    Last edited by El Crazy Xabi; 02-09-2016, 04:12 PM.

    Comment


    • Hello,

      Were you guys able to figure it out? I am running SSPACE x_64 with options (x=1 and T=16) but I am getting the following error:

      =>Mon Mar 7 15:46:00 2016: Extending of contigs with unmapped reads

      =>Mon Mar 7 15:46:00 2016: Building Bowtie index for contigs

      =>Mon Mar 7 16:58:09 2016: Mapping reads to contigs with Bowtie
      Thread 18 terminated abnormally: Can't open bwa output -- fatal
      **************************************************

      Process 'extend/format contigs' failed on Mon Mar 7 23:58:49 2016


      I would really appreciate your help.

      Comment


      • Could you present your whole command?




        Originally posted by milo0615 View Post
        Hello,

        Were you guys able to figure it out? I am running SSPACE x_64 with options (x=1 and T=16) but I am getting the following error:

        =>Mon Mar 7 15:46:00 2016: Extending of contigs with unmapped reads

        =>Mon Mar 7 15:46:00 2016: Building Bowtie index for contigs

        =>Mon Mar 7 16:58:09 2016: Mapping reads to contigs with Bowtie
        Thread 18 terminated abnormally: Can't open bwa output -- fatal
        **************************************************

        Process 'extend/format contigs' failed on Mon Mar 7 23:58:49 2016


        I would really appreciate your help.

        Comment


        • Originally posted by sunnycqcn View Post
          Could you present your whole command?
          Hi sunnycqcn,

          The command I used is as follows. Thank you for your help

          >perl $HOME/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -l libraries.txt -s gercombsadaptrim200_k44-contigs.fa -x 1 -z 200 -T 16 -k 3 -a 0.7 -m 32 -r 0.9 -p 0 -o 15 -n 10 -v 1 -b gercombsk44 &

          [1] 20196

          log:

          [stilllab@b30-fac-staff-134-71-20-58 NEW_SSPACE_Gerreg]$ Your inserted inputs on [SSPACE_Standard_v3.0_linux] at Mon Mar 7 15:40:17 2016:
          Required inputs:
          -l = libraries.txt
          Number of paired files = 2
          -s = gercombsadaptrim200_k44-contigs.fa
          -b = gercombsk44

          Optional inputs:
          -x = 1
          -z = 200
          -k = 3
          -g = 0
          -a = 0.7
          -n = 10
          -T = 16
          -p = 0

          Contig extension inputs:
          -o = 15
          -m = 32
          -r = 0.9


          =>Mon Mar 7 15:40:17 2016: Reading, filtering and converting input sequences of library file initiated

          ------------------------------------------------------------

          =>Mon Mar 7 15:46:00 2016: Extending of contigs with unmapped reads

          =>Mon Mar 7 15:46:00 2016: Building Bowtie index for contigs

          =>Mon Mar 7 16:58:09 2016: Mapping reads to contigs with Bowtie
          Thread 18 terminated abnormally: Can't open bwa output -- fatal
          **************************************************

          Process 'extend/format contigs' failed on Mon Mar 7 23:58:49 2016

          Comment


          • Originally posted by milo0615 View Post
            Hi sunnycqcn,

            The command I used is as follows. Thank you for your help

            >perl $HOME/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -l libraries.txt -s gercombsadaptrim200_k44-contigs.fa -x 1 -z 200 -T 16 -k 3 -a 0.7 -m 32 -r 0.9 -p 0 -o 15 -n 10 -v 1 -b gercombsk44 &

            [1] 20196

            log:

            [stilllab@b30-fac-staff-134-71-20-58 NEW_SSPACE_Gerreg]$ Your inserted inputs on [SSPACE_Standard_v3.0_linux] at Mon Mar 7 15:40:17 2016:
            Required inputs:
            -l = libraries.txt
            Number of paired files = 2
            -s = gercombsadaptrim200_k44-contigs.fa
            -b = gercombsk44

            Optional inputs:
            -x = 1
            -z = 200
            -k = 3
            -g = 0
            -a = 0.7
            -n = 10
            -T = 16
            -p = 0

            Contig extension inputs:
            -o = 15
            -m = 32
            -r = 0.9


            =>Mon Mar 7 15:40:17 2016: Reading, filtering and converting input sequences of library file initiated

            ------------------------------------------------------------

            =>Mon Mar 7 15:46:00 2016: Extending of contigs with unmapped reads

            =>Mon Mar 7 15:46:00 2016: Building Bowtie index for contigs

            =>Mon Mar 7 16:58:09 2016: Mapping reads to contigs with Bowtie
            Thread 18 terminated abnormally: Can't open bwa output -- fatal
            **************************************************

            Process 'extend/format contigs' failed on Mon Mar 7 23:58:49 2016
            Please see the response of 'El Crazy Xabi' above.
            Either use -x = 0 or use an older version of SSPACE.

