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  • AllPaths-LG error at FindError module

    Hello,

    I am a newbie to using AllPaths and I ran into an error while running the RunallPathsLG algorithm.

    After preparing the input files, and halfway through running the RunAllPathsLG command I get an error message with the following output:

    ------------------ FindErrors -> frag_reads_edit.fastb

    290282408 total number of original fragment reads
    96.2 mean length of original fragment reads in bases
    38.8 % gc content of fragment reads
    0.2 % of bases pre-corrected
    2299242576 estimated genome size in bases
    21.0 % genome estimated to be repetitive (at K=25 scale)
    9 estimated genome coverage by fragment reads
    0.32 estimated standard deviation of sequencing bias (at K=25 scale)
    92.7 % of bases confirmed in cycle 0
    1.32 % of bases corrected in cycle 0
    0.01 % of bases with conflicting corrections in cycle 0
    94.8 % of bases confirmed in cycle 1
    0.31 % of bases corrected in cycle 1
    0.01 % of bases with conflicting corrections in cycle 1

    ------------------ CleanCorrectedReads -> frag_reads_corr.25mer.kspec

    8.1 % of reads removed because of low frequency kmers

    ------------------ FillFragments -> filled_reads.fastb

    58.1 % of fragment pairs that were filled

    ------------------ Memory and CPU usage

    64 available cpus
    126.1 GB of total available memory
    389.0 GB of available disk space
    50.87 hours of total elapsed time
    46.76 hours of total per-module elapsed time
    596678.04 hours of total per-module user time
    12759.45 effective parallelization factor
    115.56 GB memory usage peak

    Run directory: /archive/REFERENCE/DATA/RUN
    Log directory: /archive/REFERENCE/make_log/DATA/RUN/SUBDIR/2013-05-10T07:55:31

    *** Make encountered an error, see above for error messages. ***

    I am not really sure as to where I would look for any error's. Since the makefile is generated before the actual process, I do not really understand where the error is. Has anyone encountered something like this before/does anyone have any suggestions?

    I did post the same question in the allpaths-user forum, but I havent got any reply yet.

    Any insights would be greatly appreciated.

    Thanks in advance for your time.
    Best,
    Akshaya

  • #2
    Originally posted by akshaya.ramesh View Post
    Hello,

    I am a newbie to using AllPaths and I ran into an error while running the RunallPathsLG algorithm.

    After preparing the input files, and halfway through running the RunAllPathsLG command I get an error message with the following output:

    ------------------ FindErrors -> frag_reads_edit.fastb

    290282408 total number of original fragment reads
    96.2 mean length of original fragment reads in bases
    38.8 % gc content of fragment reads
    0.2 % of bases pre-corrected
    2299242576 estimated genome size in bases
    21.0 % genome estimated to be repetitive (at K=25 scale)
    9 estimated genome coverage by fragment reads
    0.32 estimated standard deviation of sequencing bias (at K=25 scale)
    92.7 % of bases confirmed in cycle 0
    1.32 % of bases corrected in cycle 0
    0.01 % of bases with conflicting corrections in cycle 0
    94.8 % of bases confirmed in cycle 1
    0.31 % of bases corrected in cycle 1
    0.01 % of bases with conflicting corrections in cycle 1

    ------------------ CleanCorrectedReads -> frag_reads_corr.25mer.kspec

    8.1 % of reads removed because of low frequency kmers

    ------------------ FillFragments -> filled_reads.fastb

    58.1 % of fragment pairs that were filled

    ------------------ Memory and CPU usage

    64 available cpus
    126.1 GB of total available memory
    389.0 GB of available disk space
    50.87 hours of total elapsed time
    46.76 hours of total per-module elapsed time
    596678.04 hours of total per-module user time
    12759.45 effective parallelization factor
    115.56 GB memory usage peak

    Run directory: /archive/REFERENCE/DATA/RUN
    Log directory: /archive/REFERENCE/make_log/DATA/RUN/SUBDIR/2013-05-10T07:55:31

    *** Make encountered an error, see above for error messages. ***

    I am not really sure as to where I would look for any error's. Since the makefile is generated before the actual process, I do not really understand where the error is. Has anyone encountered something like this before/does anyone have any suggestions?

    I did post the same question in the allpaths-user forum, but I havent got any reply yet.

    Any insights would be greatly appreciated.

    Thanks in advance for your time.
    Best,
    Akshaya

    Hi, I have run into the same problem. Did you ever find a solution? Any help will be greatly appreciated!

    Lida

    Comment


    • #3
      This is a guess but have you looked in this directory to see if there is an error log file(s) available: /archive/REFERENCE/make_log/DATA/RUN/SUBDIR/...

      Comment


      • #4
        Originally posted by Lida View Post
        Hi, I have run into the same problem. Did you ever find a solution? Any help will be greatly appreciated!

        Lida
        Hello!