            Comment


            • Originally posted by fahmida View Post
              Please see the response of 'El Crazy Xabi' above.
              Either use -x = 0 or use an older version of SSPACE.
              Hi fahmida,

              If I use -x = 0 the assembly stats such as the N50, n>200, and max length stay the same. I have already emailed the SSPACE developers for an older version of it.

              Thank you for your help.

              -Milo

              Comment


              • I am sure the 3.0 version work well with the big genome. I assembled one genome last month, it worked well. Meanwhile, I met the same problem as same with you. So if your library file include a lot of libraries, the error file should be like as your error file. So if you can present your library file, I can know what it happen.



                Originally posted by milo0615 View Post
                Hi fahmida,

                If I use -x = 0 the assembly stats such as the N50, n>200, and max length stay the same. I have already emailed the SSPACE developers for an older version of it.

                Thank you for your help.

                -Milo

                Comment


                • I found the SSPACE basic 2.1 in GitHub, from one of the original devs, so no need to bother with Baseclear to use the -x=1

                  Comment


                  • Originally posted by sunnycqcn View Post
                    I am sure the 3.0 version work well with the big genome. I assembled one genome last month, it worked well. Meanwhile, I met the same problem as same with you. So if your library file include a lot of libraries, the error file should be like as your error file. So if you can present your library file, I can know what it happen.
                    Hi sunnycqcn,

                    My libraries.txt file looks like the following:

                    gjHS bowtie GerJamesonii_HS_1_P.fastq GerJamesonii_HS_2_P.fastq 100 0.25 FR
                    gjGA bowtie GerJamesonii_1_P.fastq GerJamesonii_2_P.fastq 125 0.25 FR


                    Thank you,

                    -Milo

                    Comment


                    • How many libraries is in your libraries files.


                      Originally posted by milo0615 View Post
                      Hi sunnycqcn,

                      My libraries.txt file looks like the following:

                      gjHS bowtie GerJamesonii_HS_1_P.fastq GerJamesonii_HS_2_P.fastq 100 0.25 FR
                      gjGA bowtie GerJamesonii_1_P.fastq GerJamesonii_2_P.fastq 125 0.25 FR


                      Thank you,

                      -Milo

                      Comment


                      • Usually, you can try a small dataset firstly.
                        Then software work well, you can run lots of data.
                        I am sure that my data run well now.




                        Originally posted by milo0615 View Post
                        Hi sunnycqcn,

                        My libraries.txt file looks like the following:

                        gjHS bowtie GerJamesonii_HS_1_P.fastq GerJamesonii_HS_2_P.fastq 100 0.25 FR
                        gjGA bowtie GerJamesonii_1_P.fastq GerJamesonii_2_P.fastq 125 0.25 FR


                        Thank you,

                        -Milo

                        Comment


                        • Hi - I have a question about the "-n" option.

                          Here's what the option does: "minimum overlap required between contigs to merge adjacent contigs"

                          Does this mean that the SSPACE will assemble to contigs together that have terminal overlaps - like minimus2 would do?

                          Comment


                          • Hi all,
                            What am I doing wrong if I get:

                            READING READS lib1:
                            ------------------------------------------------------------
                            Total inserted pairs = 3413702
                            Number of pairs containing N's = 17688
                            Remaining pairs = 3396014
                            ------------------------------------------------------------



                            LIBRARY lib1 STATS:
                            ################################################################################

                            MAPPING READS TO CONTIGS:
                            ------------------------------------------------------------
                            Number of single reads found on contigs = 0
                            Number of pairs used for pairing contigs / total pairs = 0 / 0
                            ------------------------------------------------------------

                            READ PAIRS STATS:
                            Assembled pairs: 0 (0 sequences)
                            Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 600 +/-60): 0
                            Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 0
                            Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 0
                            ---
                            Satisfied in distance/logic within a given contig pair (pre-scaffold): 0
                            Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 0
                            ---
                            Total satisfied: 0 unsatisfied: 0


                            Estimated insert size statistics (based on 0 pairs):
                            Mean insert size = 0
                            Median insert size = 0
                            REPEATS:
                            Number of repeated edges = 0
                            ------------------------------------------------------------
                            ?
                            Thanks in advance!
                            Ulrike

                            Comment

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