        I simply re-ran AllPaths and set the Threads to 32. It worked the second time. Have you tried re-running All-Paths? Also, I usually run my denovo assembly with a small portion of the data-set, you could try that as well and see if it works. If you still do not get it to work you can post in the AllPaths forum.

        Comment


        • #5
          Rerun

          Hi all
          I also encountered this problem. I re-submitted the task and now I'm waiting for the result, hopefully it would work.

          Seth

          Comment


          • #6
            Hey,

            Did you get it working? Does setting the number of threads to 32 work? I get something similar with Allpaths-LG:

            "
            Program FindErrors failed to make target $(RUN)/frag_reads_edit.readtrack
            /bin/sh: @echo: not found
            make: *** [/home/jkammone/wrk/Miikkulainen/assembly/allpaths/data2/second_allpaths_assembly/frag_reads_edit.fastb] Error 1
            make: *** Deleting file `/home/jkammone/wrk/Miikkulainen/assembly/allpaths/data2/second_allpaths_assembly/frag_reads_edit.fastb'

            Fri Jan 24 22:43:51 2014 : make process finished.


            Looks like the command FindErrors did not complete:
            The following files are missing: 1
            $(RUN)/frag_reads_edit.fastb
            The following files are incomplete: 2
            $(RUN)/frag_reads_edit.qualb
            $(RUN)/frag_reads_filt.25mer.kspec
            Cleaning up all targets of this command...
            Moving $(RUN)/frag_reads_edit.qualb to $(RUN)/makeinfo/frag_reads_edit.qualb.incomplete
            Moving $(RUN)/frag_reads_filt.25mer.kspec to $(RUN)/makeinfo/frag_reads_filt.25mer.kspec.incomplete

            Fri Jan 24 22:43:52 2014: Compiling assembly report.

            ------------------ FindErrors -> frag_reads_edit.fastb

            323559312 total number of original fragment reads

            ...

            "

            Regards.

            Comment


            • #7
              Yes, that actually fixed it. I am not an expert at this, but increasing the numbers of threads fixed the problem for me. Have you had any luck since?

              Comment


              • #8
                Hi,

                For me, changing the number of threads did not work. Moreover, I have problems with the pipeline described in the manual:

                If I run the pipeline like this (very roughly):

                1. PrepareAllPathsInputs
                2. RunAllPathsLG

                I get:

                "
                ValidateAllPathsInputs PRE=/home/jkammone/wrk/Miikkulainen/assembly/ \
                DATA=allpaths/data K=96 K_LONG=640 LONG_JUMPS=False \
                LONG_READS=False REFERENCE=False WARN_ONLY=False \
                MM=True _MM_INTERVAL=10 _MM_SUMMARY=False \
                _MM_OUT=/home/jkammone/wrk/Miikkulainen/assembly/allpat \
                hs/data/makeinfo/ValidateAllPathsInputs.report.mm.Valid \
                ateAllPathsInputs
                --------------------------------------------------------------------------------



                Redirecting standard output to the following files:
                /home/jkammone/wrk/Miikkulainen/assembly/allpaths/data/ValidateAllPathsInputs.report
                /home/jkammone/wrk/Miikkulainen/assembly/allpaths/data/makeinfo/ValidateAllPathsInputs.report.out.ValidateAllPathsInputs
                /home/jkammone/wrk/Miikkulainen/assembly/allpaths/make_log/data/second_allpaths_assembly/test/2014-01-31T10:39:42/ValidateAllPathsInputs.out

                You should not have specified a value for K_LONG.
                You should not have specified a value for LONG_READS.
                You should not have specified a value for REFERENCE.

                To see the syntax for this command, type "ValidateAllPathsInputs -h".

                make: *** [/home/jkammone/wrk/Miikkulainen/assembly/allpaths/data/ValidateAllPathsInputs.report] Error 255
                make: *** Deleting file `/home/jkammone/wrk/Miikkulainen/assembly/allpaths/data/ValidateAllPathsInputs.report'

                "

                ----


                In case I run the pipeline like this:

                1. PrepareAllPathsInputs
                2. ValidateAllPathsInputs #manual validation
                3. RunAllPathsLG (set VALIDATE_INPUTS=False)

                I get the above error message. The troublesome lines are:

                "
                Program FindErrors failed to make target $(RUN)/frag_reads_edit.readtrack
                /bin/sh: @echo: not found
                "

                I have no clue why it goes like this. AllPathsLG-forum didn't help either. I am sending email to David Jaffe to Broad to investigate.

                Thanks anyway and regards.

                Comment


                • #9
                  Hi,
                  I have the same problem in using Allpath-LG like:
                  make: *** [/media/2TB/sweetpotato.genome/data/run/makeinfo/frag_reads_edit.fastb] Error 1
                  Call to new failed, memory usage before call = 214504216k.

                  Here is the output of top:

                  Aborting.

                  I have no idea which part is wrong. Any insights would be greatly appreciated.

                  Thanks in advance for your time.

                  Comment

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